{"entity": "journal", "iuid": "e984fbe17f5d4115b69df1669e979d8a", "timestamp": "2026-08-15T12:38:23.672Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Front%20Plant%20Sci.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Front%20Plant%20Sci"}}, "title": "Front Plant Sci", "issn": "1664-462X", "issn-l": "1664-462X", "publications_count": 28, "publications": [{"entity": "publication", "iuid": "22d1c899e817411c810114fd519eebb3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/22d1c899e817411c810114fd519eebb3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/22d1c899e817411c810114fd519eebb3"}}, "title": "A Phytophthora infestans CRN1-derived small RNA is predicted to target the potato immune regulator EDS1.", "authors": [{"family": "Singh", "given": "Shailja", "initials": "S"}, {"family": "Hu", "given": "Xinyi", "initials": "X"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2026-04-10", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "17", "pages": "1791978", "issn-l": "1664-462X"}, "abstract": "The late blight pathogen, Phytophthora infestans (Pi), causes severe damage to plants in the Solanaceae family. Although knowledge regarding the P. infestans-mediated manipulation of critical components in the plant defense system is growing, many questions remain unanswered. Herein, we aimed to examine the role of Argonaute 1 (AGO1) associated small RNAs in this interaction. Of particular interest was the early communication between the host and the pathogen. To visualize the cellular dynamics underlying potential cross-kingdom RNA trafficking, we first examined the localization and accumulation patterns of plant extracellular vesicles (EVs) and multivesicular bodies (MVBs) using a handful of markers. MVBs were present not only at the plant plasma membrane but also in the germ tube of the invading pathogen. The enrichment of MVBs decreased as the infection process proceeded. At 3.0 days post-inoculation, co-localization between AGO1 from P. infestans and StARA6 was not seen even at the swollen tip of the germ tube. Three Crinkler effector genes encoding small RNAs were found after coimmunoprecipitation, sequencing and extensive bioinformatic analysis. PiCRN1 caused more severe disease compared with PiCRN3, which carries a typical Crinkler (CRN) LFLAK domain. This difference may result from activation of a CRN1-derived siRNA predicted to target the enhanced disease susceptibility 1 (EDS1) gene in potato. To examine whether the observed phenotypic effects can be attributed to any EV cargo from the potato host, we set up a procedure to isolate EVs from P. infestans-infected potato leaves. However, the tiny EV yield obtained during the early infection phase prevented us from such analysis. The understanding of effector cell trafficking and small RNA reprogramming of host plant genes remain elusive in this pathosystem.", "doi": "10.3389/fpls.2026.1791978", "pmid": "42040283", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13106546"}], "notes": [], "created": "2026-05-11T12:26:39.885Z", "modified": "2026-05-11T12:26:39.900Z"}, {"entity": "publication", "iuid": "6f056c7d9f1f4538bce79a48ffd96515", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f056c7d9f1f4538bce79a48ffd96515.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f056c7d9f1f4538bce79a48ffd96515"}}, "title": "Phenotypic characterization and candidate gene analysis of a short kernel and brassinosteroid insensitive mutant from hexaploid oat (Avena sativa).", "authors": [{"family": "Tsardakas Renhuldt", "given": "Nikos", "initials": "N"}, {"family": "Bentzer", "given": "Johan", "initials": "J"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Marmon", "given": "Sofia", "initials": "S"}, {"family": "Sirijovski", "given": "Nick", "initials": "N"}], "type": "journal article", "published": "2024-04-26", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "15", "pages": "1358490", "issn-l": "1664-462X"}, "abstract": "In an ethyl methanesulfonate oat (Avena sativa) mutant population we have found a mutant with striking differences to the wild-type (WT) cv. Belinda. We phenotyped the mutant and compared it to the WT. The mutant was crossed to the WT and mapping-by-sequencing was performed on a pool of F2 individuals sharing the mutant phenotype, and variants were called. The impacts of the variants on genes present in the reference genome annotation were estimated. The mutant allele frequency distribution was combined with expression data to identify which among the affected genes was likely to cause the observed phenotype. A brassinosteroid sensitivity assay was performed to validate one of the identified candidates. A literature search was performed to identify homologs of genes known to be involved in seed shape from other species. The mutant had short kernels, compact spikelets, altered plant architecture, and was found to be insensitive to brassinosteroids when compared to the WT. The segregation of WT and mutant phenotypes in the F2 population was indicative of a recessive mutation of a single locus. The causal mutation was found to be one of 123 single-nucleotide polymorphisms (SNPs) spanning the entire chromosome 3A, with further filtering narrowing this down to six candidate genes. In-depth analysis of these candidate genes and the brassinosteroid sensitivity assay suggest that a Pro303Leu substitution in AVESA.00010b.r2.3AG0419820.1 could be the causal mutation of the short kernel mutant phenotype. We identified 298 oat proteins belonging to orthogroups of previously published seed shape genes, with AVESA.00010b.r2.3AG0419820.1 being the only of these affected by a SNP in the mutant. The AVESA.00010b.r2.3AG0419820.1 candidate is functionally annotated as a GSK3/SHAGGY-like kinase with homologs in Arabidopsis, wheat, barley, rice, and maize, with several of these proteins having known mutants giving rise to brassinosteroid insensitivity and shorter seeds. The substitution in AVESA.00010b.r2.3AG0419820.1 affects a residue with a known gain-of function substitution in Arabidopsis BRASSINOSTEROID-INSENSITIVE2. We propose a gain-of-function mutation in AVESA.00010b.r2.3AG0419820.1 as the most likely cause of the observed phenotype, and name the gene AsGSK2.1. The findings presented here provide potential targets for oat breeders, and a step on the way towards understanding brassinosteroid signaling, seed shape and nutrition in oats.", "doi": "10.3389/fpls.2024.1358490", "pmid": "38736447", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11082396"}], "notes": [], "created": "2024-05-17T09:09:43.657Z", "modified": "2025-02-28T14:24:28.465Z"}, {"entity": "publication", "iuid": "49e0c12e6b8446b9aa084ce46b1b54b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/49e0c12e6b8446b9aa084ce46b1b54b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/49e0c12e6b8446b9aa084ce46b1b54b8"}}, "title": "Spatio-temporal transcriptome and storage compound profiles of developing faba bean (Vicia faba) seed tissues.", "authors": [{"family": "Ohm", "given": "Hannah", "initials": "H"}, {"family": "Saripella", "given": "Ganapathi Varma", "initials": "GV"}, {"family": "Hofvander", "given": "Per", "initials": "P"}, {"family": "Grimberg", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2024-02-06", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "15", "pages": "1284997", "issn-l": "1664-462X"}, "abstract": "Faba bean (Vicia faba) is a legume grown in diverse climate zones with a high potential for increased cultivation and use in food due to its nutritional seeds. In this study, we characterized seed tissue development in faba bean to identify key developmental processes; from embryo expansion at the expense of the endosperm to the maturing storage stages of the bean seed. A spatio-temporal transcriptome profiling analysis, combined with chemical nutrient analysis of protein, starch, and lipid, of endosperm and embryo tissues at different developmental stages, revealed gene expression patterns, transcriptional networks, and biochemical pathways in faba bean. We identified key players in the LAFL (LEC1, ABI3, FUS3, and LEC2) transcription factor network as well as their major repressors VAL1 and ASIL1. Our results showed that proteins accumulated not only in the embryo but also in the endosperm. Starch accumulated throughout seed development and oil content increased during seed development but at very low levels. The patterns of differentially expressed transcripts encoding proteins with functions in the corresponding metabolic pathways for the synthesis of these storage compounds, to a high extent, aligned with these findings. However, the early expression of transcripts encoding WRI1 combined with the late expression of oil body proteins indicated a not manifested high potential for lipid biosynthesis and oil storage. Altogether, this study contributes to increased knowledge regarding seed developmental processes applicable to future breeding methods and seed quality improvement for faba bean.", "doi": "10.3389/fpls.2024.1284997", "pmid": "38379954", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10877042"}], "notes": [], "created": "2024-11-25T10:33:19.933Z", "modified": "2025-02-28T14:24:23.256Z"}, {"entity": "publication", "iuid": "97328d83a5ff458481fbad51e7615b21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/97328d83a5ff458481fbad51e7615b21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/97328d83a5ff458481fbad51e7615b21"}}, "title": "Metabolomic and transcriptomic analyses identify external conditions and key genes underlying high levels of toxic glycoalkaloids in tubers of stress-sensitive potato cultivars.", "authors": [{"family": "Merino", "given": "Irene", "initials": "I"}, {"family": "Guasca", "given": "Alexandra Olarte", "initials": "AO"}, {"family": "Krmela", "given": "Ales", "initials": "A"}, {"family": "Arif", "given": "Usman", "initials": "U"}, {"family": "Ali", "given": "Ashfaq", "initials": "A"}, {"family": "Westerberg", "given": "Erik", "initials": "E"}, {"family": "Jalmi", "given": "Siddhi Kashinanth", "initials": "SK"}, {"family": "Hajslova", "given": "Jana", "initials": "J"}, {"family": "Schulzova", "given": "Vera", "initials": "V"}, {"family": "Sitbon", "given": "Folke", "initials": "F"}], "type": "journal article", "published": "2023-10-04", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "issn-l": "1664-462X", "volume": "14", "issue": null, "pages": "1210850"}, "abstract": "High levels of toxic steroidal glycoalkaloids (SGAs) in potato tubers constitute a recognized food quality problem. Tuber SGA levels vary between potato cultivars and can increase after post-harvest stresses such as wounding and light exposure. A few cultivars, e.g., 'Magnum Bonum' and 'Lenape,' have been withdrawn from commercial sales due to excessive SGA levels during some cultivation years. However, these sudden SGA increases are diffucult to predict, and their causes are not understood. To identify external and genetic factors that underlie sudden SGA increases in certain potato cultivars, we have here in a 2-year study investigated 'Magnum Bonum' and five additional table potato cultivars for their SGA levels after wounding and light exposure.