Copy number variation in fungi and its implications for wine yeast genetic diversity and adaptation
- 1Vanderbilt University, United States
In recent years, copy number (CN) variation has emerged as a new and significant source of genetic polymorphisms contributing to the phenotypic diversity of populations. CN variants are defined as genetic loci that, due to duplication and deletion, vary in their number of copies across individuals in a population. CN variants range in size from 50 base pairs to whole chromosomes, can influence gene activity, and are associated with a wide range of phenotypes in diverse organisms, including the budding yeast Saccharomyces cerevisiae. In this review, we introduce CN variation, discuss the genetic and molecular mechanisms implicated in its generation, how they can contribute to genetic and phenotypic diversity in fungal populations, and consider how CN variants may influence wine yeast adaptation in fermentation-related processes. In particular, we focus on reviewing recent work investigating the contribution of changes in CN of fermentation-related genes in yeast wine strains and offer notable illustrations of such changes, including the high levels of CN variation among the CUP genes, which confer resistance to copper, a metal with fungicidal properties, and the preferential deletion and duplication of the MAL1 and MAL3 loci, respectively, which are responsible for metabolizing maltose and sucrose. Based on the available data, we propose that CN variation is a substantial dimension of yeast genetic diversity that occurs largely independent of single nucleotide polymorphisms. As such, CN variation harbors considerable potential for understanding and manipulating yeast strains in the wine fermentation environment and beyond.
Keywords: structural variation, Alcohol fermentation, Sugar metabolism, Gene Duplication, gene loss, Population Genomics
Received: 12 Dec 2017;
Accepted: 07 Feb 2018.
Edited by:Aline Lonvaud, Université de Bordeaux, France
Reviewed by:Estefani Garcia Rios, Consejo Superior de Investigaciones Científicas (CSIC), Spain
Jan Steensels, Flanders Institute for Biotechnology, Belgium
Copyright: © 2018 Steenwyk and Rokas. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Prof. Antonis Rokas, Vanderbilt University, Nashville, United States, firstname.lastname@example.org