A highly contiguous genome assembly of Brassica nigra (BB) and revised nomenclature for the pseudochromosomes

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Abstract
Background: Brassica nigra(BB), also called black mustard, is grown as a condiment crop in India.B. nigrarepresents the B genome of U’s triangle and is one of the progenitor species ofB. juncea(AABB), an important oilseed crop of the Indian subcontinent. We report the genome assembly ofB. nigravariety Sangam.Results: The genome assembly was carried out using Oxford Nanopore long-read sequencing and optical mapping. A total of 1549 contigs were assembled, which covered ~ 515.4 Mb of the estimated ~ 522 Mb of the genome. The final assembly consisted of 15 scaffolds that were assigned to eight pseudochromosomes using a high-density genetic map ofB. nigra. Around 246 Mb of the genome consisted of the repeat elements; LTR/Gypsy types of retrotransposons being the most predominant. The B genome-specific repeats were identified in the centromeric regions of theB. nigrapseudochromosomes. A total of 57,249 protein-coding genes were identified of which 42,444 genes were found to be expressed in the transcriptome analysis. A comparison of the B genomes ofB. nigraandB. juncearevealed high gene colinearity and similar gene block arrangements. A comparison of the structure of the A, B, and C genomes of U’s triangle showed the B genome to be divergent from the A and C genomes for gene block arrangements and centromeric regions.Conclusions: A highly contiguous genome assembly of theB. nigragenome reported here is an improvement over the previous short-read assemblies and has allowed a comparative structural analysis of the A, B, and C genomes of the species belonging to the U’s triangle. Based on the comparison, we propose a new nomenclature forB. nigrapseudochromosomes, taking theB. rapapseudochromosome nomenclature as the reference.
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Funding Information
  • Department of Biotechnology (DBT), Government of India (BT/01/COE/08/06-II, BT/01/NDDB/UDSC/2016)

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