Scholarlink

<p>Plant mitochondrial genomes often contain polymorphic fragments, posing a significant challenge to complete genome assembly. Methods for assembling organelle genomes without external reference genomes use either PacBio HiFi data or error-corrected Oxford Nanopore Technologies (ONT) long-read data prior to assembly. In this study, we present a pipeline for assembling a draft mitochondrial genome using uncorrected ONT long-read data and for polishing the assembly using high-quality short-read data. This approach generates references from whole-genome assembly guided by organelle gene annotation. It facilitates users in identifying mitochondrial-derived seed contigs from a plant whole-genome assembly, extracting the raw reads that comprise them, and assembling mitochondrial genome sequences. To determine seed contigs of mitochondrial origin, a whole-genome assembly is evaluated for three criteria: 1) the mitochondrial and plastid gene densities, 2) the number of read coverage, and 3) the connectivity of contigs in the genome assembly graph. We evaluated the effectiveness of our approach by analyzing 11 publicly available plant genome sequencing datasets. We have implemented the approach as the Plant Organelle Long-read Assembly Pipeline (POLAP v0.3.7.3; <a href="https://github.com/goshng/polap">https://github.com/goshng/polap</a>).</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

POLAP: A New Pipeline for Plant Mitochondrial Genome Assembly Using Oxford Nanopore Data Through Reference Generation

  • 期刊论文

  • 发表日期：

    2025年7月1日

查看全文
  • Sang Chul Choi,
  • Sangtae Kim

摘要

Plant mitochondrial genomes often contain polymorphic fragments, posing a significant challenge to complete genome assembly. Methods for assembling organelle genomes without external reference genomes use either PacBio HiFi data or error-corrected Oxford Nanopore Technologies (ONT) long-read data prior to assembly. In this study, we present a pipeline for assembling a draft mitochondrial genome using uncorrected ONT long-read data and for polishing the assembly using high-quality short-read data. This approach generates references from whole-genome assembly guided by organelle gene annotation. It facilitates users in identifying mitochondrial-derived seed contigs from a plant whole-genome assembly, extracting the raw reads that comprise them, and assembling mitochondrial genome sequences. To determine seed contigs of mitochondrial origin, a whole-genome assembly is evaluated for three criteria: 1) the mitochondrial and plastid gene densities, 2) the number of read coverage, and 3) the connectivity of contigs in the genome assembly graph. We evaluated the effectiveness of our approach by analyzing 11 publicly available plant genome sequencing datasets. We have implemented the approach as the Plant Organelle Long-read Assembly Pipeline (POLAP v0.3.7.3; https://github.com/goshng/polap).