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

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-...

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Veröffentlicht in:Nature plants 2020-08, Vol.6 (8), p.929-941
Hauptverfasser: Perumal, Sampath, Koh, Chu Shin, Jin, Lingling, Buchwaldt, Miles, Higgins, Erin E., Zheng, Chunfang, Sankoff, David, Robinson, Stephen J., Kagale, Sateesh, Navabi, Zahra-Katy, Tang, Lily, Horner, Kyla N., He, Zhesi, Bancroft, Ian, Chalhoub, Boulos, Sharpe, Andrew G., Parkin, Isobel A. P.
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Sprache:eng
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Zusammenfassung: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 (
ISSN:2055-0278
2055-0278
DOI:10.1038/s41477-020-0735-y