TSETA (Third-generation Sequencing to Enable Tetrad Analysis) is a fungus-centric software pipeline that utilizes chromosome-level sequence assembly for genome-wide and single-nucleotide-resolution mapping of single-nucleotide polymorphisms (SNPs), meiotic recombination products, illegitimate mutations (IMs) and repeat-induced point (RIP) mutations. It utilizes a newly invented algorithm (i.e., BLASTN-guided sectional MAFFT) to perform fast, accurate, and low-cost multiple genome sequence alignments. This new algorithm outcompetes next-generation sequencing (NGS)-based variant-calling approaches for accurate and comprehensive identification of single-nucleotide variants (SNVs) and insertion/deletion mutations (Indels) among the near-complete genome sequences of any two or more intraspecific strains, as well as sequences before and after meiosis, with single-nucleotide precision. TSETA also has a powerful tool for the visualization of the results from the scale of the chromosomal landscape to individual nucleotides. The data output files are user-friendly for researchers and students lacking computational expertise to analyze and reason about data and evidence.
Trichoderma reesei is an industrially important cellulolytic filamentous fungus and a new fungal model organism for studying epigenetics, meiosis and sexual development.(A) Germination of QM6a conidia on a PDA plate. (B) Two single-ascospore cultures of T. reesei env1 mutant were inoculated on a 10-cm MEA plate under a 12-hour light and 12-hour dark photoperiod. (C) T. reesei fruiting bodies and droplets of liquid forming on their surface (D) T. reesei linear asci and each asci contains 16 ascospores. The complete genome sequence of QM6a is publicly available at https://mycocosm.jgi.doe.gov/Trire_Chr/Trire_Chr.home.html