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

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

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.

Keywords: De novo assembly; Funannotate; Genome annotation; Maker 2; PacBio long-read sequencing; QM6a; Trichoderma reesei.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Fungal / isolation & purification
  • Genome, Fungal*
  • Hypocreales / genetics*
  • Molecular Sequence Annotation*
  • Molecular Weight
  • RNA, Fungal / isolation & purification
  • Reproducibility of Results
  • Sequence Analysis, DNA / methods*
  • Software*

Substances

  • DNA, Fungal
  • RNA, Fungal

Supplementary concepts

  • Trichoderma reesei