Summary: Asparagus bean (Vigna unguiculata ssp. sesquipedialis), a subspecies of V. unguiculata, is a vital legume crop widely cultivated in Asia for its tender pods consumed as vegetables. However, the existing asparagus bean assemblies still contain numerous gaps and unanchored sequences, which presents challenges to functional genomics research. Here, we present an improved reference genome sequence of an elite asparagus bean variety, Fengchan 6, achieved through the integration of nanopore ultra‐long reads, PacBio high‐fidelity reads, and Hi‐C technology. The improved assembly is 521.3 Mb in length and demonstrates several enhancements, including a higher N50 length (46.4 Mb), an anchor ratio of 99.8%, and the presence of only one gap. Furthermore, we successfully assembled 14 telomeres and all 11 centromeres, including four telomere‐to‐telomere chromosomes. Remarkably, the centromeric regions cover a total length of 38.1 Mb, providing valuable insights into the complex architecture of centromeres. Among the 30 594 predicted protein‐coding genes, we identified 2356 genes that are tandemly duplicated in segmental duplication regions. These findings have implications for defence responses and may contribute to evolutionary processes. By utilizing the reference genome, we were able to effectively identify the presence of the gene VuMYB114, which regulates the accumulation of anthocyanins, thereby controlling the purple coloration of the pods. This discovery holds significant implications for understanding the underlying mechanisms of color determination and the breeding process. Overall, the highly improved reference genome serves as crucial resource and lays a solid foundation for asparagus bean genomic studies and genetic improvement efforts.

Fusarium wilt (FW), caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. Tracheiphilum, is a serious threat to cowpea production worldwide. Understanding the genetic architecture of FW resistance is a prerequisite to combatting this disease and developing FW resistance varieties. In the current study, a genetic diversity panel of 99 cowpea accessions was collected, and they were infected by a single strain, FW-HZ. The disease index (DI) based on the two indicators of leaf damage (LFD) and vascular discoloration (VD) varied highly across the population: most accessions were susceptible, and only seven accessions showed resistant phenotypes by both indicators. Through a genome-wide association study (GWAS), 3 and 7 single nucleotide polymorphisms (SNPs) significantly associated with LFD and VD were detected, respectively, which were distributed on chromosomes 3, 4, 5, 6 and 9, accounting for 0.68–13.92% of phenotypic variation. Based on the cowpea reference genome, 30 putative genes were identified and proposed as the likely candidates, including leucine-rich repeat protein kinase family protein, protein kinase superfamily protein and zinc finger family protein. These results provide novel insights into the genetic architecture of FW resistance and a basis for molecular breeding of FW resistant cultivars in cowpea.

Purple cowpea accumulates abundant anthocyanins in its epidermis, with R2R3-MYB transcription factors serving as potential regulators of anthocyanin accumulation. This study systematically deciphered the genome-wide characteristics of cowpea R2R3-MYB transcription factors, elucidating their critical roles in plant anthocyanin accumulation. Employing a combined strategy of HMMER Hidden Markov Model searches and BLASTP homology alignment, we successfully identified 127 non-redundant VuR2R3-MYB transcription factors. The encoded proteins exhibited remarkable physicochemical diversity: the average length reached 338.8 amino acid residues, with theoretical isoelectric points distributed between 4.79 and 10.91 residues. When performing a phylogenetic analysis with Arabidopsis homologs, 27 distinct subgroups were identified. Among them, the S4–S7 clades showed conserved protein architectures, which might play a role in regulating the phenylpropanoid pathway. An analysis of the gene architecture revealed patterns of intron/exon organization. Specifically, 85 out of 127 loci (66.9%) presented the typical two-intron configuration, whereas 18 genes had no introns. An investigation of the promoters found that, on average, each gene had 52 cis-regulatory elements. These elements were mainly light-responsive motifs and phytohormone-related elements. Chromosomal mapping indicated an uneven distribution of these genes across 11 chromosomes. Duplication analysis further showed 13 tandem repeats and 54 segmentally duplicated pairs. An analysis of evolutionary constraints demonstrated that purifying selection was predominant (Ka/Ks < 0.5) among paralogous pairs. Through comparative transcriptomics of pod color variants, 19 differentially expressed MYB regulators were identified. These included VuR2R3-MYB23 (MYB3 homolog), VuR2R3-MYB95 (MYB4 homolog), VuR2R3-MYB53 (MYB114 homolog), and VuR2R3-MYB92 (MYB5 homolog), which showed a strong correlation with the patterns of anthocyanin accumulation. Our findings are expected to contribute to elucidating the potential regulatory mechanisms through which R2R3-MYB transcription factors mediate anthocyanin biosynthesis and accumulation.