{"entity": "researcher", "timestamp": "2026-08-13T18:02:26.052Z", "family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "affiliations": ["Department of Zoology, Stockholm University, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16"}}, "publications": [{"entity": "publication", "iuid": "d822f5357c6a448b82142e0a1e71bdac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d822f5357c6a448b82142e0a1e71bdac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d822f5357c6a448b82142e0a1e71bdac"}}, "title": "Evolved and Plastic Gene Expression in Adaptation of a Specialist Fly to a Novel Niche.", "authors": [{"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}}, {"family": "Ortega Gim\u00e9nez", "given": "Jes\u00fas", "initials": "J", "orcid": "0000-0001-6599-1675", "researcher": {"href": "https://publications.scilifelab.se/researcher/e60538dadc0a4ee9ade7bc0015d67491.json"}}, {"family": "Choudhary", "given": "Shruti", "initials": "S", "orcid": "0000-0002-6146-7224", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6ebad9d4ddf40949a19776df31a00c7.json"}}, {"family": "Moss", "given": "Oliver", "initials": "O"}, {"family": "Su", "given": "Yi", "initials": "Y", "orcid": "0009-0001-4802-5210", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7f56487ba584ac5b08cfa6c06c6f7a6.json"}}, {"family": "Van Aken", "given": "Olivier", "initials": "O", "orcid": "0000-0003-4024-968X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f8174aa4d9e4031822ea281b6f0f9dd.json"}}, {"family": "Runemark", "given": "Anna", "initials": "A", "orcid": "0000-0002-8976-5530", "researcher": {"href": "https://publications.scilifelab.se/researcher/e914e2d1ccbd4d35ae574187762ae01f.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "34", "issue": "4", "pages": "e17653"}, "abstract": "How gene expression evolves to enable divergent ecological adaptation and how changes in gene expression relate to genomic architecture are pressing questions for understanding the mechanisms enabling adaptation and ecological speciation. Furthermore, how plasticity in gene expression can both contribute to and be affected by the process of ecological adaptation is crucial to understanding gene expression evolution, colonisation of novel niches and response to rapid environmental change. Here, we investigate the role of constitutive and plastic gene expression differences between host races, or host-specific ecotypes, of the peacock fly Tephritis conura, a thistle bud specialist. By cross-fostering larvae to new buds of their natal host plant or the alternative, novel host plant, we uncover extensive constitutive differences in gene expression between the host races, especially genes associated with processing of host plant chemicals. However, evidence for expression plasticity was minimal and limited to the ancestral host race. Genes with host race-specific expression are found more often than expected within a large inversion in the T. conura genome, adding to evidence that inversions are important for enabling diversification in the face of gene flow and underscores that altered gene expression may be key to understanding the evolutionary consequences of inversions.", "doi": "10.1111/mec.17653", "pmid": "39783891", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11789552"}], "notes": [], "created": "2025-01-30T10:48:38.552Z", "modified": "2025-11-28T10:51:21.794Z"}, {"entity": "publication", "iuid": "3bf46273f014498b80752db1b270c250", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3bf46273f014498b80752db1b270c250.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3bf46273f014498b80752db1b270c250"}}, "title": "Plasticity for the win: Flexible transcriptional response to host plant switches in the comma butterfly (Polygonia c-album).", "authors": [{"family": "Schneider", "given": "Katharina", "initials": "K", "orcid": "0009-0004-7727-594X", "researcher": {"href": "https://publications.scilifelab.se/researcher/27ac69b83e6e4a70ab1473838d162f61.json"}}, {"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}}, {"family": "Celorio-Mancera", "given": "Maria de la Paz", "initials": "MdlP"}, {"family": "Janz", "given": "Niklas", "initials": "N", "orcid": "0000-0002-6379-7905", "researcher": {"href": "https://publications.scilifelab.se/researcher/addc1292f6db4eeeacee907b4a534f52.json"}}, {"family": "Moberg", "given": "Dick", "initials": "D", "orcid": "0000-0001-5704-3915", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f9df1ca5bd343cdb148d7c8fbfc6f46.json"}}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.json"}}, {"family": "Nylin", "given": "S\u00f6ren", "initials": "S", "orcid": "0000-0003-4195-8920", "researcher": {"href": "https://publications.scilifelab.se/researcher/68d7f780ed30472eb2af408b0762c14d.json"}}], "type": "journal article", "published": "2024-08-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "33", "issue": "16", "pages": "e17479"}, "abstract": "Generalist plant-feeding insects are characterised by a broad host repertoire that can comprise several families or even different orders of plants. The genetic and physiological mechanisms underlying the use of such a wide host range are still not fully understood. Earlier studies indicate that the consumption of different host plants is associated with host-specific gene expression profiles. It remained, however, unclear if and how larvae can alter these profiles in the case of a changing host environment. Using the polyphagous comma butterfly (Polygonia c-album) we show that larvae can adjust their transcriptional profiles in response to a new host plant. The switch to some of the host plants, however, resulted in a larger transcriptional response and, thus, seems to be more challenging. At a physiological level, no correspondence for these patterns could be found in larval performance. This suggests that a high transcriptional but also phenotypic flexibility are essential for the use of a broad and diverse host range. We furthermore propose that host switch tests in the laboratory followed by transcriptomic investigations can be a valuable tool to examine not only plasticity in host use but also subtle and/or transient trade-offs in the evolution of host plant repertoires.", "doi": "10.1111/mec.17479", "pmid": "39036890", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-12T19:50:29.574Z", "modified": "2025-01-02T12:19:27.670Z"}, {"entity": "publication", "iuid": "2930d1923c4f4a50a0b8f52e9b9820db", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2930d1923c4f4a50a0b8f52e9b9820db.