Brassica juncea Genome Assemblies—Characteristics and Utilization

Brassica juncea (AABB, n = 18, ~922 Mb) is a natural allopolyploid of B. rapa (AA, n = 10) and B. nigra (BB, n = 8). Oleiferous types of B. juncea (mustard) are extensively cultivated in the Indian subcontinent. We reported a highly contiguous genome assembly of B. juncea variety Varuna, a mega variety belonging to the Indian gene pool of mustard using PacBio SMRT sequencing technology and optical mapping. Two genetic maps using F1DH populations—Varuna × Heera (VH) and Tumida × Varuna (TuV) were used to assign the scaffolds and contigs to 18 LGs of B. juncea. We also assembled the genome of B. nigra variety Sangam using long-read ONT sequencing and optical mapping. The two assemblies were annotated for transposons, centromeric repeats, and protein-encoding genes. Highly contiguous genome assemblies of B. juncea, B. rapa, B. nigra, and B. oleracea (CC, n = 9) by our group and others have allowed structural analysis of the genomes in terms of gene block arrangements and gene content. B. juncea is a strict allopolyploid of B. rapa and B. nigra with no apparent gene loss or genome reshuffling or homeologous exchanges. Comparison of the A, B, and C genomes shows a common inter-paleogenome non-contiguous gene block association pointing to a common origin for the three diploid genomes in contradiction to A/C and the B genomes belonging to two different plastid lineages. We propose a new nomenclature for the B genome LGs/pseudochromosomes based on the homoeology between the B genome and the A (B. rapa) genome, using the A genome nomenclature as the baseline being the first sequenced Brassica genome. Genome assemblies of B. juncea Varuna and more recently line YS and short-read sequences of extensive germplasm are proving very useful for breeding of both oleiferous and vegetable types of mustard.