{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T05:03:08Z","timestamp":1784005388278,"version":"3.55.0"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,1,31]],"date-time":"2025-01-31T00:00:00Z","timestamp":1738281600000},"content-version":"vor","delay-in-days":30,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["21-74-20145"],"award-info":[{"award-number":["21-74-20145"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The genus Capsella serves as a model for understanding speciation, hybridization, and genome evolution in plants. Here, we present a chromosome-scale genome assembly of Capsella orientalis, the maternal progenitor of a cosmopolitan allotetraploid C. bursa-pastoris. Using nanopore sequencing and data on chromatin contacts (Hi-C), we assembled the genome into eight pseudo-chromosomes with high contiguity, evidenced by a benchmarking universal single-copy orthologs (BUSCO) completeness score of 99.3%. Comparative analysis with C. rubella and C. bursa-pastoris revealed overall synteny, except for 2\u2005Mb inversion on chromosome 4 of C. rubella. Comparative genome analysis highlighted the conservation of gene content and structural integrity in the C. orientalis-derived subgenome of C. bursa-pastoris, with the exception of a 1.8\u2005Mb region absent in O subgenome but present in C. orientalis. The genome annotation includes 27,675 protein-coding genes, with most exhibiting one-to-one orthology with Arabidopsis thaliana. Notably, 2,155 genes showed no similarity to A. thaliana ones. These results establish a robust genomic resource for C. orientalis, facilitating future studies on polyploid evolution, gene regulation, and species divergence within Capsella.<\/jats:p>","DOI":"10.1093\/gbe\/evaf009","type":"journal-article","created":{"date-parts":[[2025,1,31]],"date-time":"2025-01-31T12:40:56Z","timestamp":1738327256000},"source":"Crossref","is-referenced-by-count":1,"title":["Chromosome-Scale Assembly of <i>Capsella orientalis<\/i>, Maternal Progenitor of Cosmopolitan Allotetraploid <i>C. bursa-pastoris<\/i>"],"prefix":"10.1093","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-4329-2861","authenticated-orcid":false,"given":"Alexandra M","family":"Kasianova","sequence":"first","affiliation":[{"name":"Skolkovo Institute of Science and Technology, Center of Molecular and Cellular Biology , Moscow ,","place":["Russia"]},{"name":"Institute of Information Transmission Problems, Laboratory of Plant Genomics , Moscow ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-6449-8672","authenticated-orcid":false,"given":"Vladislav D","family":"Mityukov","sequence":"additional","affiliation":[{"name":"Institute of Gene Biology, Laboratory of Structural and Functional Organisation of Chromosomes , Moscow ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7951-1644","authenticated-orcid":false,"given":"Dmitry A","family":"German","sequence":"additional","affiliation":[{"name":"Altai State University , South-Siberian Botanical Garden, Barnaul ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8086-392X","authenticated-orcid":false,"given":"Artem S","family":"Kasianov","sequence":"additional","affiliation":[{"name":"BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO , Vair\u00e3o ,","place":["Portugal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9057-3974","authenticated-orcid":false,"given":"Aleksey A","family":"Penin","sequence":"additional","affiliation":[{"name":"Institute of Information Transmission Problems, Laboratory of Plant Genomics , Moscow ,","place":["Russia"]},{"name":"Vavilov Institute of General Genetics, Laboratory of Plant Genomics , Moscow ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8940-0400","authenticated-orcid":false,"given":"Maria D","family":"Logacheva","sequence":"additional","affiliation":[{"name":"Skolkovo Institute of Science and Technology, Center of Molecular and Cellular Biology , Moscow ,","place":["Russia"]},{"name":"Institute of Information Transmission Problems, Laboratory of Plant Genomics , Moscow ,","place":["Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,1,31]]},"reference":[{"issue":"1","key":"2025020106524897900_evaf009-B1","doi-asserted-by":"publisher","first-page":"602","DOI":"10.1186\/1471-2164-15-602","article-title":"Mating system shifts and transposable element evolution in the plant genus Capsella","volume":"15","author":"\u00c5gren","year":"2014","journal-title":"BMC