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2930d1923c4f4a50a0b8f52e9b9820db"}}, "title": "Genetic constraints in genes exhibiting splicing plasticity in facultative diapause.", "authors": [{"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}}, {"family": "Pruisscher", "given": "Peter", "initials": "P"}, {"family": "Roberts", "given": "Kevin T", "initials": "KT", "orcid": "0000-0003-2785-5108", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f74402c368a41f2b5610a946770cbe1.json"}}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "volume": "132", "issue": "3", "pages": "142-155", "issn-l": "0018-067X"}, "abstract": "Phenotypic plasticity is produced and maintained by processes regulating the transcriptome. While differential gene expression is among the most important of these processes, relatively little is known about other sources of transcriptional variation. Previous work suggests that alternative splicing plays an extensive and functionally unique role in transcriptional plasticity, though plastically spliced genes may be more constrained than the remainder of expressed genes. In this study, we explore the relationship between expression and splicing plasticity, along with the genetic diversity in those genes, in an ecologically consequential polyphenism: facultative diapause. Using 96 samples spread over two tissues and 10 timepoints, we compare the extent of differential splicing and expression between diapausing and direct developing pupae of the butterfly Pieris napi. Splicing differs strongly between diapausing and direct developing trajectories but alters a smaller and functionally unique set of genes compared to differential expression. We further test the hypothesis that among these expressed loci, plastically spliced genes are likely to experience the strongest purifying selection to maintain seasonally plastic phenotypes. Genes with unique transcriptional changes through diapause consistently had the lowest nucleotide diversity, and this effect was consistently stronger among genes that were differentially spliced compared to those with just differential expression through diapause. Further, the strength of negative selection was higher in the population expressing diapause every generation. Our results suggest that maintenance of the molecular mechanisms involved in diapause progression, including post-transcriptional modifications, are highly conserved and likely to experience genetic constraints, especially in northern populations of P. napi.", "doi": "10.1038/s41437-024-00669-2", "pmid": "38291272", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10923799"}, {"db": "pii", "key": "10.1038/s41437-024-00669-2"}], "notes": [], "created": "2024-03-14T11:16:17.218Z", "modified": "2025-02-28T14:14:07.422Z"}, {"entity": "publication", "iuid": "402524da476a4884a9495be39fc7f50c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/402524da476a4884a9495be39fc7f50c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/402524da476a4884a9495be39fc7f50c"}}, "title": "Larval transcriptomes reflect the evolutionary history of plant-insect associations.", "authors": [{"family": "de la Paz Celorio-Mancera", "given": "Maria", "initials": "M", "orcid": "0000-0003-0296-0577", "researcher": {"href": "https://publications.scilifelab.se/researcher/2abfa65f99b44f1ba6f8f0e6f3d7d8a4.json"}}, {"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}}, {"family": "Pruisscher", "given": "Peter", "initials": "P"}, {"family": "Smialowska", "given": "Agata", "initials": "A"}, {"family": "Pires Braga", "given": "Mariana", "initials": "M", "orcid": "0000-0002-1253-2536", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab296645778b4d97959314bf28c8209a.json"}}, {"family": "Janz", "given": "Niklas", "initials": "N"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.json"}}, {"family": "Nylin", "given": "S\u00f6ren", "initials": "S"}], "type": "journal article", "published": "2023-02-04", "journal": {"title": "Evolution", "issn": "1558-5646", "volume": "77", "issue": "2", "pages": "519-533", "issn-l": "0014-3820"}, "abstract": "In this study, we investigated whether patterns of gene expression in larvae feeding on different plants can explain important aspects of the evolution of insect-plant associations, such as phylogenetic conservatism of host use and re-colonization of ancestral hosts that have been lost from the host repertoire. To this end, we performed a phylogenetically informed study comparing the transcriptomes of 4 nymphalid butterfly species in Polygonia and the closely related genus Nymphalis. Larvae were reared on Urtica dioica, Salix spp., and Ribes spp. Plant-specific gene expression was found to be similar across butterfly species, even in the case of host plants that are no longer used by two of the butterfly species. These results suggest that plant-specific transcriptomes