\r\n\r\nResults showed that 'Magnum Bonum' has an unusual strong SGA response to light exposure, but not to wounding, whereas 'Bintje' displayed an opposite regulation. Levels of calystegine alkaloids were not significantly altered by treatments, implicating independent metabolic regulation of SGA and calystegine levels also under conditions of high SGA accumulation. Metabolomic and transcriptomic analyses identified a small number of key genes whose expression correlated with SGA differences between cultivars. Overexpression of two key genes in transgenic low-SGA potato cultivars increased their leaf SGA levels significantly.\r\n\r\nThe results show that a strong response to light can underlie the SGA peaks that occasionally occur in certain potato cultivars and indicate that a between-cultivar variation in the expression of single SGA key genes can account for cultivar SGA differerences. We propose that current attempts to mitigate the SGA hazard will benefit from an increased consideration of cultivar-dependent SGA responses to post-harvest conditions, particularly light exposure. The identified key SGA genes can now be used as a molecular tool in this work.", "doi": "10.3389/fpls.2023.1210850", "pmid": "37860257", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10582707"}], "notes": [], "created": "2023-11-16T12:04:12.160Z", "modified": "2024-01-16T13:48:32.011Z"}, {"entity": "publication", "iuid": "9e948ecc3d964822aa93e200ba5a1016", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e948ecc3d964822aa93e200ba5a1016.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e948ecc3d964822aa93e200ba5a1016"}}, "title": "Dissecting the genetic basis of drought responses in common bean using natural variation.", "authors": [{"family": "Labastida", "given": "Diana", "initials": "D"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Rend\u00f3n-Anaya", "given": "Martha", "initials": "M"}], "type": "journal article", "published": "2023-09-14", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "14", "pages": "1143873", "issn-l": "1664-462X"}, "abstract": "The common bean (Phaseolus vulgaris L) is the most important legume for human consumption, contributing 30% of the total daily protein intake in developing countries. A major limitation for its cultivation is drought, which causes more than 60% of the annual losses. Among physiological adaptations to drought, delaying senescence and extending the photosynthetic capacity can improve crop productivity. This strategy is known as functional \"stay-green\" (SG) and has been discussed as a goal in plant breeding to alleviate the loss of yield under water scarcity conditions. The genetic components behind SG traits have been explored specially in cereals, but they are to date poorly studied in the common bean. For this, we screened 71 common bean cultivars belonging to the three most important gene-pools, Mesoamerica, Andes and Europe, selected to cover the natural variation of the species. Phenotyping experiments under terminal drought during long-days in greenhouse conditions, identified six photoperiod insensitive cultivars of European origin with a clear SG phenotype. Using SNP data produced from whole genome re-sequencing data, we obtained 10 variants significantly associated to the SG phenotype on chromosomes 1, 3, 7, 8, 9 and 10 that are in close proximity to gene models with functional annotations related to hormone signaling and anti-oxidant production. Calculating pairwise FST between subgroups of cultivars divided according to their drought response (susceptibility, escape, recovery or SG), we identified up to 29 genomic windows accounting for 1,45Mb that differentiate SG cultivars; these signals were especially strong on chromosomes 1, 5 and 10. Within these windows, we found genes directly involved in photosynthetic processes and trehalose synthesis. Altogether, these signals represent good targets for further characterization and highlight the multigenic nature of the SG response in legumes.", "doi": "10.3389/fpls.2023.1143873", "pmid": "37780498", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10538545"}], "notes": [], "created": "2023-11-27T22:01:49.292Z", "modified": "2024-01-16T13:48:32.269Z"}, {"entity": "publication", "iuid": "be11fea8451948f58662b917f457df29", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be11fea8451948f58662b917f457df29.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be11fea8451948f58662b917f457df29"}}, "title": "Limited genetic changes observed during in situ and ex situ conservation in Nordic populations of red clover (Trifolium pratense).", "authors": [{"family": "Hagenblad", "given": "Jenny", "initials": "J"}, {"family": "Aloisi", "given": "Karolina", "initials": "K"}, {"family": "Marum", "given": "Petter", "initials": "P"}, {"family": "\u00d6hlund", "given": "Linda", "initials": "L"}, {"family": "Solberg", "given": "Svein \u00d8ivind", "initials": "S\u00d8"}, {"family": "Asdal", "given": "\u00c5smund", "initials": "\u00c5"}, {"family": "Palm\u00e9", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2023-08-09", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "14", "pages": "1233838", "issn-l": "1664-462X"}, "abstract": "In situ and ex situ conservation are the two main approaches for preserving genetic diversity. The advantages and disadvantages of the two approaches have been discussed but their genetic effects have not been fully evaluated.\n\nIn this study we investigate the effects of the two conservation approaches on genetic diversity in red clover. Seed samples collected from wild populations in Sweden and Norway in 1980, their subsequent generations created during seed regeneration at the gene bank and samples recollected from the same location as the original samples, were analyzed with microsatellite markers, alongside reference samples from cultivars.\n\nOverall, there was a differentiation between cultivars and the wild material and between wild material from Sweden and Norway. In general, the original collections clustered together with the later generations of the same accession in the gene bank, and with the recollected samples from the same location, and the level of diversity remained the same among samples of the same accession. Limited gene flow from cultivated varieties to the wild populations was detected; however, some wild individuals are likely to be escapees or affected by gene flow.\n\nIn conclusion, there were examples of genetic changes within individual accessions both in situ and ex situ, as is also to be expected in any living population. However, we observed only limited genetic changes in both in situ and ex situ conservation over the generations included in this study and with the relatively large populations used in the ex situ conservation in the gene bank at NordGen.", "doi": "10.3389/fpls.2023.1233838", "pmid": "37621888", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10445542"}], "notes": [], "created": "2024-01-05T16:22:54.210Z", "modified": "2024-01-05T16:22:54.215Z"}, {"entity": "publication", "iuid": "54a263eed46a4d8ca6dbb82ac886808a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/54a263eed46a4d8ca6dbb82ac886808a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/54a263eed46a4d8ca6dbb82ac886808a"}}, "title": "Comparative transcriptome profiling provides insights into the growth promotion activity of Pseudomonas fluorescens strain SLU99 in tomato and potato plants.", "authors": [{"family": "Hanifah", "given": "Nurul Atilia Shafienaz Binti", "initials": "NASB"}, {"family": "Ghadamgahi", "given": "Farideh", "initials": "F"}, {"family": "Ghosh", "given": "Samrat", "initials": "S"}, {"family": "Ortiz", "given": "Rodomiro", "initials": "R"}, {"family": "Whisson", "given": "Stephen C", "initials": "SC"}, {"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Kalyandurg", "given": "Pruthvi B", "initials": "PB"}], "type": "journal article", "published": "2023-07-18", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "14", "pages": "1141692", "issn-l": "1664-462X"}, "abstract": "The use of biocontrol agents with plant growth-promoting activity has emerged as an approach to support sustainable agriculture. During our field evaluation of potato plants treated with biocontrol rhizobacteria, four bacteria were associated with increased plant height. Using two important solanaceous crop plants, tomato and potato, we carried out a comparative analysis of the growth-promoting activity of the four bacterial strains: Pseudomonas fluorescens SLU99, Serratia plymuthica S412, S. rubidaea AV10, and S. rubidaea EV23. Greenhouse and in vitro experiments showed that P. fluorescens SLU99 promoted plant height, biomass accumulation, and yield of potato and tomato plants, while EV23 promoted growth in potato but not in tomato plants. SLU99 induced the expression of plant hormone-related genes in potato and tomato, especially those involved in maintaining homeostasis of auxin, cytokinin, gibberellic acid and ethylene. Our results reveal potential mechanisms underlying the growth promotion and biocontrol effects of these rhizobacteria and suggest which strains may be best deployed for sustainably improving crop yield.", "doi": "10.3389/fpls.2023.1141692", "pmid": "37534284", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10393259"}], "notes": [], "created": "2023-10-11T12:16:52.510Z", "modified": "2023-10-19T13:01:31.991Z"}, {"entity": "publication", "iuid": "db4eeb97e2784ac6ab937b16a7e239da", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db4eeb97e2784ac6ab937b16a7e239da.