Publications of NIPGR Scientists

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    The ricebean genome provides insight into Vigna genome evolution and facilitates genetic enhancement
    (John Wiley & Sons, 2023) Francis, Aleena; Singh, Nagendra Pratap; Singh, Mohar; Sharma, Paras; Gayacharan; Kumar, Durgesh; Basu, Udita; Bajaj, Deepak; Varshney, Nidhi; Joshi, Dinesh Chandra; Semwal, Dinesh Prasad; Tyagi, Vandana; Wankhede, Dhammaprakash; Bharadwaj, Rakesh; Singh, Amit Kumar; Parida, Swarup K.; Chattopadhyay, Debasis
    Ricebean [Vigna umbellata (Thunb.) Ohwi and Ohashi] (2n = 2x = 22) is a warm-season dietary pulse legume crop and was originated in the Indo-China region. It is known to provide food security to the small and marginal farmers of South and South-East Asia. Ricebean is well known for its high nutritional quality and resistance to bacterial leaf spot, Mungbean yellow mosaic virus and bruchid, which are devastating for the other Vigna family crops (Dhaliwal et al., 2022). We report a reference grade de novo genome assembly, which is anchored to the genetic linkage groups and covered almost the whole estimated genome length of ricebean and so far, the largest among the sequenced Vigna species.
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    A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes
    (John Wiley & Sons, 2021) Paritosh, Kumar; Yadava, Satish Kumar; Singh, Priyansha; Bhayana, Latika; Mukhopadhyay, Arundhati; Gupta, Vibha; Bisht, Naveen C.; Zhang, Jianwei; Kudrna, David A; Copetti, Dario; Wing, Rod A; Reddy, Vijay Bhaskar; Pradhan, Akshay Kumar; Pental, Deepak
    Brassica juncea (AABB), commonly referred to as mustard, is a natural allopolyploid of two diploid species – B. rapa (AA) and B. nigra (BB). We report a highly contiguous genome assembly of an oleiferous type of B. juncea variety Varuna, an archetypical Indian gene pool line of mustard, with ~100x PacBio single‐molecule real‐time (SMRT) long‐reads providing contigs with an N50 value of >5Mb. Contigs were corrected for the misassemblies and scaffolded with BioNano optical mapping. We also assembled a draft genome of B. nigra (BB) variety Sangam using Illumina short‐read sequencing and Oxford Nanopore long‐reads and used it to validate the assembly of the B genome of B. juncea. Two different linkage maps of B. juncea, containing a large number of genotyping‐by‐sequencing markers were developed and used to anchor scaffolds/contigs to the 18 linkage groups of the species. The resulting chromosome‐scale assembly of B. juncea Varuna is a significant improvement over the previous draft assembly of B. juncea Tumida, a vegetable type of mustard. The assembled genome was characterized for transposons, centromeric repeats, gene content, and gene block associations. In comparison to the A genome, the B genome contains a significantly higher content of LTR/Gypsy retrotransposons, distinct centromeric repeats, and a large number of B. nigra specific gene clusters that break the gene collinearity between the A and the B genomes. The B. juncea Varuna assembly will be of major value to the breeding work on oleiferous types of mustard that are grown extensively in south Asia and elsewhere.