can be robust over evolutionary time. We propose that adaptations to particular larval food plants can profitably be understood as an evolved set of modules of co-expressed genes, promoting conservatism in host use and facilitating re-colonization. Moreover, we speculate that the degree of overlap between plant-specific transcriptomes may correlate with the strength of trade-offs between plants as resources and hence to the probability of colonizing hosts and complete host shifts.", "doi": "10.1093/evolut/qpac049", "pmid": "36625474", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6881564"}], "notes": [], "created": "2023-05-17T08:45:56.948Z", "modified": "2024-01-16T13:48:33.977Z"}, {"entity": "publication", "iuid": "cd197346a3404e49b2b51b03e1b7f753", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cd197346a3404e49b2b51b03e1b7f753.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cd197346a3404e49b2b51b03e1b7f753"}}, "title": "High-Quality Genome Assembly and Comprehensive Transcriptome of the Painted Lady Butterfly Vanessa cardui.", "authors": [{"family": "Zhang", "given": "Linlin", "initials": "L", "orcid": "0000-0003-0247-7710", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a9f542614414a63a2435f1e0790be58.json"}}, {"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Reed", "given": "Robert D", "initials": "RD"}], "type": "journal article", "published": "2021-07-06", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "13", "issue": "7", "issn-l": "1759-6653"}, "abstract": "The painted lady butterfly, Vanessa cardui, has the longest migration routes, the widest hostplant diversity, and one of the most complex wing patterns of any insect. Due to minimal culturing requirements, easily characterized wing pattern elements, and technical feasibility of CRISPR/Cas9 genome editing, V. cardui is emerging as a functional genomics model for diverse research programs. Here, we report a high-quality, annotated genome assembly of the V. cardui genome, generated using 84\u00d7 coverage of PacBio long-read data, which we assembled into 205 contigs with a total length of 425.4 Mb (N50 = 10.3 Mb). The genome was very complete (single-copy complete Benchmarking Universal Single-Copy Orthologs [BUSCO] 97%), with contigs assembled into presumptive chromosomes using synteny analyses. Our annotation used embryonic, larval, and pupal transcriptomes, and 20 transcriptomes across five different wing developmental stages. Gene annotations showed a high level of accuracy and completeness, with 14,437 predicted protein-coding genes. This annotated genome assembly constitutes an important resource for diverse functional genomic studies ranging from the developmental genetic basis of butterfly color pattern, to coevolution with diverse hostplants.", "doi": "10.1093/gbe/evab145", "pmid": "34282459", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6310739"}, {"db": "pmc", "key": "PMC8290113"}], "notes": [], "created": "2021-10-01T09:02:33.146Z", "modified": "2024-01-16T13:48:39.151Z"}, {"entity": "publication", "iuid": "7a887e2d751543cda0fd97112b70afe0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a887e2d751543cda0fd97112b70afe0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a887e2d751543cda0fd97112b70afe0"}}, "title": "Chromosome Level Assembly of the Comma Butterfly (Polygonia c-album).", "authors": [{"family": "Celorio-Mancera", "given": "Maria de la Paz", "initials": "MP", "orcid": "0000-0003-0296-0577", "researcher": {"href": "https://publications.scilifelab.se/researcher/2abfa65f99b44f1ba6f8f0e6f3d7d8a4.json"}}, {"family": "Rastas", "given": "Pasi", "initials": "P", "orcid": "0000-0003-2768-1339", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a8f5f2160154bdfa0b21dfc132d4871.json"}}, {"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}}, {"family": "Nylin", "given": "Soren", "initials": "S", "orcid": "0000-0003-4195-8920", "researcher": {"href": "https://publications.scilifelab.se/researcher/68d7f780ed30472eb2af408b0762c14d.json"}}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.json"}}], "type": "journal article", "published": "2021-05-07", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "13", "issue": "5", "issn-l": "1759-6653"}, "abstract": "The comma butterfly (Polygonia c-album, Nymphalidae, Lepidoptera) is a model insect species, most notably in the study of phenotypic plasticity and plant-insect coevolutionary interactions. In order to facilitate the integration of genomic tools with a diverse body of ecological and evolutionary research, we assembled the genome of a Swedish comma using 10X sequencing, scaffolding with matepair data, genome polishing, and assignment to linkage groups using a high-density linkage map. The resulting genome is 373 Mb in size, with a scaffold N50 of 11.7 Mb and contig N50 of 11,2Mb. The genome contained 90.1% of single-copy Lepidopteran orthologs in a BUSCO analysis of 5,286 genes. A total of 21,004 gene-models were annotated on the genome using RNA-Seq data from larval and adult tissue in combination with proteins from the Arthropoda database, resulting in a high-quality annotation for which functional annotations were generated. We further documented the quality of the chromosomal assembly via synteny assessment with Melitaea cinxia. The resulting annotated, chromosome-level genome will provide an important resource for investigating coevolutionary dynamics and comparative analyses in Lepidoptera.", "doi": "10.1093/gbe/evab054", "pmid": "33749729", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6179806"}, {"db": "pmc", "key": "PMC8140205"}], "notes": [], "created": "2021-06-09T12:14:35.404Z", "modified": "2024-01-16T13:48:39.799Z"}]}