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PROVIDER: PRJEB71987 | ENA |
REPOSITORIES: ENA
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Project description:Raw sequence reads of Saccharomyces strains and Saccharomyces interspecific hybrids isolated from industrial environments
| PRJNA516557 | ENA
Project description:In this work, we evaluated the genetic stabilization process, of the intra- (Saccharomyces cerevisiae) and interspecific (S. cerevisiae x Saccharomyces kudriavzevii) hybrids obtained by different non-GMO techniques, under fermentative conditions. Large-scale transitions in genome size, detected by measuring total DNA content, and genome reorganizations in both nuclear and mitochondrial DNA, evidenced by changes in molecular markers, were observed during the experiments. Interspecific hybrids seem to need fewer generations to reach genetic stability than intraspecific hybrids. The largest number of molecular patterns among the derived stable colonies was observed for intraspecific hybrids, particularly for those obtained by rare-mating in which the total amount of initial DNA was larger. Finally, a representative intraspecific stable hybrid underwent a normal industrial process to obtain active dry yeast production as an important point at which inducing changes in genome composition was possible. No changes in hybrid genetic composition after this procedure were confirmed by comparative genome hybridization. According to our results, fermentation steps 2 and 5 –comprising between 30 and 50 generations- suffice to obtain genetically stable interspecific and intraspecific hybrids, respectively. This work aimed to develop and validate a fast genetic stabilization method for newly generated Saccharomyces hybrids under selective enological conditions. A comparison of the whole stabilization process in intra- and interspecific hybrids showing different ploidy levels, as a result of using different hybridization methodologies, was also made.
2015-03-30 | GSE46192 | GEO
Project description:Four hybrid yeast strains isolated from a variety of industrial substrates were hybridized to an array-CGH platform containing probes to query the whole genomes of seven different Saccharomyces species. For most of the strains we found evidence of multiple interspecific hybridization events and multiple introgressed regions. The strains queried were GSY205 (isolated from a cider fermentation), GSY505 (a contaminant from a lager beer fermentation), GSY2232 (a commercial wine yeast strain), and GSY312 (a commercial lager beer strain). Additionally, 3 different rare viable spores derived from laboratory-created interspecific S. cerevisiae-S. bayanus (aka S. uvarum) hybrids were queried, before and after evolution in chemostats, via S. cerevisiae-S. bayanus microarrays.
2016-12-01 | GSE35549 | GEO
Project description:In this work, we evaluated the genetic stabilization process, of the intra- (Saccharomyces cerevisiae) and interspecific (S. cerevisiae x Saccharomyces kudriavzevii) hybrids obtained by different non-GMO techniques, under fermentative conditions. Large-scale transitions in genome size, detected by measuring total DNA content, and genome reorganizations in both nuclear and mitochondrial DNA, evidenced by changes in molecular markers, were observed during the experiments. Interspecific hybrids seem to need fewer generations to reach genetic stability than intraspecific hybrids. The largest number of molecular patterns among the derived stable colonies was observed for intraspecific hybrids, particularly for those obtained by rare-mating in which the total amount of initial DNA was larger. Finally, a representative intraspecific stable hybrid underwent a normal industrial process to obtain active dry yeast production as an important point at which inducing changes in genome composition was possible. No changes in hybrid genetic composition after this procedure were confirmed by comparative genome hybridization. According to our results, fermentation steps 2 and 5 –comprising between 30 and 50 generations- suffice to obtain genetically stable interspecific and intraspecific hybrids, respectively. This work aimed to develop and validate a fast genetic stabilization method for newly generated Saccharomyces hybrids under selective enological conditions. A comparison of the whole stabilization process in intra- and interspecific hybrids showing different ploidy levels, as a result of using different hybridization methodologies, was also made. A stable hybrid strain was compared with itself before and after ADY (active dry yeast) production in order to evaluate the genetic stability of this strain.