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db4eeb97e2784ac6ab937b16a7e239da"}}, "title": "Impact of xylan on field productivity and wood saccharification properties in aspen.", "authors": [{"family": "Derba-Maceluch", "given": "Marta", "initials": "M"}, {"family": "Sivan", "given": "Pramod", "initials": "P"}, {"family": "Donev", "given": "Evgeniy N", "initials": "EN"}, {"family": "Gandla", "given": "Madhavi Latha", "initials": "ML"}, {"family": "Yassin", "given": "Zakiya", "initials": "Z"}, {"family": "Vaasan", "given": "Rakhesh", "initials": "R"}, {"family": "Heinonen", "given": "Emilia", "initials": "E"}, {"family": "Andersson", "given": "Sanna", "initials": "S"}, {"family": "Amini", "given": "Fariba", "initials": "F"}, {"family": "Scheepers", "given": "Gerhard", "initials": "G"}, {"family": "Johansson", "given": "Ulf", "initials": "U"}, {"family": "Vilaplana", "given": "Francisco J", "initials": "FJ"}, {"family": "Albrectsen", "given": "Benedicte R", "initials": "BR"}, {"family": "Hertzberg", "given": "Magnus", "initials": "M"}, {"family": "J\u00f6nsson", "given": "Leif J", "initials": "LJ"}, {"family": "Mellerowicz", "given": "Ewa J", "initials": "EJ"}], "type": "journal article", "published": "2023-07-17", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "14", "pages": "1218302", "issn-l": "1664-462X"}, "abstract": "Xylan that comprises roughly 25% of hardwood biomass is undesirable in biorefinery applications involving saccharification and fermentation. Efforts to reduce xylan levels have therefore been made in many species, usually resulting in improved saccharification. However, such modified plants have not yet been tested under field conditions. Here we evaluate the field performance of transgenic hybrid aspen lines with reduced xylan levels and assess their usefulness as short-rotation feedstocks for biorefineries. Three types of transgenic lines were tested in four-year field tests with RNAi constructs targeting either Populus GT43 clades B and C (GT43BC) corresponding to Arabidopsis clades IRX9 and IRX14, respectively, involved in xylan backbone biosynthesis, GATL1.1 corresponding to AtGALT1 involved in xylan reducing end sequence biosynthesis, or ASPR1 encoding an atypical aspartate protease. Their productivity, wood quality traits, and saccharification efficiency were analyzed. The only lines differing significantly from the wild type with respect to growth and biotic stress resistance were the ASPR1 lines, whose stems were roughly 10% shorter and narrower and leaves showed increased arthropod damage. GT43BC lines exhibited no growth advantage in the field despite their superior growth in greenhouse experiments. Wood from the ASPR1 and GT43BC lines had slightly reduced density due to thinner cell walls and, in the case of ASPR1, larger cell diameters. The xylan was less extractable by alkali but more hydrolysable by acid, had increased glucuronosylation, and its content was reduced in all three types of transgenic lines. The hemicellulose size distribution in the GALT1.1 and ASPR1 lines was skewed towards higher molecular mass compared to the wild type. These results provide experimental evidence that GATL1.1 functions in xylan biosynthesis and suggest that ASPR1 may regulate this process. In saccharification without pretreatment, lines of all three constructs provided 8-11% higher average glucose yields than wild-type plants. In saccharification with acid pretreatment, the GT43BC construct provided a 10% yield increase on average. The best transgenic lines of each construct are thus predicted to modestly outperform the wild type in terms of glucose yields per hectare. The field evaluation of transgenic xylan-reduced aspen represents an important step towards more productive feedstocks for biorefineries.", "doi": "10.3389/fpls.2023.1218302", "pmid": "37528966", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10389764"}], "notes": [], "created": "2023-08-30T07:07:10.054Z", "modified": "2025-10-17T13:03:13.754Z"}, {"entity": "publication", "iuid": "97f5481181f84542aee20a1691770a1e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/97f5481181f84542aee20a1691770a1e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/97f5481181f84542aee20a1691770a1e"}}, "title": "Fluorogenic properties of 4-dimethylaminocinnamaldehyde (DMACA) enable high resolution imaging of cell-wall-bound proanthocyanidins in plant root tissues.", "authors": [{"family": "Chowdhury", "given": "Jamil", "initials": "J"}, {"family": "Ferdous", "given": "Jannatul", "initials": "J"}, {"family": "Lihavainen", "given": "Jenna", "initials": "J"}, {"family": "Albrectsen", "given": "Benedicte Riber", "initials": "BR"}, {"family": "Lundberg-Felten", "given": "Judith", "initials": "J"}], "type": "journal article", "published": "2023-01-16", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "13", "pages": "1060804", "issn-l": "1664-462X"}, "abstract": "Proanthocyanidins (PAs) are polymeric phenolic compounds found in plants and used in many industrial applications. Despite strong evidence of herbivore and pathogen resistance-related properties of PAs, their in planta function is not fully understood. Determining the location and dynamics of PAs in plant tissues and cellular compartments is crucial to understand their mode of action. Such an approach requires microscopic localization with fluorescent dyes that specifically bind to PAs. Such dyes have hitherto been lacking. Here, we show that 4-dimethylaminocinnamaldehyde (DMACA) can be used as a PA-specific fluorescent dye that allows localization of PAs at high resolution in cell walls and inside cells using confocal microscopy, revealing features of previously unreported wall-bound PAs. We demonstrate several novel usages of DMACA as a fluorophore by taking advantage of its double staining compatibility with other fluorescent dyes. We illustrate the use of the dye alone and its co-localization with cell wall polymers in different Populus root tissues. The easy-to-use fluorescent staining method, together with its high photostability and compatibility with other fluorogenic dyes, makes DMACA a valuable tool for uncovering the biological function of PAs at a cellular level in plant tissues. DMACA can also be used in other plant tissues than roots, however care needs to be taken when tissues contain compounds that autofluoresce in the red spectral region which can be confounded with the PA-specific DMACA signal.", "doi": "10.3389/fpls.2022.1060804", "pmid": "36726681", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9884812"}], "notes": [], "created": "2023-08-30T07:07:04.961Z", "modified": "2025-10-17T13:03:14.479Z"}, {"entity": "publication", "iuid": "24fade919dbc45778aef41258830ece5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/24fade919dbc45778aef41258830ece5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/24fade919dbc45778aef41258830ece5"}}, "title": "IPT9, a cis-zeatin cytokinin biosynthesis gene, promotes root growth.", "authors": [{"family": "Antoniadi", "given": "Ioanna", "initials": "I"}, {"family": "Mateo-Bonmat\u00ed", "given": "Eduardo", "initials": "E"}, {"family": "Pernisov\u00e1", "given": "Mark\u00e9ta", "initials": "M"}, {"family": "Brunoni", "given": "Federica", "initials": "F"}, {"family": "Antoniadi", "given": "Mariana", "initials": "M"}, {"family": "Villalonga", "given": "Mauricio Garcia-Atance", "initials": "MG"}, {"family": "Ament", "given": "Anita", "initials": "A"}, {"family": "Kar\u00e1dy", "given": "Michal", "initials": "M"}, {"family": "Turnbull", "given": "Colin", "initials": "C"}, {"family": "Dole\u017eal", "given": "Karel", "initials": "K"}, {"family": "P\u011bn\u010d\u00edk", "given": "Ale\u0161", "initials": "A"}, {"family": "Ljung", "given": "Karin", "initials": "K"}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O"}], "type": "journal article", "published": "2022-10-14", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "13", "pages": "932008", "issn-l": "1664-462X"}, "abstract": "Cytokinin and auxin are plant hormones that coordinate many aspects of plant development. Their interactions in plant underground growth are well established, occurring at the levels of metabolism, signaling, and transport. Unlike many plant hormone classes, cytokinins are represented by more than one active molecule. Multiple mutant lines, blocking specific parts of cytokinin biosynthetic pathways, have enabled research in plants with deficiencies in specific cytokinin-types. While most of these mutants have confirmed the impeding effect of cytokinin on root growth, the ipt29 double mutant instead surprisingly exhibits reduced primary root length compared to the wild type. This mutant is impaired in cis-zeatin (cZ) production, a cytokinin-type that had been considered inactive in the past. Here we have further investigated the intriguing ipt29 root phenotype, opposite to known cytokinin functions, and the (bio)activity of cZ. Our data suggest that despite the ipt29 short-root phenotype, cZ application has a negative impact on primary root growth and can activate a cytokinin response in the stele. Grafting experiments revealed that the root phenotype of ipt29 depends mainly on local signaling which does not relate directly to cytokinin levels. Notably, ipt29 displayed increased auxin levels in the root tissue. Moreover, analyses of the differential contributions of ipt2 and ipt9 to the ipt29 short-root phenotype demonstrated that, despite its deficiency on cZ levels, ipt2 does not show any root phenotype or auxin homeostasis variation, while ipt9 mutants were indistinguishable from ipt29. We conclude that IPT9 functions may go beyond cZ biosynthesis, directly or indirectly, implicating effects on auxin homeostasis and therefore influencing plant growth.", "doi": "10.3389/fpls.2022.932008", "pmid": "36311087", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9616112"}], "notes": [], "created": "2022-12-05T08:06:44.349Z", "modified": "2025-10-17T13:03:14.613Z"}, {"entity": "publication", "iuid": "50214f3ea74a4cd89f24e91e10750c93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50214f3ea74a4cd89f24e91e10750c93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50214f3ea74a4cd89f24e91e10750c93"}}, "title": "Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae).", "authors": [{"family": "Thureborn", "given": "Olle", "initials": "O"}, {"family": "Razafimandimbison", "given": "Sylvain G", "initials": "SG"}, {"family": "Wikstr\u00f6m", "given": "Niklas", "initials": "N"}, {"family": "Rydin", "given": "Catarina", "initials": "C"}], "type": "journal article", "published": "2022-09-08", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "issn-l": "1664-462X", "volume": "13", "issue": null, "pages": "967456"}, "abstract": "Subfamily Rubioideae is the largest of the main lineages in the coffee family (Rubiaceae), with over 8,000 species and 29 tribes. Phylogenetic relationships among tribes and other major clades within this group of plants are still only partly resolved despite considerable efforts. While previous studies have mainly utilized data from the organellar genomes and nuclear ribosomal DNA, we here use a large number of low-copy nuclear genes obtained via a target capture approach to infer phylogenetic relationships within Rubioideae. We included 101 Rubioideae species representing all but two (the monogeneric tribes Foonchewieae and Aitchinsonieae) of the currently recognized tribes, and all but one non-monogeneric tribe were represented by more than one genus. Using data from the 353 genes targeted with the universal Angiosperms353 probe set we investigated the impact of data type, analytical approach, and potential paralogs on phylogenetic reconstruction. We inferred a robust phylogenetic hypothesis of Rubioideae with the vast majority (or all) nodes being highly supported across all analyses and datasets and few incongruences between the inferred topologies. The results were similar to those of previous studies but novel relationships were also identified. We found that supercontigs [coding sequence (CDS) + non-coding sequence] clearly outperformed CDS data in levels of support and gene tree congruence. The full datasets (353 genes) outperformed the datasets with potentially paralogous genes removed (186 genes) in levels of support but increased gene tree incongruence slightly. The pattern of gene tree conflict at short internal branches were often consistent with high levels of incomplete lineage sorting (ILS) due to rapid speciation in the group. While concatenation- and coalescence-based trees mainly agreed, the observed phylogenetic discordance between the two approaches may be best explained by their differences in accounting for ILS. The use of target capture data greatly improved our confidence and understanding of the Rubioideae phylogeny, highlighted by the increased support for previously uncertain relationships and the increased possibility to explore sources of underlying phylogenetic discordance.", "doi": "10.3389/fpls.2022.967456", "pmid": "36160958", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9493367"}, {"db": "Dryad", "key": "10.5061/dryad.d7wm37q44"}], "notes": [], "created": "2022-12-19T10:35:58.954Z", "modified": "2023-10-16T12:18:04.650Z"}, {"entity": "publication", "iuid": "d24d5bdf40f2440e9b4d6964e7517574", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d24d5bdf40f2440e9b4d6964e7517574.