{"entity": "researcher", "timestamp": "2026-06-17T04:29:20.632Z", "family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "affiliations": ["Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden.", "Department of Organismal Biology - Systematic Biology, Uppsala University, 752 36, Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b"}}, "publications": [{"entity": "publication", "iuid": "eaf9b454889b42e98966f350d0a69e84", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eaf9b454889b42e98966f350d0a69e84.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eaf9b454889b42e98966f350d0a69e84"}}, "title": "A mosaic of modular variation at a single gene underpins convergent plumage coloration.", "authors": [{"family": "Lutgen", "given": "Dave", "initials": "D", "orcid": "0000-0003-0793-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/68173a10b32e4dca953933b92e0cec4e.json"}}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Chase", "given": "Madeline A", "initials": "MA", "orcid": "0000-0002-7916-3560", "researcher": {"href": "https://publications.scilifelab.se/researcher/3053121df4b64418bc1dcc2d7e50d87c.json"}}, {"family": "Kakhki", "given": "Niloofar Alaei", "initials": "NA"}, {"family": "Lammers", "given": "Fritjof", "initials": "F", "orcid": "0000-0002-3110-8220", "researcher": {"href": "https://publications.scilifelab.se/researcher/40a13a19d3594543a30c5146011aaa3a.json"}}, {"family": "de Souza", "given": "Stacey G", "initials": "SG", "orcid": "0000-0001-6596-5522", "researcher": {"href": "https://publications.scilifelab.se/researcher/63b19ded18de4742b8b0e63408500bc7.json"}}, {"family": "Ducrest", "given": "Anne-Lyse", "initials": "AL", "orcid": "0000-0001-6412-2769", "researcher": {"href": "https://publications.scilifelab.se/researcher/020a4c63ac834ff1a09234094ff552d2.json"}}, {"family": "Burri", "given": "Marta", "initials": "M"}, {"family": "Andriopoulos", "given": "Pavlos", "initials": "P", "orcid": "0000-0002-5377-2974", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef8407f9cb79440d80f580cef8536175.json"}}, {"family": "Lukhele", "given": "Sifiso M", "initials": "SM", "orcid": "0000-0003-0638-0641", "researcher": {"href": "https://publications.scilifelab.se/researcher/67a4a265644e452898bd89600ca081d8.json"}}, {"family": "Moysi", "given": "Michaella", "initials": "M"}, {"family": "Yohannes", "given": "Elizabeth", "initials": "E"}, {"family": "Abbasov", "given": "Abdin", "initials": "A", "orcid": "0009-0002-6370-9167", "researcher": {"href": "https://publications.scilifelab.se/researcher/de8b1ae2193849cc956e9750bfc47ead.json"}}, {"family": "Albayrak", "given": "Tamer", "initials": "T", "orcid": "0000-0003-4115-3946", "researcher": {"href": "https://publications.scilifelab.se/researcher/36f1ec59f0da42d89af256efda6c7db5.json"}}, {"family": "Aliabadian", "given": "Mansour", "initials": "M", "orcid": "0000-0002-3200-4853", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf133d36d2ec42bba680538cd5e69151.json"}}, {"family": "Auchli", "given": "Nicolas", "initials": "N"}, {"family": "Bontzorlos", "given": "Vasileios", "initials": "V", "orcid": "0000-0002-1276-3385", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebafa22103ec46ab87ce2b5fa878519d.json"}}, {"family": "Christoforou", "given": "Ioulios", "initials": "I"}, {"family": "Copete", "given": "Jos\u00e9 Luis", "initials": "JL", "orcid": "0000-0001-8542-0351", "researcher": {"href": "https://publications.scilifelab.se/researcher/e18b36757e804e0fb00a2f13015e79b6.json"}}, {"family": "Fulco", "given": "Egidio", "initials": "E"}, {"family": "Garcia", "given": "Jesus T", "initials": "JT"}, {"family": "Javakhishvili", "given": "Zura", "initials": "Z", "orcid": "0000-0001-7587-4974", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15c16f36f8d407d8b3c69723f6470e2.json"}}, {"family": "Kazazou", "given": "Anna", "initials": "A", "orcid": "0009-0003-6518-8833", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcdef2602fe44fd98f1b36f83acde23a.json"}}, {"family": "Lei", "given": "Fumin", "initials": "F", "orcid": "0000-0001-9920-8167", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e9cc44c016c4d099f674d182c08fbaa.json"}}, {"family": "Liu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4580-5518", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd2de623