Additional file 4 of A highly contiguous genome assembly of Brassica nigra (BB) and revised nomenclature for the pseudochromosomes
Creators: name: Paritosh, Kumar
name: Pradhan, Akshay Kumar
name: Pental, Deepak
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Additional file 4: Supplementary Figure 1. K-mer frequency distribution in ~40x PE Illumina reads of B. nigra line BnSDH-1. The frequency of the kmers of length 21bp was calculated and used to estimate the genome size with FindGSE program. The B. nigra genome was estimated to be ~522.13 Mb in size. Supplementary Figure 2. Correction of B. nigra Nanopore assembly contigs with ~100x Illumina short-reads using the Pilon program. Five rounds of Pilon based corrections of SNPs and InDels were carried out iteratively. Most of the errors were identified and corrected in the first two cycles. Green bars represents the BUSCO score of complete gene models achieved after each round of correction. Supplementary Figure 3. Relationship between the GBS markers on the genetic map of Brassica nigra Sangam x 2782 F1DH population [23] and physical position of the respective marker tags on the B. nigra Sangam genomic sequences. Genetic positions of the markers have been shown on the xaxis and position of the marker in the assembled genome on the y-axis. A linear relationship was found between the physical and genetic distances of the markers present on the LGs. The centromeric regions showed lower rate of recombination as compared to other regions of the chromosomes. Supplementary Figure 4. Distribution of different TEs on the B. nigra pseudochromosomes. LTR/Copia and LTR/Gypsy type transposable elements are the most abundant TEs. Centromeric regions show a much higher content of LTR/Copia TEs. Supplementary Figure 5. Distribution of the B genome-specific centromeric repeats on the eight pseudochromosomes of B. nigra. The earlier described six unique repeat sequences in the B genome of B. juncea [23] were found to constitute the centromeric regions of the B. nigra pseudochromosomes. The position of the centromeric repeats on the pseudochromosomes has been shown by horizontal bars; the vertical curve represents the cumulative number of the predicted centromeric repeats. Supplementary Figure 6. Genes identified in the transcriptome of leaf, stem, and developing inflorescence of B. nigra. Genes present on the eight pseudochromosomes of B. nigra are represented in track 1; each gene is represented by a line and colored based on the gene bock it belongs to, following Schranz et al. [17].. Track 2 represents the position of the centromeric repeats in each of the B. nigra pseudochromosomes. Track 3 represents the position of the genes found to be expressed in the transcriptome sequencing data; each expressing gene has been represented by a green line; genes nonexpressing in the transcriptome study are represented by red lines. Supplementary Figure 7. Orthologous gene retention in the BraA [21], BniB (this study), and BolC [22] genomes corresponding to the A. thaliana genes. Position of the A. thaliana genes have been plotted on axis X, the proportion of the genes retained in each of the three constituent paleogenomes of the A, B and C genomes has been plotted on axis Y. The constituent paleogenomes have been designated LF (least fragmented), MF1 (moderately fragmented), and MF2 (most fragmented) based on the percentage of genes retained in comparison to At, following the convention set for B. rapa [13]. Supplementary Figure 8. Comparison of the eight B. nigra (BniB) pseudochromosomes with the ten B. rapa (BraA) pseudochromosomes [21] for homologous regions. Each of the horizontal lines represents a gene. Homologous regions were identified by gene collinearity and the least Ks values amongst all the possible gene pairs. The number given to each B genome pseudochromosome in most of the cases is based on the number given to the A genome pseudochromosome with which it shows maximum homology.