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UGDR: a generic pipeline to detect recombined regions in polyploid and complex hybrid yeast genomes. BMC Bioinformatics 2022 Dec 21;23(1):555

Date

12/22/2022

Pubmed ID

36544090

Pubmed Central ID

PMC9773435

DOI

10.1186/s12859-022-05113-y

Scopus ID

2-s2.0-85144580819 (requires institutional sign-in at Scopus site)

Abstract

MOTIVATION: In eukaryotes, homologous recombination between the parental genomes frequently occurs during the evolutionary conserved process of meiosis, generating the genetic diversity transmitted by the gametes. The genome-wide determination of the frequency and location of the recombination events can now be efficiently performed by genotyping the offspring's polymorphic markers. However, genotyping recombination in complex hybrid genomes with existing methods remains challenging because of their strain and ploidy specificity and the degree of diversity and complexity of the parental genomes, especially in [Formula: see text] polyploids.

RESULTS: We present UGDR, a pipeline to genotype the polymorphisms of complex hybrid yeast genomes. It is based on optimal mapping strategies of NGS reads, comparative analyses of the allelic ratio variation and read depth coverage. We tested the UGDR pipeline with sequencing reads from recombined hybrid diploid yeast strains and various clinical strains exhibiting different degrees of ploidy. UGDR allows to plot the markers distribution and recombination profile per chromosome.

CONCLUSION: UGDR detects and plots recombination events in haploids and polyploid yeasts, which facilitates the discovery and understanding of the yeast genetic recombination map and identify new out-performing recombinants.

Author List

Bedrat A

Author

Amina Bedrat PhD Postdoctoral Researcher 3 in the Pediatrics department at Medical College of Wisconsin




MESH terms used to index this publication - Major topics in bold

Diploidy
Genome
Ploidies
Polymorphism, Genetic
Polyploidy
Yeasts