f33467b89b1cf800db4b3f5.json"}}, {"family": "Paposhvili", "given": "Nika", "initials": "N"}, {"family": "Patchett", "given": "Robert", "initials": "R", "orcid": "0000-0003-4105-3136", "researcher": {"href": "https://publications.scilifelab.se/researcher/787404ed66114f6ca1df945d9110ca8a.json"}}, {"family": "P\u00e9ter", "given": "\u00c1ron", "initials": "\u00c1", "orcid": "0000-0003-3219-9344", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b840805e45a4e0e95ade7ce7d0bdb99.json"}}, {"family": "Ritter", "given": "Raphael", "initials": "R", "orcid": "0009-0000-3060-1622", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b0db805e7214250b7df8d01e0803641.json"}}, {"family": "S\u00e1ndor", "given": "Attila D", "initials": "AD", "orcid": "0000-0001-8852-8341", "researcher": {"href": "https://publications.scilifelab.se/researcher/6db813f6be6943cc93dfbb9222bd112f.json"}}, {"family": "Schneider", "given": "Fabian", "initials": "F"}, {"family": "Shurulinkov", "given": "Petar", "initials": "P"}, {"family": "Sklyarenko", "given": "Sergey", "initials": "S", "orcid": "0000-0002-7443-347X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0de4c8591f1b4929ae73d3ea81ca2c17.json"}}, {"family": "Stumberger", "given": "Borut", "initials": "B"}, {"family": "Tagiyev", "given": "Abulfaz", "initials": "A"}, {"family": "Uboldi", "given": "Alessia", "initials": "A", "orcid": "0009-0001-3940-3697", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c73538105e441eb6a5402ad0883799.json"}}, {"family": "Vogiatzis", "given": "Nikitas", "initials": "N", "orcid": "0009-0008-9592-923X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9be0f74759fd4d429c3cb891c51d6e83.json"}}, {"family": "Taborsak-Lines", "given": "Fanny", "initials": "F"}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Yao", "given": "Liqun", "initials": "L"}, {"family": "Peichel", "given": "Catherine L", "initials": "CL", "orcid": "0000-0002-7731-8944", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b4d7c680f69458dbde56257ff4820c5.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Gagnaire", "given": "Pierre-Alexandre", "initials": "PA", "orcid": "0000-0002-1908-3235", "researcher": {"href": "https://publications.scilifelab.se/researcher/10f9487cea1d40938b3f9f00f72e6433.json"}}, {"family": "Kirschel", "given": "Alexander N G", "initials": "ANG", "orcid": "0000-0003-4379-7956", "researcher": {"href": "https://publications.scilifelab.se/researcher/d533e6378c094ef7bf44e570bcbb1145.json"}}, {"family": "Schweizer", "given": "Manuel", "initials": "M", "orcid": "0000-0002-7555-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a043d6f016b46709ace7f181d8cd3b8.json"}}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d7e24b36a24560bafa92f08848ac46.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f21e70e2864b42ab9fc532c14c069c.json"}}], "type": "journal article", "published": "2025-10-16", "journal": {"title": "Science", "issn": "1095-9203", "volume": "390", "issue": "6770", "pages": "eado8005", "issn-l": "0036-8075"}, "abstract": "The reshuffling of genomic variation from multiple origins is an important contributor to phenotypic diversification, yet insights into the evolutionary trajectories of this combinatorial process and their interplay with genetic architecture remain scarce. We show that convergent plumage color evolution in wheatears involves a monogenic architecture with modular variation introgressed at the agouti signaling protein (ASIP) locus. Introgression of a new transposable element insertion and linked protein-coding variation underpin a transspecific throat color polymorphism, which stable isotopes suggest is associated with alternative foraging niches. Cointrogression of linked regulatory ASIP variation resulted in mantle color convergence in one species, whereas convergent color evolution at the genus level required new variation. Our results demonstrate evolutionary trajectories from introgressed variation realized within the constraints of a monogenic architecture.", "doi": "10.1126/science.ado8005", "pmid": "41100596", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Short read": "Service", "NGI