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d24d5bdf40f2440e9b4d6964e7517574"}}, "title": "Single, but not dual, attack by a biotrophic pathogen and a sap-sucking insect affects the oak leaf metabolome.", "authors": [{"family": "van Dijk", "given": "Laura J A", "initials": "LJA"}, {"family": "Regazzoni", "given": "Emilia D E", "initials": "EDE"}, {"family": "Albrectsen", "given": "Benedicte R", "initials": "BR"}, {"family": "Ehrl\u00e9n", "given": "Johan", "initials": "J"}, {"family": "Abdelfattah", "given": "Ahmed", "initials": "A"}, {"family": "Stenlund", "given": "Hans", "initials": "H"}, {"family": "Pawlowski", "given": "Katharina", "initials": "K"}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM"}], "type": "journal article", "published": "2022-08-03", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "13", "pages": "897186", "issn-l": "1664-462X"}, "abstract": "Plants interact with a multitude of microorganisms and insects, both below- and above ground, which might influence plant metabolism. Despite this, we lack knowledge of the impact of natural soil communities and multiple aboveground attackers on the metabolic responses of plants, and whether plant metabolic responses to single attack can predict responses to dual attack. We used untargeted metabolic fingerprinting (gas chromatography-mass spectrometry, GC-MS) on leaves of the pedunculate oak, Quercus robur, to assess the metabolic response to different soil microbiomes and aboveground single and dual attack by oak powdery mildew (Erysiphe alphitoides) and the common oak aphid (Tuberculatus annulatus). Distinct soil microbiomes were not associated with differences in the metabolic profile of oak seedling leaves. Single attacks by aphids or mildew had pronounced but different effects on the oak leaf metabolome, but we detected no difference between the metabolomes of healthy seedlings and seedlings attacked by both aphids and powdery mildew. Our findings show that aboveground attackers can have species-specific and non-additive effects on the leaf metabolome of oak. The lack of a metabolic signature detected by GC-MS upon dual attack might suggest the existence of a potential negative feedback, and highlights the importance of considering the impacts of multiple attackers to gain mechanistic insights into the ecology and evolution of species interactions and the structure of plant-associated communities, as well as for the development of sustainable strategies to control agricultural pests and diseases and plant breeding.", "doi": "10.3389/fpls.2022.897186", "pmid": "35991442", "labels": {"Swedish Metabolomics Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9381920"}, {"db": "Dryad", "key": "10.5061/dryad.vq83bk3w9"}], "notes": [], "created": "2022-12-05T08:09:35.854Z", "modified": "2025-10-17T13:03:14.786Z"}, {"entity": "publication", "iuid": "2488c6cb0e74465fb22eafbfe10e83fc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2488c6cb0e74465fb22eafbfe10e83fc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2488c6cb0e74465fb22eafbfe10e83fc"}}, "title": "Populus SVL Acts in Leaves to Modulate the Timing of Growth Cessation and Bud Set.", "authors": [{"family": "Andr\u00e9", "given": "Domenique", "initials": "D"}, {"family": "Zambrano", "given": "Jos\u00e9 Alfredo", "initials": "JA"}, {"family": "Zhang", "given": "Bo", "initials": "B"}, {"family": "Lee", "given": "Keh Chien", "initials": "KC"}, {"family": "R\u00fchl", "given": "Mark", "initials": "M"}, {"family": "Marcon", "given": "Alice", "initials": "A"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}], "type": "journal article", "published": "2022-02-17", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "issn-l": "1664-462X", "volume": "13", "issue": null, "pages": "823019"}, "abstract": "SHORT VEGETATIVE PHASE (SVP) is an important regulator of FLOWERING LOCUS T (FT) in the thermosensory pathway of Arabidopsis. It is a negative regulator of flowering and represses FT transcription. In poplar trees, FT2 is central for the photoperiodic control of growth cessation, which also requires the decrease of bioactive gibberellins (GAs). In angiosperm trees, genes similar to SVP, sometimes named DORMANCY-ASSOCIATED MADS-BOX genes, control temperature-mediated bud dormancy. Here we show that SVL, an SVP ortholog in aspen trees, besides its role in controlling dormancy through its expression in buds, is also contributing to the regulation of short day induced growth cessation and bud set through its expression in leaves. SVL is upregulated during short days in leaves and binds to the FT2 promoter to repress its transcription. It furthermore decreases the amount of active GAs, whose downregulation is essential for growth cessation, by repressing the transcription of GA20 oxidase. Finally, the SVL protein is more stable in colder temperatures, thus integrating the temperature signal into the response. We conclude that the molecular function of SVL in the photoperiodic pathway has been conserved between Arabidopsis and poplar trees, albeit the physiological process it controls has changed. SVL is thus both involved in regulating the photoperiod response in leaves, modulating the timing of growth cessation and bud set, and in the subsequent temperature regulation of dormancy in the buds.", "doi": "10.3389/fpls.2022.823019", "pmid": "35251092", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8891642"}], "notes": [], "created": "2022-03-29T13:48:44.625Z", "modified": "2024-01-16T13:48:37.467Z"}, {"entity": "publication", "iuid": "626a62e0410d42a690604515e58e829b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/626a62e0410d42a690604515e58e829b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/626a62e0410d42a690604515e58e829b"}}, "title": "Characterization of Dynamic Regulatory Gene and Protein Networks in Wheat Roots Upon Perceiving Water Deficit Through Comparative Transcriptomics Survey.", "authors": [{"family": "Rahimi", "given": "Yousef", "initials": "Y"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Bihamta", "given": "Mohammad Reza", "initials": "MR"}, {"family": "Alipour", "given": "Hadi", "initials": "H"}, {"family": "Taleei", "given": "Alireza", "initials": "A"}, {"family": "Khoshnoodi Jabar Abadi", "given": "Shaghayegh", "initials": "S"}], "type": "journal article", "published": "2021-08-16", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "12", "pages": "710867", "issn-l": "1664-462X"}, "abstract": "A well-developed root system benefits host plants by optimizing water absorption and nutrient uptake and thereby increases plant productivity. In this study we have characterized the root transcriptome using RNA-seq and subsequential functional analysis in a set of drought tolerant and susceptible genotypes. The goal of the study was to elucidate and characterize water deficit-responsive genes in wheat landraces that had been through long-term field and biochemical screening for drought tolerance. The results confirm genotype differences in water-deficit tolerance in line with earlier results from field trials. The transcriptomics survey highlighted a total of 14,187 differentially expressed genes (DEGs) that responded to water deficit. The characterization of these genes shows that all chromosomes contribute to water-deficit tolerance, but to different degrees, and the B genome showed higher involvement than the A and D genomes. The DEGs were mainly mapped to flavonoid, phenylpropanoid, and diterpenoid biosynthesis pathways, as well as glutathione metabolism and hormone signaling. Furthermore, extracellular region, apoplast, cell periphery, and external encapsulating structure were the main water deficit-responsive cellular components in roots. A total of 1,377 DEGs were also predicted to function as transcription factors (TFs) from different families regulating downstream cascades. TFs from the AP2/ERF-ERF, MYB-related, B3, WRKY, Tify, and NAC families were the main genotype-specific regulatory factors. To further characterize the dynamic biosynthetic pathways, protein-protein interaction (PPI) networks were constructed using significant KEGG proteins and putative TFs. In PPIs, enzymes from the CYP450, TaABA8OH2, PAL, and GST families play important roles in water-deficit tolerance in connection with MYB13-1, MADS-box, and NAC transcription factors.", "doi": "10.3389/fpls.2021.710867", "pmid": "34484273", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8415571"}], "notes": [], "created": "2022-01-16T21:08:45.935Z", "modified": "2024-01-16T13:48:38.732Z"}, {"entity": "publication", "iuid": "d48dec0c5acd4c628f8923ae5339eb5d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d48dec0c5acd4c628f8923ae5339eb5d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d48dec0c5acd4c628f8923ae5339eb5d"}}, "title": "Genomic Predictions With Nonadditive Effects Improved Estimates of Additive Effects and Predictions of Total Genetic Values in Pinus sylvestris.", "authors": [{"family": "Calleja-Rodriguez", "given": "Ainhoa", "initials": "A"}, {"family": "Chen", "given": "ZhiQiang", "initials": "Z"}, {"family": "Suontama", "given": "Mari", "initials": "M"}, {"family": "Pan", "given": "Jin", "initials": "J"}, {"family": "Wu", "given": "Harry X", "initials": "HX"}], "type": "journal