Long-read-based draft genome sequence of Indian black gram IPU-94-1 ‘Uttara’: Insights into disease resistance and seed storage protein genes

Black gram [Vigna mungo (L.) Hepper var. mungo] [LAV1] is a warm-season
legume highly prized for its protein content along with significant folate
and iron proportions. To expedite the genetic enhancement of black gram, a
high-quality draft genome from the center of origin of the crop is
indispensable. Here, we established a draft genome sequence of an Indian
black gram cultivar, ‘Uttara’ (IPU 94-1), known for its high resistance to
mungbean yellow mosaic virus. Pacific Biosciences of California, Inc.
(PacBio) single-molecule real-time (SMRT) and Illumina sequencing
assembled a draft reference-guided assembly with a cumulative size of
~454.4 Mb, of which, 444.4 Mb was anchored on 11 pseudomolecules
corresponding to 11 chromosomes. Uttara assembly denotes features of a
high-quality draft genome illustrated through high N50 value (42.88 Mb),
gene completeness (benchmarking universal single-copy ortholog [BUSCO]
score 94.17%), and low levels of ambiguous nucleotides (N) percent
(0.0005%). Gene discovery using transcript evidence predicted 28,881
protein-coding genes, from which, ~95% were functionally annotated. A
global survey of genes associated with disease resistance revealed 119
nucleotide binding site–leucine rich repeat (NBS-LRR) proteins, while 23
genes encoding seed storage proteins (SSPs) were discovered in black gram.
A large set of microsatellite loci were discovered for marker development
in the crop. Our draft genome of an Indian black gram provides the
foundational genomic resources for the improvement of important agronomic
traits and ultimately will help in accelerating black gram breeding
programs.