Genomics"},{"issue":"1","key":"2025020106524897900_evaf009-B2","doi-asserted-by":"publisher","first-page":"lqaa108","DOI":"10.1093\/nargab\/lqaa108","article-title":"BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database","volume":"3","author":"Br\u016fna","year":"2021","journal-title":"NAR Genom Bioinform"},{"issue":"1","key":"2025020106524897900_evaf009-B3","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"2025020106524897900_evaf009-B4","doi-asserted-by":"publisher","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"issue":"1","key":"2025020106524897900_evaf009-B5","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"issue":"3","key":"2025020106524897900_evaf009-B6","first-page":"5","article-title":"Cruciferae of European Russia","volume":"5","author":"Dorofeyev","year":"2002","journal-title":"Turczaninowia"},{"issue":"9","key":"2025020106524897900_evaf009-B7","doi-asserted-by":"publisher","first-page":"2806","DOI":"10.1073\/pnas.1412277112","article-title":"Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris","volume":"112","author":"Douglas","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025020106524897900_evaf009-B8","first-page":"11","article-title":"A rapid DNA isolation procedure for small quantities of fresh leaf tissue","volume":"19","author":"Doyle","year":"1987","journal-title":"Phytochemical Bull"},{"issue":"1","key":"2025020106524897900_evaf009-B9","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.cels.2015.07.012","article-title":"Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom","volume":"3","author":"Durand","year":"2016","journal-title":"Cell Syst"},{"issue":"17","key":"2025020106524897900_evaf009-B10","doi-asserted-by":"publisher","first-page":"9451","DOI":"10.1073\/pnas.1921046117","article-title":"RepeatModeler2 for automated genomic discovery of transposable element families","volume":"117","author":"Flynn","year":"2020","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"2025020106524897900_evaf009-B11","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1111\/j.1756-1051.2011.01341.x","article-title":"Plant genera and species new to China recently found in northwest Xinjiang","volume":"30","author":"German","year":"2012","journal-title":"Nord J Bot"},{"key":"2025020106524897900_evaf009-B12","first-page":"5","article-title":"Some interesting records of Cruciferae in Asia","volume":"101","author":"German","year":"2009","journal-title":"Animadv Syst Herb Kryl Univ Tomsk"},{"issue":"13","key":"2025020106524897900_evaf009-B13","doi-asserted-by":"publisher","first-page":"5246","DOI":"10.1073\/pnas.0808012106","article-title":"Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck","volume":"106","author":"Guo","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"13","key":"2025020106524897900_evaf009-B14","doi-asserted-by":"publisher","first-page":"3531","DOI":"10.1093\/jxb\/erl158","article-title":"Catching a \u2018hopeful monster\u2019: shepherd\u2019s purse (Capsella bursa-pastoris) as a model system to study the evolution of flower development","volume":"57","author":"Hintz","year":"2006","journal-title":"J Exp Bot"},{"issue":"5","key":"2025020106524897900_evaf009-B15","doi-asserted-by":"publisher","first-page":"767","DOI":"10.1093\/bioinformatics\/btv661","article-title":"BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS","volume":"32","author":"Hoff","year":"2016","journal-title":"Bioinformatics"},{"key":"2025020106524897900_evaf009-B16","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1007\/978-1-4939-9173-0_5","article-title":"Whole-genome annotation with BRAKER","volume":"1962","author":"Hoff","year":"2019","journal-title":"Methods Mol Biol"},{"issue":"7","key":"2025020106524897900_evaf009-B17","doi-asserted-by":"publisher","first-page":"2253","DOI":"10.1093\/bioinformatics\/btz891","article-title":"NextPolish: a fast and efficient genome polishing tool for long-read assembly","volume":"36","author":"Hu","year":"2020","journal-title":"Bioinformatics"},{"issue":"1","key":"2025020106524897900_evaf009-B18","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1186\/s13059-024-03252-4","article-title":"NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads","volume":"25","author":"Hu","year":"2024","journal-title":"Genome Biol"},{"issue":"2","key":"2025020106524897900_evaf009-B19","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1111\/tpj.13563","article-title":"High-quality genome assembly of Capsella Bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution","volume":"91","author":"Kasianov","year":"2017","journal-title":"Plant