Other": "Service"}, "xrefs": [], "notes": [], "created": "2026-01-26T14:53:27.788Z", "modified": "2026-01-26T14:53:31.469Z"}, {"entity": "publication", "iuid": "94a6617807b3431a961787b517bc63a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/94a6617807b3431a961787b517bc63a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/94a6617807b3431a961787b517bc63a0"}}, "title": "Orthopteran Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and Evolution of Supergenes.", "authors": [{"family": "Jayaprasad", "given": "Suvratha", "initials": "S"}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Ellerstrand", "given": "Simon J", "initials": "SJ", "orcid": "0000-0003-2674-6997", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ed13c7732674cc992f2356848b97a7b.json"}}, {"family": "Rossini", "given": "Roberto", "initials": "R"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Pettersson", "given": "Olga V", "initials": "OV", "orcid": "0000-0002-5597-1870", "researcher": {"href": "https://publications.scilifelab.se/researcher/31689f508a984d0680d285c294669615.json"}}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA", "orcid": "0009-0002-8357-5186", "researcher": {"href": "https://publications.scilifelab.se/researcher/5419b796720a47c8aa7a26ca663a96bd.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3101-2285", "researcher": {"href": "https://publications.scilifelab.se/researcher/0db39539bdd94519a418e6dd7a287cc8.json"}}, {"family": "Bonath", "given": "Franziska", "initials": "F"}, {"family": "Bradford", "given": "Tessa M", "initials": "TM", "orcid": "0000-0003-0607-1398", "researcher": {"href": "https://publications.scilifelab.se/researcher/d434c308f143443b864dfb1137c9d549.json"}}, {"family": "Cooper", "given": "Steven J B", "initials": "SJB", "orcid": "0000-0002-7843-8438", "researcher": {"href": "https://publications.scilifelab.se/researcher/8df76e7fede64a0294cf68a3ae20a07c.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Kawakami", "given": "Takeshi", "initials": "T", "orcid": "0000-0002-9204-6852", "researcher": {"href": "https://publications.scilifelab.se/researcher/424031a0011f4e77bbb6f64a1d369b8b.json"}}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d7e24b36a24560bafa92f08848ac46.json"}}, {"family": "Palacios-Gimenez", "given": "Octavio M", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90e29ecd5724ff19509983e65891915.json"}}], "type": "journal article", "published": "2024-10-30", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "pages": "e17567", "issn-l": "0962-1083"}, "abstract": "The early evolution of sex chromosomes has remained obscure for more than a century. The Vandiemenella viatica species group of morabine grasshoppers is highly suited for studying the early stages of sex chromosome divergence and degeneration of the Y chromosome. This stems from the fact that neo-XY sex chromosomes have independently evolved multiple times by X-autosome fusions with different autosomes. Here, we generated new chromosome-level assemblies for two chromosomal races representing karyotypes with and without neo-sex chromosomes (P24XY and P24X0), and sequence data of a third chromosomal race with a different neo-XY chromosome system (P25XY). Interestingly, these two neo-XY chromosomal races are formed by different X-autosome fusions (involving chr1 and chrB, respectively), and we found that both neo-Y chromosomes have partly ceased to recombine with their neo-X counterpart. We show that the neo-XY chromosomes have diverged through accumulation of SNPs and structural mutations, and that many neo-Y-linked genes have degenerated since recombination ceased. However, the non-recombining regions of neo-Y chromosomes host non-degenerated genes crucial for sex determination, such as sex-lethal and transformer, alongside genes associated with spermatogenesis, fertility, and reproduction, illustrating their integrative role as a masculinizing supergene. Contrary to expectations, the neo-Y chromosomes showed (slightly) lower density of transposable elements (TEs) compared to other genomic regions. The study reveals the unique dynamics of young sex chromosomes, with evolution of recombination suppression and pronounced decay of (some) neo-sex chromosome genes, and provides a compelling case illustrating how chromosomal fusions and post-fusion mutational processes contribute to the evolution of