当前位置: X-MOL 学术Genome Biol. Evol. › 论文详情
Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)
Ultralong Oxford Nanopore Reads Enable the Development of a Reference-Grade Perennial Ryegrass Genome Assembly
Genome Biology and Evolution ( IF 3.3 ) Pub Date : 2021-07-08 , DOI: 10.1093/gbe/evab159
Daniel Frei 1 , Elisabeth Veekman 2 , Daniel Grogg 3 , Ingrid Stoffel-Studer 3 , Aki Morishima 4 , Rie Shimizu-Inatsugi 4 , Steven Yates 3 , Kentaro K Shimizu 4, 5 , Jürg E Frey 1 , Bruno Studer 3 , Dario Copetti 3, 4
Affiliation  

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.

中文翻译:

超长牛津纳米孔读数能够开发参考级多年生黑麦草基因组组装

尽管过去十年在 DNA 测序方面取得了进展,但重建大型且重复丰富的真核基因组的端粒到端粒基因组组装仍然很困难。更准确的碱基检出或更长的读长可以解决这个问题,但当前的测序平台无法同时提供这两者。多年生黑麦草(Lolium perenne L.)是一个重要物种的例子,由于缺乏参考基因组组装,阻碍了基于基因组学的方法在育种计划中的迅速采用。为了填补这一空白,我们优化了 Oxford Nanopore Technologies 的测序方案,获得 N50 为 62 kb 的测序读数,这对于植物样品来说是非常高的值。此类读数的组装产生了高度完整(2.7 Gb 中的 2.3 个)、正确(QV 45)和连续(重叠群 N50 和 N90 分别为 11.74 和 3.34 Mb)的基因组组装。我们展示了读取长度如何成为确定装配连续性的关键。序列注释揭示了转座元件和重复序列(占组装的 81.6%)的优势,并鉴定了 38,868 个蛋白质编码基因。几乎 90% 的碱基可以固定在七个假分子上,为多年生黑麦草提供了第一个高质量的单倍体参考组装。该协议将能够为更多植物样本产生更长的牛津纳米孔技术读数,并将饲草引入现代基因组学辅助育种计划。
更新日期:2021-07-08
down
wechat
bug