Abstract
Summary 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.
Highlights
Genus Brassica contains some of the most important oilseed and vegetable crops that are grown worldwide
High molecular weight DNA isolated from B. juncea variety Varuna was subjected to singlemolecule real-time (SMRT) sequencing on the PacBio RSII platform
We have reported a highly contiguous genome assembly of B. juncea variety Varuna, an oleiferous type belonging to the Indian gene pool of mustard, using long-read SMRT sequencing and optical mapping
Summary
Genus Brassica contains some of the most important oilseed and vegetable crops that are grown worldwide. Nagaharu, based on cytogenetic studies, proposed a model on the relationship of six key species of the genus[1]. Draft genomes of B. rapa (estimated genome size ~ 485 Mb), B. oleracea (~ 630 Mb) and B. napus (~1130 Mb) were assembled with short-read, high-throughput Illumina technology with some limited Sanger sequencing[2,3,4]. A draft sequence of a vegetable type of B. juncea variety Tumida (genome size ~922 Mb) was assembled[5] using ~176x Illumina reads, gap filling with 12x PacBio singlemolecule real-time (SMRT) sequences and long-range scaffolding with BioNano optical mapping
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