Journal Article

Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa

Chang, Lichun, Liang, Jianli, Wu, Jian, Freeling, Michael, Chen, Haixu, Zhang, Tingting, Lin, Runmao, Zhang, Lei, Wang, Xiaowu, Cai, Xu

2021

Overview

Background 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. Results Herein, 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. Conclusions This 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.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Animal Genetics and Genomics / auxins / Base Sequence / Bioinformatics / Biomedical and Life Sciences / Brassica rapa / Brassica rapa - genetics / Chinese cabbage / Domestication / Evolutionary Biology / Evolutionary genetics / Flowering / fractionation / Gene expression / genes / Genome, Plant / Genomes / Genomic Structural Variation / Human Genetics / Life Sciences / Microbial Genetics and Genomics / Molecular Sequence Annotation / morphs / Phylogeny / Plant Genetics and Genomics / plant hormones / Polyploidy / Speciation / species / Species Specificity / Synteny / Synteny - genetics