PacBio 长读测序、组装和 Funannotate 对里氏木霉 QM6a 全基因组的重新注释。

PacBio Long-Read Sequencing, Assembly, and Funannotate Reannotation of the Complete Genome of Trichoderma reesei QM6a.

机构信息

Taiwan International Graduate Program in Molecular and Cellular Biology, Academia Sinica, Taipei, Taiwan, Republic of China.

Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.

出版信息

Methods Mol Biol. 2021;2234:311-329. doi: 10.1007/978-1-0716-1048-0_21.

DOI:10.1007/978-1-0716-1048-0_21

PMID:33165795

Abstract

Single-molecule real-time (SMRT) sequencing developed by Pacific BioSciences (PacBio) offers three major advantages compared to second-generation sequencing: long read length and high consensus accuracy, and a low degree of bias. Together with high sequencing coverage, these advantages overcome the difficulty of sequencing genomic regions such as long AT-rich islands and repeated regions (e.g., ribosomal DNA) in the genome of Trichoderma reesei QM6a. Herein, we describe a protocol for preparing high-quality, high molecular weight genomic DNA for PacBio long-read sequencing, de novo assembly and streamlined annotation of the QM6a genome.

摘要

与第二代测序相比，Pacific BioSciences（PacBio）开发的单分子实时（SMRT）测序具有三个主要优势：读长长、一致性准确率高、偏差度低。结合高测序覆盖率，这些优势克服了在基因组中对长 AT 丰富岛和重复区域（例如，核糖体 DNA）进行测序的困难，如里氏木霉 QM6a 的基因组。在此，我们描述了一种为 PacBio 长读测序、QM6a 基因组从头组装和简化注释准备高质量、高分子量基因组 DNA 的方案。