Genome wide analysis of meiotic recombination in yeast: For a few SNPs more

Chakraborty, Parijat; Pankajam, Ajith V; Dutta, Abhishek; Nishant, K. T.

doi:10.1002/iub.1877

Cited by 10 publications

(5 citation statements)

References 65 publications

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“…Our group had previously isolated and whole-genome sequenced 52 haploid spore clones originated from thirteen sets of JAY270 four-spored tetrads (Rodrigues-Prause et al, 2018). It has been estimated that each meiotic cell division in S. cerevisiae produces about 90 crossovers distributed across the genome (Mancera et al, 2008; Chakraborty et al, 2018). These events result in the formation of recombinant chromatids that are sorted into haploid spores, each containing approximately half maternal and half paternal alleles ( Figure 1A ).…”

Section: Resultsmentioning

confidence: 99%

Controlled Reduction of Genomic Heterozygosity in an Industrial Yeast Strain Reveals Wide Cryptic Phenotypic Variation

2019

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Abundant genomic heterozygosity can be found in wild strains of the budding yeast Saccharomyces cerevisiae isolated from industrial and clinical environments. The extent to which heterozygosity influences the phenotypes of these isolates is not fully understood. One such case is the PE-2/JAY270 strain, a natural hybrid widely adopted by sugarcane bioethanol distilleries for its ability to thrive under harsh biotic and abiotic stresses during industrial scale fermentation, however, it is not known whether or how the heterozygous configuration of the JAY270 genome contributes to its many desirable traits. In this study, we took a step toward exploring this question by conducting an initial functional characterization of JAY270’s heteroalleles. We manipulated the abundance and distribution of heterozygous alleles through inbreeding and targeted uniparental disomy (UPD). Unique combinations of homozygous alleles in each inbred strain revealed wide phenotypic variation for at least two important industrial traits: Heat stress tolerance and competitive growth. Quantitative trait loci analyses allowed the identification of broad genomic regions where genetic polymorphisms potentially impacted these traits, and there was no overlap between the loci associated with each. In addition, we adapted an approach to induce bidirectional UPD of three targeted pairs of chromosomes (IV, XIV, and XV), while heterozygosity was maintained elsewhere in the genome. In most cases UPD led to detectable phenotypic alterations, often in opposite directions between the two homozygous haplotypes in each UPD pair. Our results showed that both widespread and regional homozygosity could uncover cryptic phenotypic variation supported by the heteroalleles residing in the JAY270 genome. Interestingly, we characterized multiple examples of inbred and UPD strains that displayed heat tolerance or competitive growth phenotypes that were superior to their heterozygous parent. However, we propose that homozygosity for those regions may be associated with a decrease in overall fitness in the complex and dynamic distillery environment, and that may have contributed to slowing down the erosion of heterozygosity from the JAY270 genome. This study also laid a foundation for approaches that can be expanded to the identification of specific alleles of interest for industrial applications in this and other hybrid yeast strains.

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Section: Resultsmentioning

confidence: 99%

Controlled Reduction of Genomic Heterozygosity in an Industrial Yeast Strain Reveals Wide Cryptic Phenotypic Variation

2019

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“…This technique is highly scalable, and in our case, we likely could have sequenced many more markers (and/or individuals) while maintaining a very high depth per amplicon. This method is an alternative to the increasingly popular bulk-sequencing approaches, in which sample DNA is pooled prior to sequencing (Chakraborty et al, 2018). GT-seq avoids some of the complexity of these approaches.…”

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confidence: 99%

Natural Selection Shapes Variation in Genome-wide Recombination Rate in Drosophila pseudoobscura

et al. 2020

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While recombination is widely recognized to be a key modulator of numerous evolutionary phenomena, we have a poor understanding of how recombination rate itself varies and evolves within a species. Here, we performed a comprehensive study of recombination rate (rate of meiotic crossing over) in two natural populations of Drosophila pseudoobscura from Utah and Arizona, USA. We used an amplicon sequencing approach to obtain high-quality genotypes in approximately 8000 individual backcrossed offspring (17 mapping populations with roughly 530 individuals each), for which we then quantified crossovers. Interestingly, variation in recombination rate within and between populations largely manifested as differences in genome-wide recombination rate rather than remodeling of the local recombination landscape.Comparing populations, we discovered individuals from the Utah population displayed on average 8% higher crossover rates than the Arizona population, a statistically significant difference. Using a QST-FST analysis, we found that this difference in crossover rate was dramatically higher than expected under neutrality, indicating that this difference may have been driven by natural selection. Finally, using a combination of short and long read wholegenome sequencing, we found no significant association between crossover rate and structural variation at the 200-400kb scale. Our results demonstrate that (1) there is abundant variation in genome-wide crossover rate in natural populations (2) interpopulation differences in recombination rate may be the result of local adaptation, and (3) the observed variation among individuals in recombination rate is primarily driven by global regulators of crossover rate, with little detected variation in recombination rate among strains across specific tracts of individual chromosomes.

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“…Similarly, the mean gene conversion tract length in the meiosis of Drosophila melanogaster was determined to be 476 bp ( Miller et al, 2012 ). For gene conversion in the meiosis of Saccharomyces cerevisiae , a somewhat higher value of 1.5 kbp has been obtained ( Chakraborty et al, 2018 ). The very high co-conversion rate in the experiment described above indicated that the value might well be considerable larger in H. volcanii than in all those processes in bacteria and eukaryotes.…”

Section: Discussionmentioning

confidence: 99%

Characterization of Non-selected Intermolecular Gene Conversion in the Polyploid Haloarchaeon Haloferax volcanii

et al. 2021

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Gene conversion is defined as the non-reciprocal transfer of genetic information from one site to a homologous, but not identical site of the genome. In prokaryotes, gene conversion can increase the variance of sequences, like in antigenic variation, but can also lead to a homogenization of sequences, like in the concerted evolution of multigene families. In contrast to these intramolecular mechanisms, the intermolecular gene conversion in polyploid prokaryotes, which leads to the equalization of the multiple genome copies, has hardly been studied. We have previously shown the intermolecular gene conversion in halophilic and methanogenic archaea is so efficient that it can be studied without selecting for conversion events. Here, we have established an approach to characterize unselected intermolecular gene conversion in Haloferax volcanii making use of two genes that encode enzymes involved in carotenoid biosynthesis. Heterozygous strains were generated by protoplast fusion, and gene conversion was quantified by phenotype analysis or/and PCR. It was verified that unselected gene conversion is extremely efficient and it was shown that gene conversion tracts are much longer than in antigenic variation or concerted evolution in bacteria. Two sites were nearly always co-converted when they were 600 bp apart, and more than 30% co-conversion even occurred when two sites were 5 kbp apart. The gene conversion frequency was independent from the extent of genome differences, and even a one nucleotide difference triggered conversion.

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Genome wide analysis of meiotic recombination in yeast: For a few SNPs more

Cited by 10 publications

References 65 publications

Controlled Reduction of Genomic Heterozygosity in an Industrial Yeast Strain Reveals Wide Cryptic Phenotypic Variation

Controlled Reduction of Genomic Heterozygosity in an Industrial Yeast Strain Reveals Wide Cryptic Phenotypic Variation

Natural Selection Shapes Variation in Genome-wide Recombination Rate in Drosophila pseudoobscura

Characterization of Non-selected Intermolecular Gene Conversion in the Polyploid Haloarchaeon Haloferax volcanii

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