Telomere-to-telomere genome unlocks subgenome evolution in shepherd’s purse
image: This study presents a subgenome-resolved telomere-to-telomere reference genome of Capsella bursa-pastoris, named Cbp_T2T, constructed using PacBio HiFi reads, Nanopore ultra-long reads, and Hi-C data. Notable divergences were observed between its subgenomes, and comparative genomics identified two large inversions within the species.
Credit: Xin Liu, Lu Liu, Hai-Fei Yan, Xue-Jun Ge, Hui-Run Huang
Date: May 6, 2026
Guangzhou, China: Researchers from the South China Botanical Garden, Chinese Academy of Sciences, have generated the first telomere-to-telomere (T2T) gap-free reference genome—named Cbp_T2T—for the pivotal model plant Capsella bursa-pastoris (Brassicaceae), published in Biological Diversity. By integrating PacBio HiFi, Oxford Nanopore ultra-long, and Hi-C sequencing technologies, the team assembled a 330.91 Mb allotetraploid genome comprising 16 chromosomes (eight in each subgenome), with a contig N50 of 20.28 Mb and 98.70% BUSCO completeness, representing the most contiguous C. bursa-pastoris genome to date.
The high-quality assembly uncovered striking subgenome divergence. Subgenome CbpA (related to C. grandiflora/C. rubella) and CbpB (related to C. orientalis) displayed pronounced structural variations, including 191 translocations, 48 inversions, and over 1100 duplications. Centromeric and pericentromeric regions showed markedly lower collinearity than chromosome arms. Repetitive sequences accounted for 37.04% of the genome, and 55,722 protein-coding genes were annotated.
Comparisons with a previously published genome (Cbp_version2) identified two large, lineage-specific inversions on chromosomes 6 and 7 (1.93 Mb and 2.33 Mb, respectively), indicating genomic divergence among geographically distinct accessions. The T2T assembly fully resolved telomeric and centromeric regions, which were poorly assembled in earlier versions.
This breakthrough genome clarifies subgenome evolution in polyploid Capsella, improves understanding of structural variation and adaptation, and supports future studies on polyploid speciation, mating-system shifts, and comparative genomics in cruciferous plants.
Original Source
Liu, Xin, Lu Liu, Hai-Fei Yan, Xue-Jun Ge, and Hui-Run Huang. 2025. “Telomere-To-Telomere Reference Genome Reveals Subgenome Divergence and Large Structural Variants in Capsella Bursa-pastoris (Brassicaceae).” Biological Diversity 2(1): 28–38.
https://onlinelibrary.wiley.com/doi/10.1002/bod2.70001
Keywords
Capsella bursa-pastoris, inversion, structural variant, subgenome divergence, telomere-to-telomere
About the Author
Xin Liu (Co-first Author), Master’s graduate, South China Botanical Garden, Chinese Academy of Sciences. His research focuses on the evolutionary mechanisms underlying plant genotype–phenotype associations revealed by multi-omics approaches. He has published 3 papers as first or co-first first author, with a total of 49 citations.
Lu Liu (Co-first Author), Postdoctoral Fellow at the South China Botanical Garden, Chinese Academy of Sciences. Her research focuses on conservation genetics. She has published a series of high-quality papers as first author in renowned journals including New Phytologist and Ecology and Evolution.
Hui-Run Huang (Corresponding Author), Associate Professor and Master’s Supervisor at the South China Botanical Garden, Chinese Academy of Sciences. Her research interests include genome assembly, adaptive evolution, and plant resource utilization. She has published extensively as first author or corresponding author in prestigious journals such as New Phytologist, Horticulture Research, and Journal of Systematics and Evolution.
About the Journal
Biological Diversity (ISSN: 2994-4139) is a new open-access, high-impact, English-language journal, devoted to advancing biodiversity conservation, enhancing ecosystem services, and promoting the sustainable use of resources under global change. It features innovative research addressing the global biodiversity crisis.