article", "published": "2021-07-07", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "12", "pages": "666820", "issn-l": "1664-462X"}, "abstract": "Genomic selection study (GS) focusing on nonadditive genetic effects of dominance and the first order of epistatic effects, in a full-sib family population of 695 Scots pine (Pinus sylvestris L.) trees, was undertaken for growth and wood quality traits, using 6,344 single nucleotide polymorphism markers (SNPs) generated by genotyping-by-sequencing (GBS). Genomic marker-based relationship matrices offer more effective modeling of nonadditive genetic effects than pedigree-based models, thus increasing the knowledge on the relevance of dominance and epistatic variation in forest tree breeding. Genomic marker-based models were compared with pedigree-based models showing a considerable dominance and epistatic variation for growth traits. Nonadditive genetic variation of epistatic nature (additive \u00d7 additive) was detected for growth traits, wood density (DEN), and modulus of elasticity (MOEd) representing between 2.27 and 34.5% of the total phenotypic variance. Including dominance variance in pedigree-based Best Linear Unbiased Prediction (PBLUP) and epistatic variance in genomic-based Best Linear Unbiased Prediction (GBLUP) resulted in decreased narrow-sense heritability and increased broad-sense heritability for growth traits, DEN and MOEd. Higher genetic gains were reached with early GS based on total genetic values, than with conventional pedigree selection for a selection intensity of 1%. This study indicates that nonadditive genetic variance may have a significant role in the variation of selection traits of Scots pine, thus clonal deployment could be an attractive alternative for the species. Additionally, confidence in the role of nonadditive genetic effects in this breeding program should be pursued in the future, using GS.", "doi": "10.3389/fpls.2021.666820", "pmid": "34305966", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8294091"}], "notes": [], "created": "2021-10-01T09:03:48.743Z", "modified": "2024-01-16T13:48:39.125Z"}, {"entity": "publication", "iuid": "2b54f0133c7b43f9801e3f8e05389752", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b54f0133c7b43f9801e3f8e05389752.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b54f0133c7b43f9801e3f8e05389752"}}, "title": "Cryo-Electron Microscopy of Arabidopsis thaliana Phytochrome A in Its Pr State Reveals Head-to-Head Homodimeric Architecture.", "authors": [{"family": "Wahlgren", "given": "Weixiao Yuan", "initials": "WY"}, {"family": "Golonka", "given": "David", "initials": "D"}, {"family": "Westenhoff", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-6961-8015", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f1519bb234b43c6a13833b04e6720b8.json"}}, {"family": "M\u00f6glich", "given": "Andreas", "initials": "A"}], "type": "journal article", "published": "2021-04-21", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "12", "pages": "663751", "issn-l": "1664-462X"}, "abstract": "Phytochrome photoreceptors regulate vital adaptations of plant development, growth, and physiology depending on the ratio of red and far-red light. The light-triggered Z/E isomerization of a covalently bound bilin chromophore underlies phytochrome photoconversion between the red-absorbing Pr and far-red-absorbing Pfr states. Compared to bacterial phytochromes, the molecular mechanisms of signal propagation to the C-terminal module and its regulation are little understood in plant phytochromes, not least owing to a dearth of structural information. To address this deficit, we studied the Arabidopsis thaliana phytochrome A (AtphyA) at full length by cryo-electron microscopy (cryo-EM). Following heterologous expression in Escherichia coli, we optimized the solvent conditions to overcome protein aggregation and thus obtained photochemically active, near-homogenous AtphyA. We prepared grids for cryo-EM analysis of AtphyA in its Pr state and conducted single-particle analysis. The resulting two-dimensional class averages and the three-dimensional electron density map at 17 \u00c5 showed a homodimeric head-to-head assembly of AtphyA. Docking of domain structures into the electron density revealed a separation of the AtphyA homodimer at the junction of its photosensor and effector modules, as reflected in a large void in the middle of map. The overall architecture of AtphyA resembled that of bacterial phytochromes, thus hinting at commonalities in signal transduction and mechanism between these receptors. Our work paves the way toward future studies of the structure, light response, and interactions of full-length phytochromes by cryo-EM.", "doi": "10.3389/fpls.2021.663751", "pmid": "34108981", "labels": {"Cryo-EM": "Service", "Integrated Microscopy Technologies Gothenburg": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC8182759"}], "notes": [], "created": "2021-12-14T12:25:21.473Z", "modified": "2023-12-04T10:16:21.768Z"}, {"entity": "publication", "iuid": "252b7f8a80bd4a9bbd65b8df674d1aed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/252b7f8a80bd4a9bbd65b8df674d1aed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/252b7f8a80bd4a9bbd65b8df674d1aed"}}, "title": "Reaction Wood Anatomical Traits and Hormonal Profiles in Poplar Bent Stem and Root.", "authors": [{"family": "De Zio", "given": "Elena", "initials": "E"}, {"family": "Montagnoli", "given": "Antonio", "initials": "A"}, {"family": "Karady", "given": "Michal", "initials": "M"}, {"family": "Terzaghi", "given": "Mattia", "initials": "M"}, {"family": "Sferra", "given": "Gabriella", "initials": "G"}, {"family": "Antoniadi", "given": "Ioanna", "initials": "I"}, {"family": "Scippa", "given": "Gabriella S", "initials": "GS"}, {"family": "Ljung", "given": "Karin", "initials": "K"}, {"family": "Chiatante", "given": "Donato", "initials": "D"}, {"family": "Trupiano", "given": "Dalila", "initials": "D"}], "type": "journal article", "published": "2020-12-07", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "11", "issue": null, "pages": "590985", "issn-l": "1664-462X"}, "abstract": "Reaction wood (RW) formation is an innate physiological response of woody plants to counteract mechanical constraints in nature, reinforce structure and redirect growth toward the vertical direction. Differences and/or similarities between stem and root response to mechanical constraints remain almost unknown especially in relation to phytohormones distribution and RW characteristics. Thus, Populus nigra stem and root subjected to static non-destructive mid-term bending treatment were analyzed. The distribution of tension and compression forces was firstly modeled along the main bent stem and root axis; then, anatomical features, chemical composition, and a complete auxin and cytokinin metabolite profiles of the stretched convex and compressed concave side of three different bent stem and root sectors were analyzed. The results showed that in bent stems RW was produced on the upper stretched convex side whereas in bent roots it was produced on the lower compressed concave side. Anatomical features and chemical analysis showed that bent stem RW was characterized by a low number of vessel, poor lignification, and high carbohydrate, and thus gelatinous layer in fiber cell wall. Conversely, in bent root, RW was characterized by high vessel number and area, without any significant variation in carbohydrate and lignin content. An antagonistic interaction of auxins and different cytokinin forms/conjugates seems to regulate critical aspects of RW formation/development in stem and root to facilitate upward/downward organ bending. The observed differences between the response stem and root to bending highlight how hormonal signaling is highly organ-dependent.", "doi": "10.3389/fpls.2020.590985", "pmid": "33363556", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7754185"}], "notes": [], "created": "2021-01-12T12:46:48.308Z", "modified": "2025-10-17T13:03:16.508Z"}, {"entity": "publication", "iuid": "0b15b32dffe24e6c9ddd62c29e602101", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b15b32dffe24e6c9ddd62c29e602101.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b15b32dffe24e6c9ddd62c29e602101"}}, "title": "Evolutionary History of the Marchantia polymorpha Complex.", "authors": [{"family": "Linde", "given": "Anna-Malin", "initials": "AM"}, {"family": "Sawangproh", "given": "Weerachon", "initials": "W"}, {"family": "Cronberg", "given": "Nils", "initials": "N"}, {"family": "Sz\u00f6v\u00e9nyi", "given": "P\u00e9ter", "initials": "P"}, {"family": "Lagercrantz", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2020-06-26", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "11", "issue": null, "pages": "829", "issn-l": "1664-462X"}, "abstract": "The potential role of introgression in evolution has gained increased interest in recent years. Although some fascinating examples have been reported, more information is needed to generalize the importance of hybridization and introgression for adaptive divergence. As limited data exist on haploid dominant species, we analyzed genomes of three subspecies of the liverwort Marchantia polymorpha. We used available genomic data for subsp. ruderalis and carried out whole-genome (PacBio) sequencing for one individual each of subsp. montivagans and subsp. polymorpha as well as Illumina resequencing of additional genomes for all three subspecies. The three subspecies were compared against M. paleacea as outgroup. Our analyses revealed separation of the three taxa, but all three possible topologies were richly represented across the genomes, and the underlying divergence order less obvious. This uncertainty could be the result of the divergence of the three subspecies close in time, or that introgression has been frequent since divergence. In particular, we found that pseudo-chromosome 2 in subsp. montivagans was much more diverged than other parts of the genomes. This could either be explained by specific capture of chromosome 2 from an unknown related species through hybridization or by conservation of chromosome 2 despite intermittent or ongoing introgression affecting more permeable parts of the genomes. A higher degree of chromosomal rearrangements on pseudo-chromosome 2 support the second hypothesis. Species tree analyses recovered an overall topology where subsp. montivagans diverged first and subsp. ruderalis and subsp. polymorpha appeared as sister lineages. Each subspecies was associated with its own chloroplast and mitochondrial haplotype group. Our data suggest introgression but refute a previous hypothesis that subsp. ruderalis is a new stabilized hybrid between the other two