A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes

Kumar Paritosh, Satish Kumar Yadava, Priyansha Singh, Latika Bhayana, Arundhati Mukhopadhyay, Vibha Gupta, Naveen Chandra Bisht, Jianwei Zhang, David A. Kudrna, Dario Copetti, Rod A. Wing, Vijaya Bhasker Reddy Lachagari, Akshay Kumar Pradhan, Deepak Pental

Research output: Contribution to journalArticlepeer-review

51 Scopus citations


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 ~100× PacBio single-molecule real-time (SMRT) long reads providing contigs with an N50 value of >5 Mb. 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.

Original languageEnglish (US)
Pages (from-to)602-614
Number of pages13
JournalPlant Biotechnology Journal
Issue number3
StatePublished - Mar 2021


  • Brassica juncea
  • Brassica nigra
  • breeding
  • evolution
  • gene blocks
  • genome assembly
  • long-read sequencing
  • oilseed mustard

ASJC Scopus subject areas

  • Biotechnology
  • Agronomy and Crop Science
  • Plant Science


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