J"},{"key":"2025020106524897900_evaf009-B20","doi-asserted-by":"publisher","first-page":"714711","DOI":"10.3389\/fpls.2021.714711","article-title":"lepidium-like, a naturally occurring mutant of Capsella bursa-pastoris, and its implications on the evolution of petal loss in Cruciferae","volume":"12","author":"Klepikova","year":"2021","journal-title":"Front Plant Sci"},{"issue":"5","key":"2025020106524897900_evaf009-B21","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nat Biotechnol"},{"issue":"9","key":"2025020106524897900_evaf009-B22","doi-asserted-by":"publisher","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res"},{"issue":"10","key":"2025020106524897900_evaf009-B23","doi-asserted-by":"publisher","first-page":"4647","DOI":"10.1093\/molbev\/msab199","article-title":"BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes","volume":"38","author":"Manni","year":"2021","journal-title":"Mol Biol Evol"},{"issue":"1","key":"2025020106524897900_evaf009-B24","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1186\/s12915-024-01832-1","article-title":"Origin and diversity of Capsella bursa-pastoris from the genomic point of view","volume":"22","author":"Penin","year":"2024","journal-title":"BMC Biol"},{"issue":"1","key":"2025020106524897900_evaf009-B25","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1186\/s12859-023-05499-3","article-title":"Mabs, a suite of tools for gene-informed genome assembly","volume":"24","author":"Schelkunov","year":"2023","journal-title":"BMC Bioinformatics"},{"issue":"9","key":"2025020106524897900_evaf009-B26","doi-asserted-by":"publisher","first-page":"1044","DOI":"10.1038\/s41587-020-0503-6","article-title":"Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes","volume":"38","author":"Shafin","year":"2020","journal-title":"Nat Biotechnol"},{"issue":"17","key":"2025020106524897900_evaf009-B27","doi-asserted-by":"publisher","first-page":"R920","DOI":"10.1016\/j.cub.2018.06.033","article-title":"Capsella","volume":"28","author":"Sicard","year":"2018","journal-title":"Curr Biol"},{"issue":"9","key":"2025020106524897900_evaf009-B28","doi-asserted-by":"publisher","first-page":"3156","DOI":"10.1105\/tpc.111.088237","article-title":"Genetics, evolution, and adaptive significance of the selfing syndrome in the genus Capsella","volume":"23","author":"Sicard","year":"2011","journal-title":"Plant Cell"},{"issue":"7","key":"2025020106524897900_evaf009-B29","doi-asserted-by":"publisher","first-page":"831","DOI":"10.1038\/ng.2669","article-title":"The Capsella rubella genome and the genomic consequences of rapid mating system evolution","volume":"45","author":"Slotte","year":"2013","journal-title":"Nat Genet"},{"issue":"5","key":"2025020106524897900_evaf009-B30","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1038\/s43588-021-00073-4","article-title":"Time- and memory-efficient genome assembly with Raven","volume":"1","author":"Vaser","year":"2021","journal-title":"Nat Comput Sci"},{"issue":"1","key":"2025020106524897900_evaf009-B31","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1186\/s13059-024-03359-8","article-title":"SynGAP: a synteny-based toolkit for gene structure annotation polishing","volume":"25","author":"Wu","year":"2024","journal-title":"Genome Biol"},{"issue":"1","key":"2025020106524897900_evaf009-B32","doi-asserted-by":"publisher","first-page":"btac808","DOI":"10.1093\/bioinformatics\/btac808","article-title":"YaHS: yet another Hi-C scaffolding tool","volume":"39","author":"Zhou","year":"2023","journal-title":"Bioinformatics"}],"container-title":["Genome Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gbe\/article-pdf\/17\/1\/evaf009\/61711576\/evaf009.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gbe\/article-pdf\/17\/1\/evaf009\/61711576\/evaf009.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,1]],"date-time":"2025-02-01T06:53:01Z","timestamp":1738392781000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gbe\/article\/doi\/10.1093\/gbe\/evaf009\/7993349"}},"subtitle":[],"editor":[{"given":"Vincent","family":"Castric","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,1]]},"references-count":32,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2025,1,6]]}},"URL":"https:\/\/doi.org\/10.1093\/gbe\/evaf009","relation":{},"ISSN":["1759-6653"],"issn-type":[{"value":"1759-6653","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,1]]},"published":{"date-parts":[[2025,1]]},"article-number":"evaf009"}}