subspecies.", "doi": "10.3389/fpls.2020.00829", "pmid": "32670318", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7332582"}], "notes": [], "created": "2020-08-25T13:05:18.846Z", "modified": "2024-01-16T13:48:42.341Z"}, {"entity": "publication", "iuid": "348be40f9f6a4ce29625b02c375ccea8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/348be40f9f6a4ce29625b02c375ccea8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/348be40f9f6a4ce29625b02c375ccea8"}}, "title": "Hybrid Aspen Expressing a Carbohydrate Esterase Family 5 Acetyl Xylan Esterase Under Control of a Wood-Specific Promoter Shows Improved Saccharification.", "authors": [{"family": "Wang", "given": "Zhao", "initials": "Z"}, {"family": "Pawar", "given": "Prashant Mohan-Anupama", "initials": "PM"}, {"family": "Derba-Maceluch", "given": "Marta", "initials": "M"}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "Chong", "given": "Sun-Li", "initials": "SL"}, {"family": "Tenkanen", "given": "Maija", "initials": "M"}, {"family": "J\u00f6nsson", "given": "Leif J", "initials": "LJ"}, {"family": "Mellerowicz", "given": "Ewa J", "initials": "EJ"}], "type": "journal article", "published": "2020-04-08", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "11", "issue": null, "pages": "380", "issn-l": "1664-462X"}, "abstract": "Fast-growing broad-leaf tree species can serve as feedstocks for production of bio-based chemicals and fuels through biochemical conversion of wood to monosaccharides. This conversion is hampered by the xylan acetylation pattern. To reduce xylan acetylation in the wood, the Hypocrea jecorina acetyl xylan esterase (HjAXE) from carbohydrate esterase (CE) family 5 was expressed in hybrid aspen under the control of the wood-specific PtGT43B promoter and targeted to the secretory pathway. The enzyme was predicted to deacetylate polymeric xylan in the vicinity of cellulose due to the presence of a cellulose-binding module. Cell-wall-bound protein fractions from developing wood of transgenic plants were capable of releasing acetyl from finely ground wood powder, indicative of active AXE present in cell walls of these plants, whereas no such activity was detected in wild-type plants. The transgenic lines grew in height and diameter as well as wild-type trees, whereas their internodes were slightly shorter, indicating higher leaf production. The average acetyl content in the wood of these lines was reduced by 13%, mainly due to reductions in di-acetylated xylose units, and in C-2 and C-3 mono-acetylated xylose units. Analysis of soluble cell wall polysaccharides revealed a 4% reduction in the fraction of xylose units and an 18% increase in the fraction of glucose units, whereas the contents of cellulose and lignin were not affected. Enzymatic saccharification of wood from transgenic plants resulted in 27% higher glucose yield than for wild-type plants. Brunauer-Emmett-Teller (BET) analysis and Simons' staining pointed toward larger surface area and improved cellulose accessibility for wood from transgenic plants compared to wood from wild-type plants, which could be achieved by HjAXE deacetylating xylan bound to cellulose. The results show that CE5 family can serve as a source of enzymes for in planta reduction of recalcitrance to saccharification.", "doi": "10.3389/fpls.2020.00380", "pmid": "32322259", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7156598"}], "notes": [], "created": "2020-11-24T20:26:42.680Z", "modified": "2025-10-17T13:03:57.020Z"}, {"entity": "publication", "iuid": "4709badbd0ff4384bde2d08fb256b773", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4709badbd0ff4384bde2d08fb256b773.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4709badbd0ff4384bde2d08fb256b773"}}, "title": "Ethylene Signaling Is Required for Fully Functional Tension Wood in Hybrid Aspen.", "authors": [{"family": "Seyfferth", "given": "Carolin", "initials": "C"}, {"family": "Wessels", "given": "Bernard A", "initials": "BA"}, {"family": "Gorzs\u00e1s", "given": "Andr\u00e1s", "initials": "A"}, {"family": "Love", "given": "Jonathan W", "initials": "JW"}, {"family": "R\u00fcggeberg", "given": "Markus", "initials": "M"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Vain", "given": "Thomas", "initials": "T"}, {"family": "Antos", "given": "Kamil", "initials": "K"}, {"family": "Tuominen", "given": "Hannele", "initials": "H"}, {"family": "Sundberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Felten", "given": "Judith", "initials": "J"}], "type": "journal article", "published": "2019-09-26", "journal": {"volume": "10", "issn": "1664-462X", "issue": null, "pages": "1101", "title": "Front Plant Sci", "issn-l": "1664-462X"}, "abstract": "Tension wood (TW) in hybrid aspen trees forms on the upper side of displaced stems to generate a strain that leads to uplifting of the stem. TW is characterized by increased cambial growth, reduced vessel frequency and diameter, and the presence of gelatinous, cellulose-rich (G-)fibers with its microfibrils oriented parallel to the fiber cell axis. Knowledge remains limited about the molecular regulators required for the development of this special xylem tissue with its characteristic morphological, anatomical, and chemical features. In this study, we use transgenic, ethylene-insensitive (ETI) hybrid aspen trees together with time-lapse imaging to show that functional ethylene signaling is required for full uplifting of inclined stems. X-ray diffraction and Raman microspectroscopy of TW in ETI trees indicate that, although G-fibers form, the cellulose microfibril angle in the G-fiber S-layer is decreased, and the chemical composition of S- and G-layers is altered than in wild-type TW. The characteristic asymmetric growth and reduction of vessel density is suppressed during TW formation in ETI trees. A genome-wide transcriptome profiling reveals ethylene-dependent genes in TW, related to cell division, cell wall composition, vessel differentiation, microtubule orientation, and hormone crosstalk. Our results demonstrate that ethylene regulates transcriptional responses related to the amount of G-fiber formation and their properties (chemistry and cellulose microfibril angle) during TW formation. The quantitative and qualitative changes in G-fibers are likely to contribute to uplifting of stems that are displaced from their original position.", "doi": "10.3389/fpls.2019.01101", "pmid": "31611886", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6775489"}], "notes": [], "created": "2019-12-02T16:50:54.206Z", "modified": "2020-01-21T13:56:15.400Z"}, {"entity": "publication", "iuid": "c1b33788aae54878be32e5126d6426ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1b33788aae54878be32e5126d6426ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1b33788aae54878be32e5126d6426ea"}}, "title": "Diplodia Tip Blight on Its Way to the North: Drivers of Disease Emergence in Northern Europe.", "authors": [{"family": "Brodde", "given": "Laura", "initials": "L"}, {"family": "Adamson", "given": "Kalev", "initials": "K"}, {"family": "Julio Camarero", "given": "J", "initials": "J"}, {"family": "Casta\u00f1o", "given": "Carles", "initials": "C"}, {"family": "Drenkhan", "given": "Rein", "initials": "R"}, {"family": "Lehtij\u00e4rvi", "given": "Asko", "initials": "A"}, {"family": "Luchi", "given": "Nicola", "initials": "N"}, {"family": "Migliorini", "given": "Duccio", "initials": "D"}, {"family": "S\u00e1nchez-Miranda", "given": "\u00c1ngela", "initials": "\u00c1"}, {"family": "Stenlid", "given": "Jan", "initials": "J"}, {"family": "\u00d6zda\u011f", "given": "\u015eule", "initials": "\u015e"}, {"family": "Oliva", "given": "Jon\u00e0s", "initials": "J"}], "type": "journal article", "published": "2019-01-09", "journal": {"volume": "9", "issn": "1664-462X", "issue": null, "pages": "1818", "title": "Front Plant Sci", "issn-l": "1664-462X"}, "abstract": "Disease emergence in northern and boreal forests has been mostly due to tree-pathogen encounters lacking a co-evolutionary past. However, outbreaks involving novel interactions of the host or the pathogen with the environment have been less well documented. Following an increase of records in Northern Europe, the first large outbreak of Diplodia sapinea on Pinus sylvestris was discovered in Sweden in 2016. By reconstructing the development of the epidemic, we found that the attacks started approx. 10 years back from several isolated trees in the stand and ended up affecting almost 90% of the trees in 2016. Limited damage was observed in other plantations in the surroundings of the affected stand, pointing to a new introduced pathogen as the cause of the outbreak. Nevertheless, no genetic differences based on SSR markers were found between isolates of the outbreak area and other Swedish isolates predating the outbreak or from other populations in Europe and Asia Minor. On a temporal scale, we saw that warm May and June temperatures were associated with higher damage and low tree growth, while cold and rainy conditions seemed to favor growth and deter disease. At a spatial scale, we saw that spread occurred predominantly in the SW aspect-area of the stand. Within that area and based on tree-ring and isotope (\u03b413C) analyses, we saw that disease occurred on trees that over the years had shown a lower water-use efficiency (WUE). Spore traps showed that highly infected trees were those producing the largest amount of inoculum. D. sapinea impaired latewood growth and reduced C reserves in needles and branches. D. sapinea attacks can cause serious economic damage by killing new shoots, disrupting the crown, and affecting the quality of stems. Our results show that D. sapinea has no limitations in becoming a serious pathogen in Northern Europe. Management should focus on reducing inoculum, especially since climate change may bring more favorable conditions for this pathogen. Seedlings for planting should be carefully inspected as D. sapinea may be present in a latent stage in asymptomatic tissues.", "doi": "10.3389/fpls.2018.01818", "pmid": "30687338", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6334237"}], "notes": [], "created": "2019-11-25T15:06:47.043Z", "modified": "2021-06-21T13:43:01.570Z"}, {"entity": "publication", "iuid": "35234fdfb5a84f84b1abdd29c159662c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/35234fdfb5a84f84b1abdd29c159662c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/35234fdfb5a84f84b1abdd29c159662c"}}, "title": "Comparative Analysis of the Nodule Transcriptomes of Ceanothus thyrsiflorus (Rhamnaceae, Rosales) and Datisca glomerata (Datiscaceae, Cucurbitales).", "authors": [{"family": "Salgado", "given": "Marco G", "initials": "MG"}, {"family": "van Velzen", "given": "Robin", "initials": "R"}, {"family": "Nguyen", "given": "Thanh Van", "initials": "TV"}, {"family": "Battenberg", "given": "Kai", "initials": "K"}, {"family": "Berry", "given": "Alison M", "initials": "AM"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Pawlowski", "given": "Katharina", "initials": "K"}], "type": "journal