論文

査読有り 国際誌
2021年7月10日

Ultralong Oxford Nanopore reads enable the development of a reference-grade perennial ryegrass genome assembly.

Genome biology and evolution
  • Daniel Frei
  • Elisabeth Veekman
  • Daniel Grogg
  • Ingrid Stoffel-Studer
  • Aki Morishima
  • Rie Shimizu-Inatsugi
  • Steven Yates
  • Kentaro K Shimizu
  • Jürg E Frey
  • Bruno Studer
  • Dario Copetti
  • 全て表示

記述言語
英語
掲載種別
研究論文(学術雑誌)
DOI
10.1093/gbe/evab159

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 a N50 of 62 kb-an unprecedented 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.

リンク情報
DOI
https://doi.org/10.1093/gbe/evab159
PubMed
https://www.ncbi.nlm.nih.gov/pubmed/34247248
ID情報
  • DOI : 10.1093/gbe/evab159
  • PubMed ID : 34247248

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