Abstract
BackgroundDespite the prevalence and recurrence of polyploidization in the speciation of flowering plants, its impacts on crop intraspecific genome diversification are largely unknown. Brassica rapa is a mesopolyploid species that is domesticated into many subspecies with distinctive morphotypes.ResultsHerein, we report the consequences of the whole-genome triplication (WGT) on intraspecific diversification using a pan-genome analysis of 16 de novo assembled and two reported genomes. Among the genes that derive from WGT, 13.42% of polyploidy-derived genes accumulate more transposable elements and non-synonymous mutations than other genes during individual genome evolution. We denote such genes as being “flexible.” We construct the Brassica rapa ancestral genome and observe the continuing influence of the dominant subgenome on intraspecific diversification in B. rapa. The gene flexibility is biased to the more fractionated subgenomes (MFs), in contrast to the more intact gene content of the dominant LF (least fractionated) subgenome. Furthermore, polyploidy-derived flexible syntenic genes are implicated in the response to stimulus and the phytohormone auxin; this may reflect adaptation to the environment. Using an integrated graph-based genome, we investigate the structural variation (SV) landscapes in 524 B. rapa genomes. We observe that SVs track morphotype domestication. Four out of 266 candidate genes for Chinese cabbage domestication are speculated to be involved in the leafy head formation.ConclusionsThis pan-genome uncovers the possible contributions of allopolyploidization on intraspecific diversification and the possible and underexplored role of SVs in favorable trait domestication. Collectively, our work serves as a rich resource for genome-based B. rapa improvement.
Highlights
Polyploidization plays a positive role in increasing the richness of the plant kingdom by supporting plant speciation through frequent and recurrent polyploidization and rediploidization events [1,2,3,4,5]
To anchor the contigs of each accession to the 10 pseudochromosomes of B. rapa, 12 of the 16 accessions with relatively higher contig N50 values were sequenced with Hi-C technology; a procedure that aids in assembly [50]
The present study found that the average ratio of flexible syntenic gene (FSG) on the least fractionated (LF), MF1, and MF2 subgenomes was 8.57%, 9.27%, and 9.55%, respectively, and the ratio of FSGs was significantly lower in the LF subgenome (Fig. 3e, Additional file 2: Figure S20 and Additional file 3: Table S24), revealing that the biased gene flexibility during intraspecific diversification was associated with the increase of the dominance of the LF subgenome
Summary
Polyploidization plays a positive role in increasing the richness of the plant kingdom by supporting plant speciation through frequent and recurrent polyploidization and rediploidization events [1,2,3,4,5]. Cai et al Genome Biology (2021) 22:166 undoubtedly be discovered due to the increasing number of sequenced plant species. Subgenome dominance is a common phenomenon that is widely observed in allopolyploids, including cotton [8], Brassica [9], and wheat [10]. This subgenome dominance reflects gene fractionation bias and expression dominance between homoeologous genes from different subgenomes [11,12,13]. Despite the prevalence and recurrence of polyploidization in the speciation of flowering plants, its impacts on crop intraspecific genome diversification are largely unknown. Brassica rapa is a mesopolyploid species that is domesticated into many subspecies with distinctive morphotypes
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