supergenes.", "doi": "10.1111/mec.17567", "pmid": "39475093", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-10-31T12:37:22.766Z", "modified": "2024-11-25T10:27:35.236Z"}, {"entity": "publication", "iuid": "ca128e901f5f4cf484de05f16bcca9cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ca128e901f5f4cf484de05f16bcca9cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ca128e901f5f4cf484de05f16bcca9cc"}}, "title": "Contemporary intergeneric hybridization and backcrossing among birds-of-paradise.", "authors": [{"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications.scilifelab.se/researcher/e272339ca04d4daf935b708b04c5c53e.json"}}, {"family": "Soares", "given": "Andr\u00e9 E R", "initials": "AER"}, {"family": "M\u00fcller", "given": "Ingo A", "initials": "IA"}, {"family": "P\u00e4ckert", "given": "Martin", "initials": "M", "orcid": "0000-0001-5045-0139", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b587876461a4066b09d2bd5d3eaffc1.json"}}, {"family": "Frahnert", "given": "Sylke", "initials": "S"}, {"family": "van Grouw", "given": "Hein", "initials": "H"}, {"family": "Kamminga", "given": "Pepijn", "initials": "P"}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2024-09-00", "journal": {"title": "Evolution Letters", "issn": "2056-3744", "issn-l": "2056-3744", "volume": "8", "issue": "5", "pages": "680-694"}, "abstract": "Despite large differences in morphology, behavior and lek-mating strategies the birds-of-paradise are known to hybridize occasionally, even across different genera. Many of these bird-of-paradise hybrids were originally described as distinct species based on large morphological differences when compared to recognized species. Nowadays, these specimens are generally recognized as hybrids based on morphological assessments. Having fascinated naturalists for centuries, hybrid specimens of birds-of-paradise have been collected and the specimens kept in Natural History Collections. In the present study, we utilize this remarkable resource in a museomics framework and evaluate the genomic composition of most described intergeneric hybrids and some intrageneric hybrids. We show that the majority of investigated specimens are first-generation hybrids and that the parental species, in most cases, are in line with prior morphological assessments. We also identify two specimens that are the result of introgressive hybridization between different genera. Additionally, two specimens exhibit hybrid morphologies but have no identifiable signals of hybridization, which may indicate that minor levels of introgression can have large morphological effects. Our findings provide direct evidence of contemporary introgressive hybridization taking place between genera of birds-of-paradise in nature, despite markedly different morphologies and lek-mating behaviors.", "doi": "10.1093/evlett/qrae023", "pmid": "39328285", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11424083"}, {"db": "pii", "key": "qrae023"}], "notes": [], "created": "2024-10-18T07:14:19.442Z", "modified": "2024-11-25T10:23:13.047Z"}, {"entity": "publication", "iuid": "2c9906a7c1a0408f8006e723a38f488c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c9906a7c1a0408f8006e723a38f488c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c9906a7c1a0408f8006e723a38f488c"}}, "title": "An annotated chromosome-scale reference genome for Eastern black-eared wheatear (Oenanthe melanoleuca).", "authors": [{"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Palacios-Gimenez", "given": "Octavio Manuel", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90e29ecd5724ff19509983e65891915.json"}}, {"family": "Lutgen", "given": "Dave", "initials": "D", "orcid": "0000-0003-0793-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/68173a10b32e4dca953933b92e0cec4e.json"}}, {"family": "Olsen", "given": "Remi Andr\u00e9", "initials": "RA"}, {"family": "Alaei Kakhki", "given": "Niloofar", "initials": "N"}, {"family": "Andriopoulos", "given": "Pavlos", "initials": "P", "orcid": "0000-0002-5377-2974", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef8407f9cb79440d80f580cef8536175.json"}}, {"family": "Bontzorlos", "given": "Vasileios", "initials": "V", "orcid": "0000-0002-1276-3385", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebafa22103ec46ab87ce2b5fa878519d.json"}}, {"family": "Schweizer", "given": "Manuel", "initials": "M", "orcid": "0000-0002-7555-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a043d6f016b46709ace7f181d8cd3b8.