A chromosome‐scale assembly of the black gram (Vigna mungo) genome

Abstract

Black gram (Vigna mungo) is an important short duration grain legume crop. Black gram seeds provide an inexpensive source of dietary protein. Here, we applied the 10X Genomics linked‐read technology to obtain a de novo whole genome assembly of V. mungo cultivated variety Chai Nat 80 (CN80). The preliminary assembly contained 12,228 contigs and had an N50 length of 5.2 Mb. Subsequent scaffolding using the long‐range Chicago and HiC techniques yielded the first high‐quality, chromosome‐level assembly of 499 Mb comprising 11 pseudomolecules. Comparative genomics analyses based on sequence information from single‐copy orthologous genes revealed that black gram and mungbean (Vigna radiata) diverged about 2.7 million years ago . The transversion rate (4DTv) analysis in V. mungo revealed no evidence supporting a recent genome‐wide duplication event observed in the tetraploid créole bean (Vigna reflexo‐pilosa). The proportion of repetitive elements in the black gram genome is slightly lower than the numbers reported for related Vigna species. The majority of long terminal repeat retrotransposons appeared to integrate into the genome within the last five million years. We also examined alternative splicing events in V. mungo using full‐length transcript sequences. While intron retention was the most prevalent mode of alternative splicing in several plant species, alternative 3' acceptor site selection represented the majority of events in black gram. Our high‐quality genome assembly along with the genomic variation information from the germplasm provides valuable resources for accelerating the development of elite varieties through marker‐assisted breeding and for future comparative genomics and phylogenetic studies in legume species.

Bruchid beetle ovipositioning mediated defense responses in black gram pods

“…The whole-genome sequencing of black gram is now available but poorly annotated [ 22 ]; therefore, the raw reads were assembled by the Trinity de novo software for RNAseq data. The raw reads were also aligned with the available black gram genome sequence and found to be > 90% similar (Additional Fig.…”

Macrophomina phaseolina–host interface: Insights into an emerging dry root rot pathogen of mungbean and urdbean, and its mitigation strategies

“…All of the available germplasm, landraces, and related and wild spe- There is high genome conservation among mungbean, urdbean, and cowpea (Pootakham et al, 2020), so it is possible that the gene(s)…”

“…for M. phaseolina resistance in cowpea may be similar to that in mungbean and urdbean. Based on the mungbean genome sequence (Kang et al, 2014), marker 1_0853 is located on chromosome 7 and corresponds to gene Vradi07 g27890 encoding PEI7; in the urdbean genome sequence (Pootakham et al, 2020) the marker localizes on chromosome 1 also corresponds to a gene producing a pectin esterase inhibitor. Further investigations are required to develop mapping populations from these dry root rot-resistance sources to identify the disease resistance QTLs and to determine if PEI is responsible for the resistance.…”

“…There is high genome conservation among mungbean, urdbean, and cowpea (Pootakham et al, 2020), so it is possible that the gene(s) for M . phaseolina resistance in cowpea may be similar to that in mungbean and urdbean.…”

Morpho-Physiological Traits and Functional Markers Based Molecular Dissection of Heat-Tolerance in Urdbean

“…However, in urdbean, use of molecular markers for mapping and characterization of traits related to heat tolerance is poorly understood. Currently, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) are available for molecular characterization in urdbean ( Raizada and Souframanien, 2019 ; Souframanien et al, 2020 ; Pootakham et al, 2021 ). Hence, this experiment was designed with the following objectives: (i) to evaluate a set of urdbean genotypes under field conditions with natural heat stress conditions (flowering and podding stage coincides with high temperature), and to compare it with normal field conditions (comparatively less exposure to high temperature during flowering and podding), (ii) to precisely phenotype selected contrasting heat tolerant and sensitive genotypes for different physiological and biochemical traits, and (iii) to characterize heat tolerant and sensitive genotypes with heat-related genic markers.…”