Origin and diversity ofCapsella bursa-pastorisfrom the genomic point view

Abstract

AbstractBackgroundCapsella bursa-pastoris, a cosmopolitan weed of hybrid origin, is an emerging model object for the study of early consequences of polyploidy, being a fast growing annual and a close relative ofArabidopsis thaliana. The development of this model is hampered by the absence of a reference genome sequence.Resultswe present here a subgenome-resolved chromosome-scale assembly and a genetic map of the genome ofCapsella bursa-pastoris. 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 – both 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 ofC. bursa-pastoris. The whole-genome analysis of 119 samples belonging toC. bursa-pastorisand its parental speciesC. grandiflora/rubellaandC. orientalisreveals introgression fromC. orientalisbut not fromC. grandiflora/rubella.ConclusionsC. bursa-pastorisdo not show genome dominance. In the earliest stages of evolution of this species a homeologous exchange occurred; its presence in all present-day populations ofC. bursa-pastorisindicates on a single origin of this species. The evidence coming from whole-genome analysis challenges the current view thatC. grandiflora/rubellawas a direct progenitor ofC. bursa-pastoris; we hypothesize that it was an extinct (or undiscovered) species sister toC. grandiflora/rubella.