Ultralong Oxford Nanopore Reads Enable the Development of a Reference-Grade Perennial Ryegrass Genome Assembly.

Autor:	Frei D; Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland., Veekman E; DLF Seeds S/A, Store Heddinge, Denmark., Grogg D; Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland., Stoffel-Studer I; Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland., Morishima A; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland., Shimizu-Inatsugi R; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland., Yates S; Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland., Shimizu KK; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.; Kihara Institute for Biological Research, Yokohama City University, Maioka, Totsuka-ward, Yokohama, Japan., Frey JE; Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland., Studer B; Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland., Copetti D; Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland.; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
Jazyk:	angličtina
Zdroj:	Genome biology and evolution [Genome Biol Evol] 2021 Aug 03; Vol. 13 (8).
DOI:	10.1093/gbe/evab159
Abstrakt:	Despite the progress made in DNA sequencing over the last decade, reconstructing telomere-to-telomere genome assemblies of large and repeat-rich eukaryotic genomes is still difficult. More accurate basecalls or longer reads could address this issue, but no current sequencing platform can provide both simultaneously. Perennial ryegrass (Lolium perenne L.) is an example of an important species for which the lack of a reference genome assembly hindered a swift adoption of genomics-based methods into breeding programs. To fill this gap, we optimized the Oxford Nanopore Technologies' sequencing protocol, obtaining sequencing reads with an N50 of 62 kb-a very high value for a plant sample. The assembly of such reads produced a highly complete (2.3 of 2.7 Gb), correct (QV 45), and contiguous (contig N50 and N90 11.74 and 3.34 Mb, respectively) genome assembly. We show how read length was key in determining the assembly contiguity. Sequence annotation revealed the dominance of transposable elements and repeated sequences (81.6% of the assembly) and identified 38,868 protein coding genes. Almost 90% of the bases could be anchored to seven pseudomolecules, providing the first high-quality haploid reference assembly for perennial ryegrass. This protocol will enable producing longer Oxford Nanopore Technology reads for more plant samples and ushering forage grasses into modern genomics-assisted breeding programs. (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu