Genome evolution across 1,011 Saccharomyces cerevisiaeSaccharomyces\ cerevisiae isolates

International audienceLarge-scale population genomic surveys are essential to explore the phenotypic diversity of natural populations. Here we report the whole-genome sequencing and phenotyping of 1,011 $Saccharomyces\ cerevisiae$ isolates, which together provide an accurate evolutionary picture of the genomic variants that shape the species-wide phenotypic landscape of this yeast. Genomic analyses support a single ‘out-of-China’ origin for this species, followed by several independent domestication events. Although domesticated isolates exhibit high variation in ploidy, aneuploidy and genome content, genome evolution in wild isolates is mainly driven by the accumulation of single nucleotide polymorphisms. A common feature is the extensive loss of heterozygosity, which represents an essential source of inter-individual variation in this mainly asexual species. Most of the single nucleotide polymorphisms, including experimentally identified functional polymorphisms, are present at very low frequencies. The largest numbers of variants identified by genome-wide association are copy-number changes, which have a greater phenotypic effect than do single nucleotide polymorphisms. This resource will guide future population genomics and genotype–phenotype studies in this classic model system

Aborting meiosis allows recombination in sterile diploid yeast hybrids

International audienceHybrids between diverged lineages contain novel genetic combinations but an impaired meiosis often makes them evolutionary dead ends. Here, we explore to what extent an aborted meiosis followed by a return-to-growth (RTG) promotes recombination across a panel of 20 Saccharomyces cerevisiae and S. paradoxus diploid hybrids with different genomic structures and levels of sterility. Genome analyses of 275 clones reveal that RTG promotes recombination and generates extensive regions of loss-of-heterozygosity in sterile hybrids with either a defective meiosis or a heavily rearranged karyotype, whereas RTG recombination is reduced by high sequence divergence between parental subgenomes. The RTG recombination preferentially arises in regions with low local heterozygosity and near meiotic recombination hotspots. The loss-of-heterozygosity has a profound impact on sexual and asexual fitness, and enables genetic mapping of phenotypic differences in sterile lineages where linkage analysis would fail. We propose that RTG gives sterile yeast hybrids access to a natural route for genome recombination and adaptation

Polymorphism in the Alpha Cardiac Muscle Actin 1 Gene Is Associated to Susceptibility to Chronic Inflammatory Cardiomyopathy

International audienceAimsChagas disease, caused by the protozoan Trypanosoma cruzi is endemic in Latin America, and may lead to a life-threatening inflammatory dilated, chronic Chagas cardiomyopathy (CCC). One third of T. cruzi-infected individuals progress to CCC while the others remain asymptomatic (ASY). A possible genetic component to disease progression was suggested by familial aggregation of cases and the association of markers of innate and adaptive immunity genes with CCC development. Since mutations in multiple sarcomeric genes, including alpha-cardiac actin (ACTC1) have been involved in hereditary dilated cardiomyopathy, we investigated the involvement of the ACTC1 gene in CCC pathogenesis.Methods and ResultsWe conducted a proteomic and genetic study on a Brazilian study population. The genetic study was done on a main cohort including 118 seropositive asymptomatic subjects and 315 cases and the replication was done on 36 asymptomatic and 102 CCC cases. ACTC1 protein and mRNA levels were lower in myocardial tissue from patients with end-stage CCC than those found in hearts from organ donors. Genotyping a case-control cohort of CCC and ASY subjects for all informative single nucleotide polymorphism (SNP) in the ACTC1 gene identified rs640249 SNP, located at the 5’ region, as associated to CCC. Associations are borderline after correction for multiple testing. Correlation and haplotype analysis led to the identification of a susceptibility haplotype. Functional assays have shown that the rs640249A/C polymorphism affects the binding of transcriptional factors in the promoter regions of the ACTC1 gene. Confirmation of the detected association on a larger independent replication cohort will be useful.ConclusionsGenetic variations at the ACTC1 gene may contribute to progression to chronic Chagas Cardiomyopathy among T. cruzi-infected patients, possibly by modulating transcription factor binding to ACTC1 promoter regions

Correlation analysis for the rs640249 polymorphism in two different reference populations.

