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

Abstract

Background Brassica 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. 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 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. Conclusions A 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.

Reference flow: reducing reference bias using multiple population genomes

“…To better understand where variant-aware methods reduce bias the most, we studied the relationship between highly biased HET sites and various categories of repeat families (Fig. 4) and classes (Additional file 1: Figure S11) annotated by RepeatMasker [30]. Using alignment to GRCh38, many strongly biased HETs are in L1 (10,288 or 23%) and Alu Fig.…”

A chromosome-scale assembly ofBrassica carinata(BBCC) accession HC20 containing resistance to multiple pathogens and an early generation assessment of introgressions intoB. juncea(AABB)

“…We have followed the LG nomenclature of B. oleracea var capitata (BolC) (Liu et al . 2014) for the BcaC chromosomes, and the nomenclature described for B. nigra (BniB) Sangam (Paritosh et al ., 2020) for the BcaB chromosomes (Table S6).…”

“…A de-novo prediction approach was used for the identification of transposable elements (TEs). A repeat library developed earlier for the Brassica genomes (Paritosh et al ., 2020; Paritosh et al ., 2021) was used as a reference. B. carinata genome was found to contain ~557.4 Mb (50.13 %) of repeat elements belonging to three broad categories – DNA transposons, retrotransposons, and other repeat elements.…”

“…Highly contiguous genome assemblies based on long-read sequencing on PacBio or Oxford Nanopore platforms supplemented with optical maps and/or chromosome capture (Hi-C) are currently available for all the species of the U’s triangle - B. rapa (Belser et al ., 2018; Zhang et al ., 2018) , B. nigra (Paritosh et al ., 2020; Perumal et al ., 2020), B. oleracea (Belser et al ., 2018; Guo et al ., 2021; Lv et al ., 2020), B. juncea (Kang et al ., 2021; Paritosh et al ., 2021), B. napus (Chen et al ., 2021; Lee et al ., 2020; Rousseau-Gueutin et al ., 2020; Song et al ., 2020) and B. carinata (Song et al ., 2021). Both breeding activity and genomic information are sparse in the case of the B genome containing Brassicas that are grown mostly by small farm holders in the developing nations.…”

Subgenome Discrimination in Brassica and Raphanus Allopolyploids Using Microsatellites

“…To analyze genome-specific microsatellites, we downloaded 100-bp whole-genome sequence reads of the four diploid A, C, B, and R genomes from NCBI ( Table 1 ). High-quality reads representing 0.04–0.06× of the A, C, B, and R genomes [ 30 , 31 , 32 , 33 ] were selected using the FastQC tool in the RepeatExplorer version 2 pipeline [ 34 ]. Following a script provided in RepeatExplorer2, a long single contig was generated by concatenating all reads from each species and inserting 50-bp Ns between reads.…”