Adzuki bean (Vigna angularis var. angularis) is a dietary legume crop in East Asia. The presumed progenitor (Vigna angularis var. nipponensis) is widely found in East Asia, suggesting speciation and domestication in these temperate climate regions. Here, we report a draft genome sequence of adzuki bean. The genome assembly covers 75% of the estimated genome and was mapped to 11 pseudo-chromosomes. Gene prediction revealed 26,857 high confidence protein-coding genes evidenced by RNAseq of different tissues. Comparative gene expression analysis with V. radiata showed that the tissue specificity of orthologous genes was highly conserved. Additional re-sequencing of wild adzuki bean, V. angularis var. nipponensis, and V. nepalensis, was performed to analyze the variations between cultivated and wild adzuki bean. The determined divergence time of adzuki bean and the wild species predated archaeology-based domestication time. The present genome assembly will accelerate the genomics-assisted breeding of adzuki bean.

Mungbean (Vigna radiata L.), a fast-growing legume species, is an important source of carbohydrates and proteins in developing countries of Asia. Here, we constructed a near-complete genome sequence of mungbean with a scaffold N50 value of 5.2 Mb and only a 0.4% gap, with a total scaffold size of 475 Mb. We identified several misassembled pseudomolecules (Chr03, Chr04, Chr05, and Chr08) in the previous draft assembly; Chr03, Chr04, and Chr08 were assembled into one chromosome, and Chr05 was broken into two chromosomes in the improved reference genome assembly, thus providing more accurate linkage information to breeders. Additionally, using an ultra-high-resolution linkage map constructed based on resequencing data, we identified several quantitative trait loci (QTLs) and the underlying candidate genes affecting synchronous pod maturity (SPM). Mungbean homologs of two soybean ([Glycine max (L.) Merr.] flowering genes, E3 (phytochrome A) and J (early flowering 3), were identified as candidate genes for the QTLs, and the candidate genes for plant height, node number, and SPM showed critical nucleotide substitutions between the reference cultivar and other genotypes (landraces and wild accessions). Based on the analysis of genetic diversity among 276 accessions collected from 23 countries, we identified 36 selective sweep regions and observed that the overall genetic diversity of cultivars decreased to 30% of that in wild accessions postdomestication. The near-complete genome sequence of mungbean represents an important resource for genome-assisted improvement in the mungbean breeding program.

SummaryThe use of next‐generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies.

Jatropha curcas (physic nut), a non-edible oilseed crop, represents one of the most promising alternative energy sources due to its high seed oil content, rapid growth and adaptability to various environments. We report ~339 Mbp draft whole genome sequence of J. curcas var. Chai Nat using both the PacBio and Illumina sequencing platforms. We identified and categorized differentially expressed genes related to biosynthesis of lipid and toxic compound among four stages of seed development. Triacylglycerol (TAG), the major component of seed storage oil, is mainly synthesized by phospholipid:diacylglycerol acyltransferase in Jatropha, and continuous high expression of homologs of oleosin over seed development contributes to accumulation of high level of oil in kernels by preventing the breakdown of TAG. A physical cluster of genes for diterpenoid biosynthetic enzymes, including casbene synthases highly responsible for a toxic compound, phorbol ester, in seed cake, was syntenically highly conserved between Jatropha and castor bean. Transcriptomic analysis of female and male flowers revealed the up-regulation of a dozen family of TFs in female flower. Additionally, we constructed a robust species tree enabling estimation of divergence times among nine Jatropha species and five commercial crops in Malpighiales order. Our results will help researchers and breeders increase energy efficiency of this important oil seed crop by improving yield and oil content, and eliminating toxic compound in seed cake for animal feed.