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f21e70e2864b42ab9fc532c14c069c.json"}}], "type": "journal article", "published": "2023-06-01", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "issn-l": "2160-1836", "volume": "13", "issue": "6", "pages": null}, "abstract": "Pervasive convergent evolution and in part high incidences of hybridization distinguish wheatears (songbirds of the genus Oenanthe) as a versatile system to address questions at the forefront of research on the molecular bases of phenotypic and species diversification. To prepare the genomic resources for this venture, we here generated and annotated a chromosome-scale assembly of the Eastern black-eared wheatear (Oenanthe melanoleuca). This species is part of the Oenanthe hispanica complex that is characterized by convergent evolution of plumage coloration and high rates of hybridization. The long-read-based male nuclear genome assembly comprises 1.04 Gb in 32 autosomes, the Z chromosome, and the mitogenome. The assembly is highly contiguous (contig N50, 12.6 Mb; scaffold N50, 70 Mb), with 96% of the genome assembled at the chromosome level and 95.5% benchmarking universal single-copy orthologs (BUSCO) completeness. The nuclear genome was annotated with 18,143 protein-coding genes and 31,333 mRNAs (annotation BUSCO completeness, 98.0%), and about 10% of the genome consists of repetitive DNA. The annotated chromosome-scale reference genome of Eastern black-eared wheatear provides a crucial resource for research into the genomics of adaptation and speciation in an intriguing group of passerines.", "doi": "10.1093/g3journal/jkad088", "pmid": "37097035", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10234393"}, {"db": "pii", "key": "7141353"}], "notes": [], "created": "2023-08-15T06:59:21.634Z", "modified": "2024-01-16T13:48:33.264Z"}, {"entity": "publication", "iuid": "53bd8defe0fc42c288b7636a3e4b140b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/53bd8defe0fc42c288b7636a3e4b140b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/53bd8defe0fc42c288b7636a3e4b140b"}}, "title": "Satellite DNA evolution in Corvoidea inferred from short and long reads.", "authors": [{"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}], "type": "journal article", "published": "2022-04-30", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083"}, "abstract": "Satellite DNA (satDNA) is a fast-evolving portion of eukaryotic genomes. The homogeneous and repetitive nature of such satDNA causes problems during the assembly of genomes, and therefore it is still difficult to study it in detail in nonmodel organisms as well as across broad evolutionary timescales. Here, we combined the use of short- and long-read data to explore the diversity and evolution of satDNA between individuals of the same species and between genera of birds spanning ~40 millions of years of bird evolution using birds-of-paradise (Paradisaeidae) and crow (Corvus) species. These avian species highlighted the presence of a GC-rich Corvoidea satellitome composed of 61 satellite families and provided a set of candidate satDNA monomers for being centromeric on the basis of length, abundance, homogeneity and transcription. Surprisingly, we found that the satDNA of crow species rapidly diverged between closely related species while the satDNA appeared more similar between birds-of-paradise species belonging to different genera.", "doi": "10.1111/mec.16484", "pmid": "35488497", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2022-08-23T20:55:31.742Z", "modified": "2024-01-16T13:48:36.942Z"}, {"entity": "publication", "iuid": "6f70e1a8af3e47a5a3fa4fba74483b35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f70e1a8af3e47a5a3fa4fba74483b35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f70e1a8af3e47a5a3fa4fba74483b35"}}, "title": "The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities.", "authors": [{"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Palacios-Gimenez", "given": "Octavio M", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90e29ecd5724ff19509983e65891915.json"}}, {"family": "Blommaert", "given": "Julie", "initials": "J", "orcid": "0000-0003-1411-2313", "researcher": {"href": "https://publications.scilifelab.se/researcher/761067515ad240c9b82f0ea7625b1320.json"}}, {"family": "Liu", "given": "Jing", "initials": "J"}, {"family": "Haryoko", "given": "Tri", "initials": "T", "orcid": "0000-0002-8549-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e409936447e49ef9cb6fe1c75417fb0.json"}}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Zhou", "given": "Qi", "initials": "Q", "orcid": "0000-0002-7419-2047", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69266aa587d4126a23aa91c5bedfff8.json"}}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}], "type": "journal article", "published": "2021-09-13", "journal": {"title": "Philos. Trans. R. Soc. Lond., B, Biol. Sci.", "issn": "1471-2970", "issn-l": "0962-8436", "volume": "376", "issue": "1833", "pages": "20200186"}, "abstract": "It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the 'toxic-Y' effect in Drosophila males. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.", "doi": "10.1098/rstb.2020.0186", "pmid": "34304594", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8310711"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.5450746"}], "notes": [], "created": "2021-10-01T09:03:22.481Z", "modified": "2024-01-16T13:48:38.503Z"}, {"entity": "publication", "iuid": "9f8b33bd6320451d949e1d5d6500a865", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f8b33bd6320451d949e1d5d6500a865.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f8b33bd6320451d949e1d5d6500a865"}}, "title": "Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise.", "authors": [{"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Xu", "given": "Luohao", "initials": "L", "orcid": "0000-0002-3714-8047", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7a6a94d73cf4c50a22734e2a54099ba.json"}}, {"family": "Burri", "given": "Reto", "initials": "R"}, {"family": "Sullivan", "given": "Shawn", "initials": "S"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Liachko", "given": "Ivan", "initials": "I"}, {"family": "Haryoko", "given": "Tri", "initials": "T"}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA"}, {"family": "Zhou", "given": "Qi", "initials": "Q", "orcid": "0000-0002-7419-2047", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69266aa587d4126a23aa91c5bedfff8.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "volume": "21", "issue": "1", "pages": "263-286", "issn-l": "1755-098X"}, "abstract": "Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies now enable assembling genomes at unprecedented quality and contiguity. However, the difficulty in assembling repeat-rich and GC-rich regions (genomic \"dark matter\") limits insights into the evolution of genome structure and regulatory networks. Here, we compare the efficiency of currently available sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter. By adopting different de novo assembly strategies, we compare individual draft assemblies to a curated multiplatform reference assembly and identify the genomic features that cause gaps within each assembly. We show that a multiplatform assembly implementing long-read, linked-read and proximity sequencing technologies performs best at recovering transposable elements, multicopy MHC genes, GC-rich microchromosomes and the repeat-rich W chromosome. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is now possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects for optimized completeness of both the coding and noncoding parts of nonmodel genomes.", "doi": "10.1111/1755-0998.13252", "pmid": "32937018", "labels": {"Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7757076"}], "notes": [], "created": "2020-10-13T18:30:03.195Z", "modified": "2024-01-16T13:48:41.036Z"}, {"entity": "publication", "iuid": "c7e200350fda45a291ec77006ecc5bbb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7e200350fda45a291ec77006ecc5bbb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7e200350fda45a291ec77006ecc5bbb"}}, "title": "Discovery and population genomics of structural variation in a songbird genus.", "authors": [{"family": "Weissensteiner", "given": "Matthias H", "initials": "MH", "orcid": "0000-0001-9302-798X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5550a93e906d4e25985cd7641f8be554.