Gapless pangenome analyses reveal fast Brassica rapa subspeciation

Abstract

Brassica rapa (Br) encompasses many morphotypes and subspecies, so it is a good model with which to investigate plant diversification and subspeciation. Here, we resequenced the genomes of 1720 Br accessions and de novo assembled 11 representative telomere-to-telomere gapless genomes for seven elite subspecies that underwent intensive morphotypification and developed distinct agronomic traits valued to agriculture. We identified 6992 unknown genes, 110 complete (peri)centromeres, and five new satellites associated with Br morphotypes and subspecies and Brassica species evolution. The pangenome, built on 11 gapless and 20 published genomes, reveals structural variations and gene diversities among Br subspecies. Pangenome-wide association studies uncovered that the gene BrLH1 controls leaf-head formation. We show that structural changes have occurred in satellites, (peri)centromeres, and genes, contributing to fast subspeciation and morphotypification during the short history of Br cultivation, providing invaluable resources for Brassica breeding.

STRUCTURED ABSTRACT INTRODUCTION : The drivers leading to the rapid rise and diversification of angiosperms since the Middle Cretaceous period remain mysterious. Recent advances in genomics and pangenomics have opened new avenues to study fast evolution and development in flowering plants. However, the lack of high-quality gapless genomic and pangenomic resources has restricted our ability to fully understand genomic and pangenomic structures and diversity, as well as their links with phenotypic variations in plants. Crops that have rapidly diversified during domestication may serve as suitable targets to answer such questions. RATIONALE : Brassica rapa (Br) is a diploid species that has evolved morphologically and physiologically diverse subspecies and morphotypes over a short history of domestication. These encompass eight forms that include turnip, pak choi, and Chinese cabbage. Using Br and its subspecies as a model, we aimed to uncover hidden links between functional satellites and centromere dynamics, structural variations (SVs) and gene functions, as well as genomic and pangenomic causes for phenotypic changes that have driven rapid plant speciation and subspeciation. RESULTS : We resequenced the genomes of 1720 different Br accessions and de novo assembled telomere-to-telomere (T2T) gapless genomes for 11 representatives of seven morphotypes and subspecies that serve as elite breeding parents. We identified 6992 previously unannotated genes, 110 complete centromeres and pericentromeres, and five new satellites associated with evolution of Br morphotypes and subspecies and Brassica species. We constructed a high-quality centromere and SV map for Br, enabling the analysis of centromeric elements, SV diversity, and their rapid evolution. We established the most comprehensive gapless pangenome to date, which comprises 31 accessions (including 11 T2T and 20 previously published genomes), and elucidated the pangenomic basis for morphotype diversification and subspeciation in Br. Particularly, we found that 200, 203, and 503 presence-absence variants (PAVs) are potentially relevant (80% conformity) to the diversification of Chinese cabbage, caixin, and turnip, respectively. Through pangenome-wide association studies (pan-GWAS) and forward genetics analysis, we also identified and functionally validated BrLH1 as a key player in the control of leafy head development in Chinese cabbage and Br subspecies. CONCLUSION : We show that structural changes have occurred in satellites, centromeres, and genes that contributed to fast subspeciation and morphotypification during the short history of Br cultivation. These genomic and pangenomic resources will provide valuable insights into the genetic basis for phenotypic diversity across Br, with implications for breeding and domestication processes.

EDITOR’S SUMMARY Pangenomes were developed to better encompass genetic variation across a species, but this concept is now being expanded to include variation across subspecies as well as genera. A pair of papers in this issue report pangenome creation for crops, which particularly benefit from this analysis approach given their high levels of diversification and ploidy (see the Perspective by Soltis and Soltis). Ma et al. created a pangenome for Brassica rapa by integrating genetic variation from 1720 accessions spanning seven subspecies. Huang et al. created a pangenome for the polyploid sugarcane (Saccharum) that combines nine assemblies from four species. These references were able to help identify structural variations and regions potentially underlying important phenotypes. These pangenomes will serve as a valuable resource for research focusing on the improvement of these crops and will offer insight into domestication processes. —Corinne Simonti and Madeleine Seale