Cowpea (Vigna unguiculata) is widely cultivated across semiarid regions of Africa, Asia, and Latin America because it can grow under limited rainfall and poor soil conditions. Its grain-type subspecies, V. unguiculata subsp. unguiculata, is an important protein source, while V. unguiculata subsp. sesquipedalis, also known as yardlong bean, is grown mainly for fresh pods. Earlier cowpea genome references supported genetic studies, but many remained fragmented, especially in repetitive regions such as centromeres and telomeres. This limited the detection of structural variants, repeat landscapes, and functional genes. Given these challenges, in-depth research into complete cowpea genomes and centromere evolution is needed.
Researchers from the Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Henan University, Huazhong Agricultural University, The University of Queensland, and the Chinese Academy of Tropical Agricultural Sciences reported (DOI: 10.1093/hr/uhaf359) the study in Horticulture Research on December 29, 2025. The study assembled complete genomes for the grain-type inbred line HJD and the vegetable-type line FC6, using them to examine cowpea subspecies divergence and centromere evolution in Phaseoleae legumes.
The team integrated Pacific Biosciences (PacBio) high-fidelity sequencing reads, Oxford Nanopore Technologies (ONT) ultralong reads, and high-throughput chromosome conformation capture (Hi-C) data to generate gapless assemblies across 11 chromosomes for both HJD and FC6. Multiple quality checks confirmed the high accuracy and completeness of the assemblies, including Benchmarking Universal Single-Copy Orthologs (BUSCO) scores of 98.40% for HJD and 98.50% for FC6 and base accuracy above 99.99%. Compared with the earlier IT97K-499-35 reference, the new telomere-to-telomere (T2T) genomes anchored approximately 50 megabases (Mb) of additional sequence to chromosomes, much of it repetitive DNA.
The improved references also strengthened genetic analysis. When resequencing data from 270 cowpea accessions were aligned, the T2T genomes reduced unmapped reads by 33% compared with IT97K-499-35. The researchers identified 201 and 140 previously unannotated centromeric genes in HJD and FC6, respectively, with Gene Ontology (GO) enrichment related to cellular respiration, immune signaling, and defense responses. A major inversion on chromosome 1, spanning roughly 9–13 Mb, showed strong differentiation between the two subspecies, suggesting a role in cowpea diversification.
The authors said the complete genomes make it possible to examine chromosome regions that were once largely missing from cowpea research. They said the findings show that centromeres are dynamic genomic regions shaped by tandem repeat arrays (TRAs), transposable elements (TEs), and structural rearrangements, rather than fixed landmarks. By connecting complete genome structure with subspecies divergence, they said the study gives researchers a clearer framework for understanding how cowpea evolved into different agricultural types and how hidden genome regions may contribute to useful traits.
Beyond cowpea, the study offers new insight into chromosome evolution across Phaseoleae, a legume group that includes soybean, mung bean, common bean, and cowpea. Comparative analysis showed that centromere composition and position are relatively conserved within cowpea but vary markedly among Phaseoleae species. Frequent centromere repositioning often coincided with chromosomal inversions, and segmental duplications (SDs) were enriched at inversion breakpoints. These results suggest that repetitive sequences and structural variation are major forces shaping legume genome evolution. For applied research, the new references can support gene discovery, marker development, recombination mapping, and more precise cowpea improvement.
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References
DOI
10.1093/hr/uhaf359
Original Source URL
https://doi.org/10.1093/hr/uhaf359
Funding information
This work was financially supported by the State Key Laboratory for Tropical Crop Breeding and the start-up package from the Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences.
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.