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

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.

Genomic insights into the origin, domestication and diversification of Brassica juncea

“…3a and 7 ), by consistent syntenic gene ordering (Supplementary Fig. 8 ) using genome-ordered graphical genotypes 28 , and by the good collinearity of SY to those of B. rapa 29 and B. nigra 30 and other previously reported Brassica genomes 19 , 25 , 31 (Supplementary Fig. 9 ).…”

“…SY is a yellow-seeded landrace of B. juncea and represents a new form evolved from hybridization between two big gene pools. Therefore, SY is different from previously sequenced stem 19 and Indian 25 mustard. The chromosome-scale reference genome of SY, in conjunction with re-sequencing of 480 accessions, captured major genetic variation and allowed detailed reconstruction of the evolutionary and domestication history of this diverse ancient crop species.…”

“…The final SY assembly captured 933.5 Mb of genome sequence, with 867.3 Mb (~92.9%) anchored into chromosomes (Fig. 1 and Supplementary Table 4 ), which is superior to previous assemblies of stem 19 and Indian 25 mustard in terms of genome size, contiguity and anchorage. We simultaneously assembled the CP (153,465 bp) and MT (219,803 bp) genomes of SY (Supplementary Figs.…”

“…The SY assembly contained 50.36% TEs (Table 1 and Supplementary Table 10 ), slightly more than the published genomes of B. juncea T84-66 (43.5%) 19 and Varuna (45.8%) 25 and B. rapa (37.51%) 32 , but less than B. nigra (53.73%) 30 . In accordance with previous Brassica genomes 19 , 25 , 29 – 33 , LTR/ gypsy retroelements were the predominant TE family (Supplementary Table 10 ). We distinguished the chromosomal centromeric from pericentromeric regions by specific repeats 30 , 34 – 37 (Fig.…”

Metabolite Profiling and Transcriptome Analysis Provide Insight into Seed Coat Color in Brassica juncea

“…Brassica species are ideal models for studying polyploid genome evolution [53], and B. juncea has the yellow-seeded trait genus naturally [8]. Therefore, we used the genome sequence of B. juncea [1,54] to perform comprehensive transcriptome and metabolic profiling of developing seeds in yellow-and dark-seeded B. juncea. In this study, our results identified differentially abundant metabolic compounds, including phenolic acids, flavonoids, lipid compounds, hydroxycinnamic acids, and novel unknown compounds.…”