article", "published": "2018-11-14", "journal": {"volume": "9", "issn": "1664-462X", "issue": null, "pages": "1629", "title": "Front Plant Sci", "issn-l": "1664-462X"}, "abstract": "Two types of nitrogen-fixing root nodule symbioses are known, rhizobial and actinorhizal symbioses. The latter involve plants of three orders, Fagales, Rosales, and Cucurbitales. To understand the diversity of plant symbiotic adaptation, we compared the nodule transcriptomes of \r\n            Datisca glomerata (Datiscaceae, Cucurbitales) and Ceanothus thyrsiflorus (Rhamnaceae, Rosales); both species are nodulated by members of the uncultured Frankia clade, cluster II. The analysis focused on various features. In both species, the expression of orthologs of legume Nod factor receptor genes was elevated in nodules compared to roots. Since arginine has been postulated as export form of fixed nitrogen from symbiotic Frankia in nodules of D. glomerata, the question was whether the nitrogen metabolism was similar in nodules of C. thyrsiflorus. Analysis of the expression levels of key genes encoding enzymes involved in arginine metabolism revealed up-regulation of arginine catabolism, but no up-regulation of arginine biosynthesis, in nodules compared to roots of D. glomerata, while arginine degradation was not upregulated in nodules of C. thyrsiflorus. This new information corroborated an arginine-based metabolic exchange between host and microsymbiont for D. glomerata, but not for C. thyrsiflorus. Oxygen protection systems for nitrogenase differ dramatically between both species. Analysis of the antioxidant system suggested that the system in the nodules of D. glomerata leads to greater oxidative stress than the one in the nodules of C. thyrsiflorus, while no differences were found for the defense against nitrosative stress. However, induction of nitrite reductase in nodules of C. thyrsiflorus indicated that here, nitrite produced from nitric oxide had to be detoxified. Additional shared features were identified: genes encoding enzymes involved in thiamine biosynthesis were found to be upregulated in the nodules of both species. Orthologous nodule-specific subtilisin-like proteases that have been linked to the infection process in actinorhizal Fagales, were also upregulated in the nodules of D. glomerata and C. thyrsiflorus. Nodule-specific defensin genes known from actinorhizal Fagales and Cucurbitales, were also found in C. thyrsiflorus. In summary, the results underline the variability of nodule metabolism in different groups of symbiotic plants while pointing at conserved features involved in the infection process.", "doi": "10.3389/fpls.2018.01629", "pmid": "30487804", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6246699"}], "notes": [], "created": "2019-01-04T14:04:17.164Z", "modified": "2020-01-21T13:56:14.792Z"}, {"entity": "publication", "iuid": "b105e92bc27d4c6f92109308208147d7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b105e92bc27d4c6f92109308208147d7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b105e92bc27d4c6f92109308208147d7"}}, "title": "Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies", "authors": [{"family": "Akhter", "given": "Shirin", "initials": "S"}, {"family": "Kretzschmar", "given": "Warren W", "initials": "WW"}, {"family": "Nordal", "given": "Veronika", "initials": "V"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}, {"family": "Sundstr\u00f6m", "given": "Jens F", "initials": "JF"}], "type": "journal-article", "published": "2018-11-13", "journal": {"volume": "9", "issn": "1664-462X", "issue": null, "pages": null, "title": "Front Plant Sci", "issn-l": "1664-462X"}, "abstract": "Recent efforts to sequence the genomes and transcriptomes of several gymnosperm species have revealed an increased complexity in certain gene families in gymnosperms as compared to angiosperms. One example of this is the gymnosperm sister clade to angiosperm TM3-like MADS-box genes, which at least in the conifer lineage has expanded in number of genes. We have previously identified a member of this sub-clade, the conifer gene \n            DEFICIENS AGAMOUS LIKE 19 (DAL19), as being specifically upregulated in cone-setting shoots. Here, we show through Sanger sequencing of mRNA-derived cDNA and mapping to assembled conifer genomic sequences that DAL19 produces six mature mRNA splice variants in Picea abies. These splice variants use alternate first and last exons, while their four central exons constitute a core region present in all six transcripts. Thus, they are likely to be transcript isoforms. Quantitative Real-Time PCR revealed that two mutually exclusive first DAL19 exons are differentially expressed across meristems that will form either male or female cones, or vegetative shoots. Furthermore, mRNA in situ hybridization revealed that two mutually exclusive last DAL19 exons were expressed in a cell-specific pattern within bud meristems. Based on these findings in DAL19, we developed a sensitive approach to transcript isoform assembly from short-read sequencing of mRNA. We applied this method to 42 putative MADS-box core regions in P. abies, from which we assembled 1084 putative transcripts. We manually curated these transcripts to arrive at 933 assembled transcript isoforms of 38 putative MADS-box genes. 152 of these isoforms, which we assign to 28 putative MADS-box genes, were differentially expressed across eight female, male, and vegetative buds. We further provide evidence of the expression of 16 out of the 38 putative MADS-box genes by mapping PacBio Iso-Seq circular consensus reads derived from pooled sample sequencing to assembled transcripts. In summary, our analyses reveal the use of mutually exclusive exons of MADS-box gene isoforms during early bud development in P. abies, and we find that the large number of identified MADS-box transcripts in P. abies results not only from expansion of the gene family through gene duplication events but also from the generation of numerous splice variants.", "doi": "10.3389/fpls.2018.01625", "pmid": "30483285", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2018-12-10T06:26:27.642Z", "modified": "2020-01-21T13:56:17.461Z"}, {"entity": "publication", "iuid": "d18c20155398484b887a4a0859d2af8d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d18c20155398484b887a4a0859d2af8d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d18c20155398484b887a4a0859d2af8d"}}, "title": "How Does the Sweet Violet (Viola odorata L.) Fight Pathogens and Pests - Cyclotides as a Comprehensive Plant Host Defense System.", "authors": [{"family": "Slazak", "given": "Blazej", "initials": "B"}, {"family": "Kapusta", "given": "Ma\u0142gorzata", "initials": "M"}, {"family": "Str\u00f6mstedt", "given": "Adam A", "initials": "AA"}, {"family": "S\u0142omka", "given": "Aneta", "initials": "A"}, {"family": "Krychowiak", "given": "Marta", "initials": "M"}, {"family": "Shariatgorji", "given": "Mohammadreza", "initials": "M"}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE"}, {"family": "Bohdanowicz", "given": "Jerzy", "initials": "J"}, {"family": "Kuta", "given": "El\u017cbieta", "initials": "E"}, {"family": "G\u00f6ransson", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2018-09-11", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "9", "issue": null, "pages": "1296", "issn-l": "1664-462X"}, "abstract": "Cyclotides are cyclic plant polypeptides of 27-37 amino acid residues. They have been extensively studied in bioengineering and drug development contexts. However, less is known about the relevance of cyclotides for the plants producing them. The anti-insect larvae effects of kB1 and antibacterial activity of cyO2 suggest that cyclotides are a part of plant host defense. The sweet violet (Viola odorata L.) produces a wide array of cyclotides, including kB1 (kalata B1) and cyO2 (cycloviolacin O2), with distinct presumed biological roles. Here, we evaluate V. odorata cyclotides' potency against plant pathogens and their mode of action using bioassays, liposome experiments and immunogold labeling for transmission electron microscopy (TEM). We explore the link between the biological activity and distribution in plant generative, vegetative tissues and seeds, depicted by immunohistochemistry and matrix assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI). Cyclotides cyO2, cyO3, cyO13, and cyO19 are shown to have potent activity against model fungal plant pathogens (Fusarium oxysporum, F. graminearum, F. culmorum, Mycosphaerella fragariae, Botrytis cinerea) and fungi isolated from violets (Colletotrichum utrechtense and Alternaria alternata), with minimal inhibitory concentrations (MICs) ranging from 0.8 \u03bcM to 25 \u03bcM. Inhibition of phytopathogenic bacteria - Pseudomonas syringae pv. syringae, Dickeya dadantii and Pectobacterium atrosepticum - is also observed with MIC = 25-100 \u03bcM. A membrane-disrupting antifungal mode of action is shown. Finding cyO2 inside the fungal spore cells in TEM images may indicate that other, intracellular targets may be involved in the mechanism of toxicity. Fungi can not break down cyclotides in the course of days. varv A (kalata S) and kB1 show little potency against pathogenic fungi when compared with the tested cycloviolacins. cyO2, cyO3, cyO19 and kB1 are differentially distributed and found in tissues vulnerable to pathogen (epidermis, rizodermis, vascular bundles, protodermis, procambium, ovary walls, outer integuments) and pest (ground tissues of leaf and petiole) attacks, respectively, indicating a link between the cyclotides' sites of accumulation and biological role. Cyclotides emerge as a comprehensive defense system in V. odorata, in which different types of peptides have specific targets that determine their distribution in plant tissues.", "doi": "10.3389/fpls.2018.01296", "pmid": "30254654", "labels": {"Spatial Mass Spectrometry": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC6141879"}], "notes": [], "created": "2020-01-24T09:22:46.676Z", "modified": "2021-12-03T11:55:39.597Z"}, {"entity": "publication", "iuid": "adbb3f0858c64bf782b0320bc06f1884", "links": {"self": {"href": "https://publications.scilifelab.se/publication/adbb3f0858c64bf782b0320bc06f1884.json"}, "display": {"href": "https://publications.scilifelab.se/publication/adbb3f0858c64bf782b0320bc06f1884"}}, "title": "Ethylene-Related Gene Expression Networks in Wood Formation.", "authors": [{"family": "Seyfferth", "given": "Carolin", "initials": "C"}, {"family": "Wessels", "given": "Bernard", "initials": "B"}, {"family": "Jokipii-Lukkari", "given": "Soile", "initials": "S"}, {"family": "Sundberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Felten", "given": "Judith", "initials": "J"}, {"family": "Tuominen", "given": "Hannele", "initials": "H"}], "type": "journal article", "published": "2018-03-14", "journal": {"volume": "9", "issn": "1664-462X", "issue": null, "pages": "272", "title": "Front Plant Sci", "issn-l": "1664-462X"}, "abstract": "Thickening of tree stems is the result of secondary growth, accomplished by the meristematic activity of the vascular cambium. Secondary growth of the stem entails developmental cascades resulting in the formation of secondary phloem outwards and secondary xylem (i.e., wood) inwards of the stem. Signaling and transcriptional reprogramming by the phytohormone ethylene modifies cambial growth and cell differentiation, but the molecular link between ethylene and secondary growth remains unknown. We addressed this shortcoming by analyzing expression profiles and co-expression networks of ethylene pathway genes using the AspWood transcriptome database which covers all stages of secondary growth in aspen (", "doi": "10.3389/fpls.2018.00272", "pmid": "29593753", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5861219"}, {"db": "European Nucleotide Archive", "description": "https://www.ebi.ac.uk/ena/data/view/PRJEB11181", "key": "ERP012528"}], "notes": [], "created": "2018-10-31T19:45:23.194Z", "modified": "2024-01-16T13:48:46.764Z"}, {"entity": "publication", "iuid": "e5950d53038144a4b77f202d0af62c98", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5950d53038144a4b77f202d0af62c98.