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.