YMAP

Yeast Mapping Analysis Pipeline
An online webserver for the visualization of yeast genome sequence datasets that provides intuitive maps of aneuploidies and the degree of heterozygosity across all chromosomes.

YMAP detects copy number variations (CNVs) and loss of heterozygosity (LOH) events in eukaryotic genomes.  It produces maps for lab strains with available haplotype maps and for clinical strains (in which a phylogeny is known). If a reference genome is uploaded, it can map chromosomes for additional yeast genomes.

YMAP was originally designed to work with SNP microarrays (Abbey et al. 2011) and was then modified to use Illumina gDNA input (Abbey et al. 2014).
Examples of informative YMAP output produced by our lab and others include:
Susceptibility to Medium-Chain Fatty Acids is Associated with Trisomy of Chromosome 7 in Candida albicans.

Ma Q, Ola M, Iracane E, and Butler G. mSphere. 2019;4:e00402-19. doi: 10.1128/mSphere.00402-19A

 
‘Parameiosis’ Drives Depolyploidization and Homologous Recombination in Candida albicans.

Anderson MZ, Thomson GJ, Hirakawa MP, and Bennett RJ. Nature Communications. 2019;10:4388. doi: 10.1038/s41467-019-12376-2

 
Genome Plasticity in Candida albicans is Driven by Long Repeat Sequences.

Todd RT, Wikoff TD, Forche A, and Selmecki A. eLife. 2019;8:e45954. doi: 10.7554/eLife.45954

 
The Evolution of Drug Resistance in Clinical Isolates of Candida albicans.

Ford C, Funt J Abbey D, Issi L, Guiducci C, Martinez D, Delorey T, Li B, White T, Cuomo C, Rao R, Berman J, Thompson D, and Regev A. eLife. 2015;4:e00662. doi: 10.7554/eLife.00662

 
Parasexual Ploidy Reduction Drives Population Heterogeneity Through Random and Transient Aneuploidy in Candida albicans.

Hickman MA, Paulson C, Dudley A, and Berman J. Genetics. 2015 Jul;200(3):781-94. doi: 10.1534/genetics.115.178020

 
The “Obligate Diploid” Candida albicans Forms Mating-Competent Haploids.

Hickman MA, Zeng G, Forche A, Hirakawa MP, Abbey D, Harrison BD, Wang YM, Su C, Bennett RJ, Wang Y, and Berman J. Nature. 2013;494:55–59. doi: 10.1038/nature11865

Stress Alters Rates and Types of Loss of Heterozygosity in Candida albicans.

A Forche, D Abbey, T Pisithkul, MA Weinzierl, T Ringstrom, D Bruck, K Petersen, and Berman J. mBio. 2011;2:e00129-11. doi: 10.1128/mBio.00129-11

© 2020 Judith Berman. Created by Naama Dror.