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

Kumar Paritosh,Deepak Pental,Akshay Kumar Pradhan

doi:10.1186/s12864-020-07271-w

Abstract

BackgroundBrassica nigra (BB), also called black mustard, is grown as a condiment crop in India. B. nigra represents the B genome of U’s triangle and is one of the progenitor species of B. juncea (AABB), an important oilseed crop of the Indian subcontinent. We report the genome assembly of B. nigra variety Sangam.ResultsThe 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 of B. 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 the B. nigra pseudochromosomes. 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 of B. nigra and B. juncea revealed 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.ConclusionsA highly contiguous genome assembly of the B. nigra genome 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 for B. nigra pseudochromosomes, taking the B. rapa pseudochromosome nomenclature as the reference.

Highlights

Brassica nigra (BB), called black mustard, is grown as a condiment crop in India
U [1] based on his observations and preceding cytogenetic work [2] proposed a model on the relationship of some of the cultivated Brassica species
The most significant observation is that the three diploid species of the U’s triangle – B. rapa, B. nigra, B. oleracea, and the other diploid species belonging to the tribe Brassiceae have originated through genome triplication, referred to as the b event [5]

Summary

Introduction

Brassica nigra (BB), called black mustard, is grown as a condiment crop in India. B. nigra represents the B genome of U’s triangle and is one of the progenitor species of B. juncea (AABB), an important oilseed crop of the Indian subcontinent. U [1] based on his observations and preceding cytogenetic work [2] proposed a model on the relationship of some of the cultivated Brassica species. The model, known as U’s triangle, described the relationship of three diploid species – B. rapa (Bra, AA, n = 10), B. nigra (Bni, BB, n = 8), and B. oleracea (Bol, CC, n = 9) with three allopolyploid species – B. juncea (Bju, AABB, n = 18), B. The most significant observation is that the three diploid species of the U’s triangle – B. rapa, B. nigra, B. oleracea, and the other diploid species belonging to the tribe Brassiceae have originated through genome triplication, referred to as the b event [5]. The presence of two plastid lineages [6,7,8,9] points to a minimum of two independent b events [20]

Methods

Results

Discussion

Conclusion