Origin and diversity of Capsella bursa-pastoris from the genomic point of view

Capsella 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 of Arabidopsis thaliana. The development of this model is hampered by the absence of a reference genome seque...

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Published in:BMC biology 2024-03, Vol.22 (1), p.52-15, Article 52
Main Authors: Penin, Aleksey A, Kasianov, Artem S, Klepikova, Anna V, Omelchenko, Denis O, Makarenko, Maksim S, Logacheva, Maria D
Format: Article
Language:English
Subjects:
Allopolyploid
Annotations
Anopheles
Arabidopsis
Biological diversity
Capsella - genetics
Capsella bursa-pastoris
Chromosome-scale assembly
Chromosomes
Dominance
Evolutionary biology
Extinct species
Genes
Genetic aspects
Genetic diversity
Genetics
Genome assembly
Genome evolution
Genomes
Genomics
Morphology
Nucleotide sequence
Polyploidy
Populations
Quality control
Rubella
Shepherd's purse
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Summary:Capsella 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 of Arabidopsis thaliana. The development of this model is hampered by the absence of a reference genome sequence. We present here a subgenome-resolved chromosome-scale assembly and a genetic map of the genome of Capsella 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 of C. bursa-pastoris. The whole-genome analysis of 119 samples belonging to C. bursa-pastoris and its parental species C. grandiflora/rubella and C. orientalis reveals introgression from C. orientalis but not from C. grandiflora/rubella. C. bursa-pastoris 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 C. bursa-pastoris indicates on a single origin of this species. The evidence coming from whole-genome analysis challenges the current view that C. grandiflora/rubella was a direct progenitor of C. bursa-pastoris; we hypothesize that it was an extinct (or undiscovered) species sister to C. grandiflora/rubella.
ISSN:1741-7007
1741-7007
DOI:10.1186/s12915-024-01832-1