ArticleGenome biology2021
Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 102 papers.
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102 citing papers in PubMed, 160 citations in OpenAlex.
- Machine learning-guided leaf margin classification and discovery that BcPHB promoter selection rewires a BcPHB-BcLMI1 module to shape leaf margins in Brassica campestris.Molecular horticulture · 2026Article
- Insight Into the Genetic Architecture of Local (Mal)Adaptation in Wild and Feral Brassica rapa Populations.Molecular ecology · 2026Article
- Article
- Pan-Genomic Dissection of GH1 β-Glucosidases inPlants (Basel, Switzerland) · 2026Article
- Dynamic evolution of FLC/MAF-like genes accompanying Brassicaceae radiation.Annals of botany · 2026Article
- Dynamic chromatin accessibility reveals BrKAN2 as a key regulator of Chinese cabbage leaf heading.Molecular horticulture · 2026Article
- Genomic analysis of 3,330 accessions provides insights into the evolutionary history and self-incompatibility locus of the Brassica A genome.Nature genetics · 2026Article
- From gapless pan-genomes to field impact: a functional roadmap for acceleratingHorticulture research · 2026Article
- Rare Natural SNP Activates SHOOT APICAL MERISTEM ENLARGER1 to Increase Branch Number and Silique Number on the Main Inflorescence in Brassica napus.Plant biotechnology journal · 2026Article
- Metabolomic analysis of a core collection of Brassica rapa and Brassica oleracea unveils unexpected chemical diversity with potential applications in chemical ecology and breeding.BMC plant biology · 2026Article
- A comprehensive analysis of two Chinese cucumber genomes and a mutant population as resources for precision breeding.Horticulture research · 2026Article
- Genome Assembly of Three Shrub Mangroves in the Genus Acanthus Reveals Two Polyploidy Events and Expansion of Genes Linked to Root Adaptation in Coastal Habitats.GigaScience · 2026Article
- Article
- Allopolyploidization-driven short-term evolution of miRNAs in Brassica A genome.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Chromosome level assembly of five Brassica rapa and oleracea accessions expand the resistance genes reservoir.Scientific data · 2025Article
- Pangenome analyses of tea plants reveal structural variations driving gene expression alterations and agronomic trait diversification.Nature communications · 2025Article
- The wucai genome and DNA methylation regulation on the inner leaves' yellowing response to low temperature.Horticulture research · 2025Article
- Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus.Genome biology · 2025Article
- Assembling the chromosome-level genome of Arctium Lappa L. provides new insights into carotenoid biosynthesis.BMC plant biology · 2025Article
- Pan-centromere landscape and dynamic evolution in Brassica plants.Nature plants · 2025Article
42 more citing papers are in PubMed but not listed here.
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10 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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