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5950d53038144a4b77f202d0af62c98"}}, "title": "The Arabidopsis TOR Kinase Specifically Regulates the Expression of Nuclear Genes Coding for Plastidic Ribosomal Proteins and the Phosphorylation of the Cytosolic Ribosomal Protein S6.", "authors": [{"family": "Dobrenel", "given": "Thomas", "initials": "T"}, {"family": "Mancera-Mart\u00ednez", "given": "Eder", "initials": "E"}, {"family": "Forzani", "given": "C\u00e9line", "initials": "C"}, {"family": "Azzopardi", "given": "Marianne", "initials": "M"}, {"family": "Davanture", "given": "Marl\u00e8ne", "initials": "M"}, {"family": "Moreau", "given": "Manon", "initials": "M"}, {"family": "Schepetilnikov", "given": "Mikhail", "initials": "M"}, {"family": "Chicher", "given": "Johana", "initials": "J"}, {"family": "Langella", "given": "Olivier", "initials": "O"}, {"family": "Zivy", "given": "Michel", "initials": "M"}, {"family": "Robaglia", "given": "Christophe", "initials": "C"}, {"family": "Ryabova", "given": "Lyubov A", "initials": "LA"}, {"family": "Hanson", "given": "Johannes", "initials": "J"}, {"family": "Meyer", "given": "Christian", "initials": "C"}], "type": "journal article", "published": "2016-11-07", "journal": {"volume": "7", "issn": "1664-462X", "issue": null, "pages": "1611", "title": "Front Plant Sci", "issn-l": "1664-462X"}, "abstract": "Protein translation is an energy consuming process that has to be fine-tuned at both the cell and organism levels to match the availability of resources. The target of rapamycin kinase (TOR) is a key regulator of a large range of biological processes in response to environmental cues. In this study, we have investigated the effects of TOR inactivation on the expression and regulation of Arabidopsis ribosomal proteins at different levels of analysis, namely from transcriptomic to phosphoproteomic. TOR inactivation resulted in a coordinated down-regulation of the transcription and translation of nuclear-encoded mRNAs coding for plastidic ribosomal proteins, which could explain the chlorotic phenotype of the TOR silenced plants. We have identified in the 5' untranslated regions (UTRs) of this set of genes a conserved sequence related to the 5' terminal oligopyrimidine motif, which is known to confer translational regulation by the TOR kinase in other eukaryotes. Furthermore, the phosphoproteomic analysis of the ribosomal fraction following TOR inactivation revealed a lower phosphorylation of the conserved Ser240 residue in the C-terminal region of the 40S ribosomal protein S6 (RPS6). These results were confirmed by Western blot analysis using an antibody that specifically recognizes phosphorylated Ser240 in RPS6. Finally, this antibody was used to follow TOR activity in plants. Our results thus uncover a multi-level regulation of plant ribosomal genes and proteins by the TOR kinase.", "doi": "10.3389/fpls.2016.01611", "pmid": "27877176", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5100631"}], "notes": [], "created": "2017-05-03T12:59:43.460Z", "modified": "2025-10-17T13:03:19.236Z"}, {"entity": "publication", "iuid": "82b076288ef3473ab74749e0f01fd49b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/82b076288ef3473ab74749e0f01fd49b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/82b076288ef3473ab74749e0f01fd49b"}}, "title": "The Aquaporin Splice Variant NbXIP1;1\u03b1 Is Permeable to Boric Acid and Is Phosphorylated in the N-terminal Domain.", "authors": [{"family": "Ampah-Korsah", "given": "Henry", "initials": "H"}, {"family": "Anderberg", "given": "Hanna I", "initials": "HI"}, {"family": "Engfors", "given": "Angelica", "initials": "A"}, {"family": "Kirscht", "given": "Andreas", "initials": "A"}, {"family": "Norden", "given": "Kristina", "initials": "K"}, {"family": "Kjellstrom", "given": "Sven", "initials": "S"}, {"family": "Kjellbom", "given": "Per", "initials": "P"}, {"family": "Johanson", "given": "Urban", "initials": "U"}], "type": "journal article", "published": "2016-06-16", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "7", "issue": null, "pages": "862", "issn-l": "1664-462X"}, "abstract": "Aquaporins (AQPs) are membrane channel proteins that transport water and uncharged solutes across different membranes in organisms in all kingdoms of life. In plants, the AQPs can be divided into seven different subfamilies and five of these are present in higher plants. The most recently characterized of these subfamilies is the XIP subfamily, which is found in most dicots but not in monocots. In this article, we present data on two different splice variants (\u03b1 and \u03b2) of NbXIP1;1 from Nicotiana benthamiana. We describe the heterologous expression of NbXIP1;1\u03b1 and \u03b2 in the yeast Pichia pastoris, the subcellular localization of the protein in this system and the purification of the NbXIP1;1\u03b1 protein. Furthermore, we investigated the functionality and the substrate specificity of the protein by stopped-flow spectrometry in P. pastoris spheroplasts and with the protein reconstituted in proteoliposomes. The phosphorylation status of the protein and localization of the phosphorylated amino acids were verified by mass spectrometry. Our results show that NbXIP1;1\u03b1 is located in the plasma membrane when expressed in P. pastoris, that it is not permeable to water but to boric acid and that the protein is phosphorylated at several amino acids in the N-terminal cytoplasmic domain of the protein. A growth assay showed that the yeast cells expressing the N-terminally His-tagged NbXIP1;1\u03b1 were more sensitive to boric acid as compared to the cells expressing the C-terminally His-tagged isoform. This might suggest that the N-terminal His-tag functionally mimics the phosphorylation of the N-terminal domain and that the N-terminal domain is involved in gating of the channel.", "doi": "10.3389/fpls.2016.00862", "pmid": "27379142", "labels": {"Structural Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC4909777"}], "notes": [], "created": "2020-01-27T10:05:59.459Z", "modified": "2021-05-24T15:39:50.282Z"}, {"entity": "publication", "iuid": "69c152e0a26d4b63a13a2298e1176dc8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69c152e0a26d4b63a13a2298e1176dc8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69c152e0a26d4b63a13a2298e1176dc8"}}, "title": "Genetic architecture of main effect QTL for heading date in European winter wheat.", "authors": [{"family": "Zanke", "given": "Christine", "initials": "C"}, {"family": "Ling", "given": "Jie", "initials": "J"}, {"family": "Plieske", "given": "J\u00f6rg", "initials": "J"}, {"family": "Kollers", "given": "Sonja", "initials": "S"}, {"family": "Ebmeyer", "given": "Erhard", "initials": "E"}, {"family": "Korzun", "given": "Viktor", "initials": "V"}, {"family": "Argillier", "given": "Odile", "initials": "O"}, {"family": "Stiewe", "given": "Gunther", "initials": "G"}, {"family": "Hinze", "given": "Maike", "initials": "M"}, {"family": "Beier", "given": "Sebastian", "initials": "S"}, {"family": "Ganal", "given": "Martin W", "initials": "MW"}, {"family": "R\u00f6der", "given": "Marion S", "initials": "MS"}], "type": "journal article", "published": "2014-05-20", "journal": {"volume": "5", "issn": "1664-462X", "issue": null, "pages": "217", "title": "Front Plant Sci", "issn-l": "1664-462X"}, "abstract": "A genome-wide association study (GWAS) for heading date (HD) was performed with a panel of 358 European winter wheat (Triticum aestivum L.) varieties and 14 spring wheat varieties through the phenotypic evaluation of HD in field tests in eight environments. Genotyping data consisted of 770 mapped microsatellite loci and 7934 mapped SNP markers derived from the 90K iSelect wheat chip. Best linear unbiased estimations (BLUEs) were calculated across all trials and ranged from 142.5 to 159.6 days after the 1st of January with an average value of 151.4 days. Considering only associations with a -log10 (P-value) \u2265 3.0, a total of 340 SSR and 2983 SNP marker-trait associations (MTAs) were detected. After Bonferroni correction for multiple testing, a total of 72 SSR and 438 SNP marker-trait associations remained significant. Highly significant MTAs were detected for the photoperiodism gene Ppd-D1, which was genotyped in all varieties. Consistent associations were found on all chromosomes with the highest number of MTAs on chromosome 5B. Linear regression showed a clear dependence of the HD score BLUEs on the number of favorable alleles (decreasing HD) and unfavorable alleles (increasing HD) per variety meaning that genotypes with a higher number of favorable or a low number of unfavorable alleles showed lower HD and therefore flowered earlier. For the vernalization gene Vrn-A2 co-locating MTAs on chromosome 5A, as well as for the photoperiodism genes Ppd-A1 and Ppd-B1 on chromosomes 2A and 2B were detected. After the construction of an integrated map of the SSR and SNP markers and by exploiting the synteny to sequenced species, such as rice and Brachypodium distachyon, we were able to demonstrate that a marker locus on wheat chromosome 5BL with homology to the rice photoperiodism gene Hd6 played a significant role in the determination of the heading date in wheat.", "doi": "10.3389/fpls.2014.00217", "pmid": "24904613", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC4033046"}], "notes": [], "created": "2017-05-04T14:58:35.795Z", "modified": "2020-01-21T13:56:02.806Z"}], "created": "2017-05-09T09:11:56.945Z", "modified": "2020-11-27T13:14:06.421Z"}