Elucidating the major hidden genomic components of the A, C, and AC genomes and their influence on Brassica evolution

Abstract

Decoding complete genome sequences is prerequisite for comprehensive genomics studies. However, the currently available reference genome sequences of Brassica rapa (A genome), B. oleracea (C) and B. napus (AC) cover 391, 540, and 850 Mbp and represent 80.6, 85.7, and 75.2% of the estimated genome size, respectively, while remained are hidden or unassembled due to highly repetitive nature of these genome components. Here, we performed the first comprehensive genome-wide analysis using low-coverage whole-genome sequences to explore the hidden genome components based on characterization of major repeat families in the B. rapa and B. oleracea genomes. Our analysis revealed 10 major repeats (MRs) including a new family comprising about 18.8, 10.8, and 11.5% of the A, C and AC genomes, respectively. Nevertheless, these 10 MRs represented less than 0.7% of each assembled reference genome. Genomic survey and molecular cytogenetic analyses validates our insilico analysis and also pointed to diversity, differential distribution, and evolutionary dynamics in the three Brassica species. Overall, our work elucidates hidden portions of three Brassica genomes, thus providing a resource for understanding the complete genome structures. Furthermore, we observed that asymmetrical accumulation of the major repeats might be a cause of diversification between the A and C genomes.

Long-reads assembly of theBrassica napusreference genome, Darmor-bzh

“…Likewise, the repetitive content of these ten genomes is similar, between 54% for Darmor-bzh and 60% for no2127. Concerning the diploid genomes and as already reported [50] , B. oleracea (C) genome assemblies contain more repetitive elements than the B. rapa (A) and B. nigra (B) genome assemblies (Table 4).…”

“…As pericentromeric region assembly was greatly improved in Darmor-bzh v10, we compared the number of RGA in such regions between the two assemblies and found 74 RGAs in Darmor-bzh v10 compared to no RGAs in Darmor-bzh v5 ( Figure 7D). To further highlight the interest of assembling such regions using ONT technologies, we compared the size and number (including RGA) of a resistance QTL to phoma stem canker overlapping the A01 centromere [47,50]. In this new assembly, we were able to identify 45 candidate RGA compared to 29 in Darmor-bzh v5 ( Figure 7E).…”

Re-exploration of U’s Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences

“…The dnaLCW method is a fast and comparatively easy method that does not require a PCR based gap filling to assemble the chloroplast and rDNA sequences. With slight modification, dnaLCW also allows the characterization of the major repeats in the Brassica genome 55 . Briefly, high-quality Illumina paired-end reads were denovo assembled using the CLC genome assembler (ver.…”

A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance

“…Through subfunctionalization or reciprocal loss of duplicated genes in differentiated populations of an ancestral species, WGDs can also promote reproductive isolation and thus facilitate speciation 13 . Brassicaceae (also known as Cruciferae), a monophyletic group distributed worldwide, has been highly diversified by complicated WGD events and subsequent evolution, with 350 genera and 4000 species 14,15 . It contains many important crops (e.g., cabbage, rapeseed and mustard) that have been domesticated for food, biofuels, and ornamentals 16 .…”