Ploidy Variation in Kluyveromyces marxianus Separates Dairy and Non-dairy Isolates

Abstract

Kluyveromyces marxianus is traditionally associated with fermented dairy products, but can also be isolated from diverse non-dairy environments. Because of thermotolerance, rapid growth and other traits, many different strains are being developed for food and industrial applications but there is, as yet, little understanding of the genetic diversity or population genetics of this species. K. marxianus shows a high level of phenotypic variation but the only phenotype that has been clearly linked to a genetic polymorphism is lactose utilisation, which is controlled by variation in the LAC12 gene. The genomes of several strains have been sequenced in recent years and, in this study, we sequenced a further nine strains from different origins. Analysis of the Single Nucleotide Polymorphisms (SNPs) in 14 strains was carried out to examine genome structure and genetic diversity. SNP diversity in K. marxianus is relatively high, with up to 3% DNA sequence divergence between alleles. It was found that the isolates include haploid, diploid, and triploid strains, as shown by both SNP analysis and flow cytometry. Diploids and triploids contain long genomic tracts showing loss of heterozygosity (LOH). All six isolates from dairy environments were diploid or triploid, whereas 6 out 7 isolates from non-dairy environment were haploid. This also correlated with the presence of functional LAC12 alleles only in dairy haplotypes. The diploids were hybrids between a non-dairy and a dairy haplotype, whereas triploids included three copies of a dairy haplotype.

High complexity and degree of genetic variation inBrettanomyces bruxellensispopulation

“…This type of event leads to a decrease of the genetic variability allowing the expression of recessive alleles, and therefore can result in a beneficial adaptation in some environments. The prevalence of LOH events has recently been observed in several yeast species such as S. cerevisiae (Peter, et al 2018), Candida albicans (Ropars, et al 2018) and Kluyveromyces marxianus (Ortiz-Merino, et al 2018). Moreover, previous studies of B. bruxellensis isolates revealed the presence of several regions which underwent LOH.…”

“…With the currently available sequencing technologies, it is now possible to explore the intraspecific variability of a species at the genome-wide level. Such population genomic studies have been performed on multiple yeast species, including S. cerevisiae (Peter, et al 2018;Skelly, et al 2013;Bergström, et al 2014;Strope, et al 2015;Almeida, et al 2015;Zhu, et al 2016;Gonçalves, et al 2016, Gallone, et al 2016 and Schizosaccharomyces pombe (Fawcett, et al 2014;Jeffares, et al 2015) but also non-model yeast species (Leducq, et al 2016;Carreté, et al 2018;Hirakawa, et al 2015;Ford, et al 2015;Ropars, et al 2018;Friedrich, et al 2015;Ortiz-Merino, et al 2018), granting better insights into their respective evolutionary histories as well as genotype-phenotype relationships.…”

Snf2 controls pulcherriminic acid biosynthesis and connects pigmentation and antifungal activity of the yeastMetschnikowia pulcherrima

“…The 5S rRNA genes are dispersed at many locations around the genome, as in M. bicuspidata (35). The distribution of empirical allele frequencies from single nucleotide variants found after mapping of Illumina data to the PacBio assembly indicated that the wildtype strain is haploid (36), in contrast to the other reported genome sequences of strains from the M. pulcherrima/M. fructicola subclade that are highly heterozygous and probably interspecies hybrids (37,38).…”

Kluyveromyces marxianus as a robust synthetic biology platform host

“…The resulting strains were tested for mating type and heterothallic status by using a pheromone assay described below, or by crossing them with reference heterothallic haploid strains, allowing haploid heterothaliic MATa or MATα strains to be successfully isolated. Some double-transposase inactivated strains did not mate with the reference strains, possibly because these are stable diploids or triploids (12) or possibly due to chromosomal rearrangements (43). Although we performed the gene inactivations individually, we later tested and verified that simultaneous targeting of both transposases with CRISPR NHEJ works efficiently in K. marxianus.…”

“…As a homothallic yeast, K. marxianus lacks a permanent mating type, because K. marxianus haploid cells naturally change their mating type (either the a-mating type, MATa, or ɑ-mating type, MATɑ) leading to uncontrolled MATa/MATɑ diploidization within a population (11). This stochastic ploidy makes it impossible to carry out quantitative biological studies of interesting traits that are ploidy-specific (12), as it leads to populations with mixed phenotypes, and prevents K. marxianus domestication through selective crossing.…”