TSETA

TSETA maps genome-wide, single-nucleotide-resolution genetic variation from third-generation sequencing to enable tetrad analysis and detect single-nucleotide polymorphisms (SNPs), meiotic recombination products, illegitimate mutations (IMs), and repeat-induced point (RIP) mutations in fungal genomes.

Key Features:

• Chromosome-level Sequence Assembly: Utilizes high-precision chromosome-level sequence assembly to support comprehensive, single-nucleotide-resolution mapping across fungal genomes.
• BLASTN-guided sectional MAFFT Alignment: Implements a BLASTN-guided sectional MAFFT algorithm for fast and accurate multiple-genome sequence alignments of near-complete genome sequences.
• SNV and Indel Detection: Identifies single-nucleotide variants (SNVs) and insertion/deletion mutations (Indels) with nucleotide-level precision across aligned genomes.
• Comparison to NGS-based Variant Calling: Provides alignment and variant-calling capabilities that surpass conventional next-generation sequencing (NGS)-based methods for intraspecific and pre- versus post-meiotic comparisons.
• Visualization Capabilities: Enables visualization of genomic data from chromosomal landscapes down to individual nucleotides to facilitate interpretation of recombination and mutation events.

Scientific Applications:

• Genetic Diversity Studies: Mapping SNPs and other variants to assess genetic diversity within and between fungal species or strains.
• Evolutionary Biology: Analyzing meiotic recombination products, IMs, and RIP mutation patterns to investigate evolutionary processes.
• Functional Genomics: Providing nucleotide-resolution variant maps to support studies of gene function and regulation in fungi.

Methodology:

Computational methods explicitly include chromosome-level sequence assembly and BLASTN-guided sectional MAFFT for multiple genome sequence alignments of near-complete genomes, identification of SNVs and Indels, and comparison to NGS-based variant-calling methods.