UGDR

UGDR detects recombined regions in polyploid and complex hybrid yeast genomes by mapping NGS reads and genotyping polymorphic markers to identify recombination events.

Key Features:

• Optimal Mapping of NGS Reads: Employs advanced mapping strategies for NGS reads to accurately align reads and identify polymorphic markers in complex hybrid genomes.
• Comparative Allelic Ratio Analysis: Performs comparative analysis of allelic ratio variations to distinguish parental alleles in hybrid genomes.
• Read Depth Coverage Assessment: Evaluates read depth coverage to improve detection accuracy of recombination events across genomic regions.
• Recombination Event Plotting: Visualizes marker distribution and recombination profiles on a per-chromosome basis.

Scientific Applications:

• Yeast genetics: Generates recombination maps to identify superior recombinants in yeast.
• Ploidy-resolved analyses: Applies to haploid, diploid (including recombined hybrid diploid strains), and polyploid yeasts, as well as clinical strains with varying ploidy levels.
• Evolutionary biology and breeding: Supports evolutionary studies and breeding programs aimed at enhancing desirable traits through recombination analysis.

Methodology:

Mapping of NGS reads, comparative allelic ratio analysis, read depth coverage assessment, and per-chromosome recombination plotting; tested using sequencing data from recombined hybrid diploid yeast strains and clinical strains with varying ploidy levels.