<p>Genotype data from the European reference population (CEU) and from the West Africa reference population (YRI) were downloaded from HapMap. A 2 Mb region surrounding the ACTC1 gene was analyzed in these two populations. The data were analyzed with Haploview Software. <b>A)</b> Correlations were assessed by calculating r² values. The rs640249 polymorphism was found to be correlated with three other polymorphisms in the CEU reference population (rs641563; rs639735; rs479623). <b>B</b>) In the West Africa reference population, the rs640249 polymorphism was correlated only with rs641563. </p

<i>In silico</i> analysis predicted differential binding patterns for rs640249 and rs641563 polymorphisms. Gel shift experiment has confirmed this differential binding for rs640249 polymorphism.

<p>The probability of these polymorphisms creating or altering DNA–protein interaction was determined by in silico analysis (<a href="http://www.gene-regulation.com/cgi-bin/pub/programs/match/bin/match.cgi" target="_blank"><u>http://www.gene-regulation.com/cgi-bin/pub/programs/match/bin/match.cgi</u></a>). An 75% threshold score (similarity matrix) was used. For each polymorphism (A, rs1800925; B, rs641563) putative bindings are described. The similarity matrix score is indicated in brackets. <b>C</b>: Electrophoretic mobility shift assays were performed in vitro as described in Materials and Methods. A differential binding pattern was detected for the rs640249A allele. </p

Relative quantification of alpha-cardiac actin 1 (ACTC1) by immunoblotting.

<div><p>Myocardial samples were obtained from the left ventricular free wall of the hearts of patients with severe CCC and end-stage heart failure, at the time of heart transplantation. Samples from five hearts from CCC patients (at least two positive results in three independent anti-<i>T</i>. <i>cruzi</i> serology tests, as indicated above), and from healthy hearts from organ donors not used for transplantation for technical reasons were used. Immunoblotting and protein quantification were done in duplicate. A. The immunoblot and the protein quantification result of the first experiment are presented here. The central line represents the median. Representative results from two experiments are shown here. A Mann-Whitney test was performed and differences were considered significant if <i>P</i><0.001.</p> <p><b>B</b>. Real-time quantitative PCR was carried out on the same samples. All the samples were tested in triplicate with GAPDH, the expression of which has been shown to vary little between human myocardial tissue samples. Data were normalized and the relative levels of each mRNA were calculated by the 2^-ΔCt method.</p></div

The same trends for association were detected in a small, independent replication cohort.

<p>The two main polymorphisms, rs640249 and rs641563, were genotyped in the independent replication cohort. This second cohort focused exclusively on male patients with Chagas disease, who have a higher risk of progression to CCC. This replication cohort included asymptomatic (<i>n</i> = 36) and CCC patients (<i>n</i> = 102). Of the 106 patients with CCC, 48 had severe ventricular dysfunction (left ventricular ejection fraction <40%). The rs640249 genotype distribution is illustrated in A. The results for the rs641563 polymorphism are in B. Haplotype analysis was then performed in C.</p

The rs640249A-rs641563A haplotype is associated with resistance to CCC.

<p>Based on the genotypes obtained, we performed a haplotype analysis of the rs7719175 and rs1800925 polymorphisms. Only three haplotypes were found in our study population: <b>A</b>) Distribution of the three main haplotype combinations in the CCC patients and ASY subjects: homozygous rs640249C-rs641563C (black bar); heterozygous rs640249C-rs641563C + rs640249A-rs641563A (gray bar) and homozygous rs640249A-rs641563A (white bar). <b>B</b>) Haplotype combinations between cases and controls, taking sex into account. <b>C</b>) Distribution of the three main haplotype combinations between patients with severe and moderate CCC, taking sex into account.</p