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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.

SUBMITTER: Perumal S

PROVIDER: S-EPMC7419231 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Characterization of B-Genome Specific High Copy hAT MITE Families in Brassica nigra Genome.

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

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Brassica nigra

Project description:Brassica nigra grown for its oil rich seeds and spice

| PRJNA18141 | ENA

Brassica nigra

Project description:Lagercrantz_95 genetic map

| PRJNA175368 | ENA

Conserved microstructure of the Brassica B Genome of Brassica nigra in relation to homologous regions of Arabidopsis thaliana, B. rapa and B. oleracea.

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