Abstract
Vigna reflexo-pilos a a (cr?ole bean) is a wild legume belonging to the subgenus Ceratoropis and is widely distributed in Asia. Cr?ole bean is the only tetraploid species in the genus Vigna and it has been shown to derive from the hybridization of Vigna hirtella and Vigna trinervia. In this study we combined the long-read PacBio technology with the chromatin contact mapping (Hi-C) technique to obtain a chromosome-level assembly of V. reflexo-pilosa. The final assembly contained 998 724 903 bases with an N50 length of 42 545 650 bases. Our gene prediction recovered 99.4% of the highly conserved orthologs based on the BUSCO analysis. To investigate homoeolog expression bias and expression level dominance in the tetraploid we also sequenced and assembled the genomes of its progenitors. Overall the majority of the homoeolog pairs (72.9%) displayed no expression bias and among those that exhibited biased expression 16.3% showed unbalanced homoeolog expression bias toward the V. trinervia subgenome. Moreover 41.2% and 36.2% of the expressed gene pairs exhibited transgressive expression and expression level dominance respectively. Interestingly the genome-wide expression level dominance in the tetraploid was biased toward the V. trinervia subgenome. The analysis of methylation patterns also revealed that the average methylation levels in coding regions were higher in the V. hirtella subgenome than those in the V. trinervia subgenome. The genomic/transcriptomic resources for these three species are useful not only for the development of elite cultivars in Vigna breeding programs but also to researchers studying comparative genomics and investigating genomic/epigenomic changes following polyploid events. ? 2023 The Author(s). Published by Oxford University Press.
