Generation of new genetic diversity by crossover (CO) and non-crossover (NCO) is a fundamental process in eukaryotes. Fungi have played critical roles in studying this process because they permit tetrad analysis, which has been used by geneticists for several decades to determine meiotic recombination products. New genetic variations can also be generated in zygotes via illegitimate mutation (IM) and repeat-induced point mutation (RIP). RIP is a genome defense mechanism for preventing harmful expansion of transposable elements or duplicated sequences in filamentous fungi. Although the exact mechanism of RIP is unknown, the C:G to T:A mutations might result from DNA cytosine methylation. A comprehensive approach for understanding the molecular mechanisms underlying these important processes is to perform high-throughput mapping of CO, NCO, RIP and IM in zygotes bearing large numbers of heterozygous variant markers. To this aim, we developed ‘TSETA’, a versatile and user-friendly pipeline that utilizes high-quality and chromosome-level genome sequences involved in a single meiotic event of the industrial workhorse fungus Trichoderma reesei. TSETA not only can be applied to most sexual eukaryotes for genome-wide tetrad analysis, it also outcompetes most currently used methods for calling out single nucleotide polymorphisms between two or more intraspecies strains or isolates.
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