Genome sequence of mungbean and insights into evolution within Vigna species

Abstract

Mungbean (Vigna radiata) is a fast-growing, warm-season legume crop that is primarily cultivated in developing countries of Asia. Here we construct a draft genome sequence of mungbean to facilitate genome research into the subgenus Ceratotropis, which includes several important dietary legumes in Asia, and to enable a better understanding of the evolution of leguminous species. Based on the de novo assembly of additional wild mungbean species, the divergence of what was eventually domesticated and the sampled wild mungbean species appears to have predated domestication. Moreover, the de novo assembly of a tetraploid Vigna species (V. reflexo-pilosa var. glabra) provides genomic evidence of a recent allopolyploid event. The species tree is constructed using de novo RNA-seq assemblies of 22 accessions of 18 Vigna species and protein sets of Glycine max. The present assembly of V. radiata var. radiata will facilitate genome research and accelerate molecular breeding of the subgenus Ceratotropis.

Figure 1. Summary of the de novo genome assembly and sequencing analysis of mungbean.

(a) SNP distributions between domesticated and wild mungbeans are depicted in the outer circle of the circular map. The middle circle represents the proportions of repeated elements including LTR/Gypsy (orange), LTR/Copia (yellow), LINE (blue) and DNA transposons (green). The inner circle shows gene densities across the chromosomes. On Vr05, two QTL locations were identified at the outermost layer, and they were consistent with G. max QTLs based on the syntenic relationship, as described schematically. (b) An OrthoMCL clustering analysis of five gene sets from A. thaliana, M. truncatula, G. max, O. sativa and V. radiata. Each value within Venn diagram shows the number of orthologue/paralogue clusters. (c) Frequency distribution of Ks values in V. radiata (red), V. reflexo-pilosa (sky blue) and G. max (green).

Figure 2. Analysis of syntenic relationships in legumes within the millettioid clade.

(a) Estimation of divergence times between V. radiata and C. cajan, and between V. radiata and G. max. (b) Visualization of chromosomal rearrangements among V. radiata var. radiata, G. max and C. cajan. Chromosomes among V. radiata var. radiata, C. cajan and G. max (A genome) are connected by red lines, and chromosomes between V. radiata var. radiata and G. max (B genome) are linked by blue lines. (c) Syntenic relationship between V. radiata and G. max; the x-axis indicates chromosomal locations and the y-axis indicates Ks value. Each dot represents the location of a synteny block with its Ks median value, showing both conservation and chromosomal rearrangements of syntenic blocks. (d) Depiction of the syntenic relationship between V. radiata and C. cajan.

Figure 3. Species tree for 22 Vigna accessions and close legume relative, G. max.

Average divergence dates were depicted for the nodes estimated by a Bayesian MCMC method. The horizontal bars represent the 95% highest posterior density (HPD) interval at each node estimated by tested genes. The colour of the square on each node represents the posterior probability according to colour gradation from black (0) through blue (0.5) to red (1). The root divergence time was set to a 19 MYA between V. radiata var. radiata and G. max following the estimation of Lavin et al.

Figure 4. Schematic illustration of allopolyploidization history of the V. reflexo-pilosa var. glabra.

Red arrow indicates the putative date (maximum 0.09 MYA) of polyploidization event of V. reflexo-pilosa var. glabra. The number at each node represents the divergence time estimated by a Bayesian MCMC method.