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The development of this model is hampered by the absence of a reference genome sequence.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We present here a subgenome-resolved chromosome-scale assembly and a genetic map of the genome of <jats:italic>Capsella bursa-pastoris<\/jats:italic>. It shows that the subgenomes are mostly colinear, with no massive deletions, insertions, or rearrangements in any of them. A subgenome-aware annotation reveals the lack of genome dominance\u2014both subgenomes carry similar number of genes. While most chromosomes can be unambiguously recognized as derived from either paternal or maternal parent, we also found homeologous exchange between two chromosomes. It led to an emergence of two hybrid chromosomes; this event is shared between distant populations of <jats:italic>C. bursa-pastoris<\/jats:italic>. The whole-genome analysis of 119 samples belonging to <jats:italic>C. bursa-pastoris<\/jats:italic> and its parental species <jats:italic>C. grandiflora\/rubella<\/jats:italic> and <jats:italic>C. orientalis<\/jats:italic> reveals introgression from <jats:italic>C. orientalis<\/jats:italic> but not from <jats:italic>C. grandiflora\/rubella<\/jats:italic>.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p><jats:italic>C. bursa-pastoris<\/jats:italic> does not show genome dominance. In the earliest stages of evolution of this species, a homeologous exchange occurred; its presence in all present-day populations of <jats:italic>C. bursa-pastoris<\/jats:italic> indicates on a single origin of this species. The evidence coming from whole-genome analysis challenges the current view that <jats:italic>C. grandiflora\/rubella<\/jats:italic> was a direct progenitor of <jats:italic>C. bursa-pastoris<\/jats:italic>; we hypothesize that it was an extinct (or undiscovered) species sister to <jats:italic>C. grandiflora\/rubella<\/jats:italic>.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12915-024-01832-1","type":"journal-article","created":{"date-parts":[[2024,3,5]],"date-time":"2024-03-05T01:01:47Z","timestamp":1709600507000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Origin and diversity of Capsella bursa-pastoris from the genomic point of view"],"prefix":"10.1186","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9057-3974","authenticated-orcid":false,"given":"Aleksey A.","family":"Penin","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Artem S.","family":"Kasianov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna V.","family":"Klepikova","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Denis O.","family":"Omelchenko","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maksim S.","family":"Makarenko","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria D.","family":"Logacheva","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,3,5]]},"reference":[{"key":"1832_CR1","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1038\/nrg.2017.26","volume":"18","author":"Y Van de Peer","year":"2017","unstructured":"Van de Peer Y, Mizrachi E, Marchal K. 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