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Catal\u00e1n", "given": "Ana", "initials": "A"}, {"family": "Francoijs", "given": "Kees-Jan", "initials": "KJ"}, {"family": "Knief", "given": "Ulrich", "initials": "U", "orcid": "0000-0001-6959-3033", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d8858c7c7b44a008a172bc637957ce1.json"}}, {"family": "Heim", "given": "Wieland", "initials": "W", "orcid": "0000-0002-3262-2491", "researcher": {"href": "https://publications.scilifelab.se/researcher/a88dd35e7b8a46b49c9e2ccc6d712b45.json"}}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Pophaly", "given": "Saurabh D", "initials": "SD"}, {"family": "Sedlazeck", "given": "Fritz J", "initials": "FJ"}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Warmuth", "given": "Vera M", "initials": "VM"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW"}], "type": "journal article", "published": "2020-07-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "3403"}, "abstract": "Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping.", "doi": "10.1038/s41467-020-17195-4", "pmid": "32636372", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-17195-4"}, {"db": "pmc", "key": "PMC7341801"}, {"db": "Dryad", "key": "10.5061/dryad.ns1rn8ppj"}], "notes": [], "created": "2020-08-25T12:55:18.199Z", "modified": "2024-01-16T13:48:42.202Z"}, {"entity": "publication", "iuid": "1138e1f8b82c448587d58bae89ae15a5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1138e1f8b82c448587d58bae89ae15a5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1138e1f8b82c448587d58bae89ae15a5"}}, "title": "Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds.", "authors": [{"family": "Xu", "given": "Luohao", "initials": "L"}, {"family": "Auer", "given": "Gabriel", "initials": "G"}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Deng", "given": "Yuan", "initials": "Y"}, {"family": "Feng", "given": "Shaohong", "initials": "S"}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f3c7981a1c43909817e72519232ff8.json"}}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK"}, {"family": "Christidis", "given": "Les", "initials": "L"}, {"family": "Prost", "given": "Stefan", "initials": "S"}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Zhou", "given": "Qi", "initials": "Q", "orcid": "0000-0002-7419-2047", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69266aa587d4126a23aa91c5bedfff8.json"}}], "type": "journal article", "published": "2019-05-00", "journal": {"volume": "3", "issn": "2397-334X", "issue": "5", "pages": "834-844", "title": "Nat Ecol Evol", "issn-l": "2397-334X"}, "abstract": "Songbirds have a species number close to that of mammals and are classic models for studying speciation and sexual selection. Sex chromosomes are hotspots of both processes, yet their evolutionary history in songbirds remains unclear. We characterized genomes of 11 songbird species, with 5 genomes of bird-of-paradise species. We conclude that songbird sex chromosomes have undergone four periods of recombination suppression before species radiation, producing a gradient of pairwise sequence divergence termed 'evolutionary strata'. The latest stratum was probably due to a songbird-specific burst of retrotransposon CR1-E1 elements at its boundary, instead of the chromosome inversion generally assumed for suppressing sex-linked recombination. The formation of evolutionary strata has reshaped the genomic architecture of both sex chromosomes. We find stepwise variations of Z-linked inversions, repeat and guanine-cytosine (GC) contents, as well as W-linked gene loss rate associated with the age of strata. A few W-linked genes have been preserved for their essential functions, indicated by higher and broader expression of lizard orthologues compared with those of other sex-linked genes. We also find a different degree of accelerated evolution of Z-linked genes versus autosomal genes among species, potentially reflecting diversified intensity of sexual selection. Our results uncover the dynamic evolutionary history of songbird sex chromosomes and provide insights into the mechanisms of recombination suppression.", "doi": "10.1038/s41559-019-0850-1", "pmid": "30936435", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-019-0850-1"}], "notes": [], "created": "2019-12-02T17:20:28.490Z", "modified": "2024-01-16T13:48:44.423Z"}]}