A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome

Abstract

It is only recently, with the advent of long-read sequencing technologies, that we are beginning to uncover previously uncharted regions of complex and inherently recursive plant genomes. To comprehensively study and exploit the genome of the neglected oilseed Brassica nigra, we generated two high-quality nanopore de novo genome assemblies. The N50 contig lengths for the two assemblies were 17.1 Mb (12 contigs), one of the best among 324 sequenced plant genomes, and 0.29 Mb (424 contigs), respectively, reflecting recent improvements in the technology. Comparison with a de novo short-read assembly corroborated genome integrity and quantified sequence-related error rates (0.2%). The contiguity and coverage allowed unprecedented access to low-complexity regions of the genome. Pericentromeric regions and coincidence of hypomethylation enabled localization of active centromeres and identified centromere-associated ALE family retro-elements that appear to have proliferated through relatively recent nested transposition events (<1 Ma). Genomic distances calculated based on synteny relationships were used to define a post-triplication Brassica-specific ancestral genome, and to calculate the extensive rearrangements that define the evolutionary distance separating B. nigra from its diploid relatives.

Long-read assembly of the Brassica napus reference genome Darmor-bzh

“…At the beginning of 2020, 2 genomes of B. rapa (Chiifu) and B. oleracea (D134) were released and sequenced using PacBio long reads [ 5 , 6 ]. A first long-read assembly based on ONT of the other diploid species, B. nigra NI100, has been available since the beginning of 2020 [ 7 ]. The earlier availability of the diploid genomes may be explained by their smaller genome size (<600 Mb) compared with their tetraploid derivatives.…”

Genome-wide Detection of Cytosine Methylations in Plant from Nanopore sequencing data using Deep Learning

“…Recently Parkin et al . sequenced ∼78× Nanopore reads of B. nigra (genotype Ni100), along with ∼20× bisulfite sequencing reads 33 . A high-contiguity B. nigra genome (491M, 8 chromosomes) was assembled in their work.…”

Assembly and Validation of Two Gap-free Reference Genomes forXian/indicaRice Reveals Insights into Plant Centromere Architecture

“…Centromeres are essential for maintaining the integrity of chromosomes during cell division, and ensure the fidelity of their inheritance. Unfortunately, until now, centromeres have remained largely under-explored, especially in larger genomes (Perumal et al, 2020). To functionally identify the location and sequence of centromeres in our gap-free genomes, we used the rice CENH3 antibody to immunoprecipitate chromatin from rice nuclei and then sequenced Illumina sequenced the captured DNA fragments (i.e.…”