2015-03-30 | E-GEOD-46192 | biostudies-arrayexpress
Project description:CGH arrays for Smukowski Heil, et al MBE 2017. Hybridization is often considered maladaptive, but sometimes hybrids can invade new ecological niches and adapt to novel or stressful environments better than their parents. The genomic changes that occur following hybridization that facilitate genome resolution and/or adaptation are not well understood. Here, we address these questions using experimental evolution of de novo interspecific hybrid yeast Saccharomyces cerevisiae x Saccharomyces uvarum and their parentals. We evolved these strains in nutrient limited conditions for hundreds of generations and sequenced the resulting cultures to identify genomic changes. Analysis of 16 hybrid clones and 16 parental clones identified numerous point mutations, copy number changes, and loss of heterozygosity events, including species biased amplification of nutrient transporters. We focused on a particularly interesting example, in which we saw repeated loss of heterozygosity at the high affinity phosphate transporter gene PHO84 in both intra- and interspecific hybrids. Using allele replacement methods, we tested the fitness of different alleles in hybrid and S. cerevisiae strain backgrounds and found that the loss of heterozygosity is indeed the result of selection on one allele over the other in both S. cerevisiae and the hybrids. This is an example where hybrid genome resolution is driven by positive selection on existing heterozygosity, and demonstrates that even infrequent outcrossing may have lasting impacts on adaptation.
2017-02-21 | GSE95086 | GEO
Project description:We profiled the transcriptomes of four Saccharomyces species, as well as pairwise hybrids between three of the species with S. cerevisiae For pairwise comparisons between Saccharomyces cerevisiae and each of S. paradoxus, S. mikatae, and S. bayanus, we performed 3'-end RNA-seq on RNA from each parent species and each interspecific hybrid.
2013-10-21 | E-GEOD-38875 | biostudies-arrayexpress
Project description:High throughput sequencing was used to investigate the production of small RNAs from cultivated tomato cultivar M82 and its wild relative Solanum pennellii. In order to understand the pattern of inheritance of the samll RNAs, interspecific hybrids (F1 and F2) along with series of introgressed lines comprising precise short genomic regions from S. pennellii in M82 background were used.
2012-05-29 | GSE23562 | GEO
Project description:Genome rearrangements are associated with eukaryotic evolutionary processes ranging from tumorigenesis to speciation. Such rearrangements are especially common following the shock of interspecific hybridization, and some of these could be expected to have strong selective value. To test this expectation we created de novo interspecific yeast hybrids between two diverged but largely syntenic species, Saccharomyces cerevisiae and S. uvarum, then experimentally evolved them under continuous ammonium limitation. We discovered that a characteristic interspecific genome rearrangement arose multiple times in independently evolved populations. We uncovered nine different breakpoints, all occurring in a ~1 kb region of chromosome 14, and all producing an “interspecific fusion junction” within the MEP2 gene coding sequence, such that the 5’ portion derives from S. cerevisiae and the 3’ portion derives from S. uvarum. In most cases the rearrangements altered both chromosomes, resulting in what can be considered to be an introgression of a several-kb region of S. uvarum into an otherwise intact S. cerevisiae chromosome 14, while the S. uvarum chromosome 14 experienced an interspecific reciprocal translocation at the same breakpoint within MEP2, yielding a chimaeric chromosome. The net result is the presence in the cell of two MEP2 fusion genes having identical breakpoints. Given that MEP2 encodes for a high-affinity ammonium permease, that MEP2 fusion genes arise repeatedly under ammonium-limitation, and that three independent evolved isolates carrying MEP2 fusion genes are each more fit than their common ancestor, the novel MEP2 fusion genes are very likely adaptive under ammonium limitation. Our results suggest that when homoploid hybrids form, the admixture of two genomes enables swift and otherwise unlikely evolutionary innovations. Furthermore, the architecture of the MEP2 rearrangement suggests a model for rapid introgression, a phenomenon seen in numerous eukaryotic phyla, that does not invoke repeated backcrossing to one of the parental species. Nomenclature: GSY86 TimeZeroInoculum = ancestral interspecific hybrid used to inoculate ammonium-limited chemostats into 3 replicate vessels A, B, C. 150gen = various single-clone isolates from 150 generations of evolutions from vessels A, B or C. 200gen = various isolates from 200 generations of evolutions from vessels A, B or C.
2013-04-01 | GSE18060 | GEO
Project description:We analyzed allele-specific expression (ASE) in leaf and floral tissues of F1 interspecific hybrids generated between the two closely related species of Arabidopsis thaliana and Arabidopsis lyrata with a whole-genome SNP tiling array (AtSNPtile1). 24 sampes, 12 DNA samples from parents and hybrids, 12 RNA sample from leaf and flowers of hybrids
2011-07-26 | E-GEOD-29037 | biostudies-arrayexpress
Project description:Genome rearrangements are associated with eukaryotic evolutionary processes ranging from tumorigenesis to speciation. Such rearrangements are especially common following the shock of interspecific hybridization, and some of these could be expected to have strong selective value. To test this expectation we created de novo interspecific yeast hybrids between two diverged but largely syntenic species, Saccharomyces cerevisiae and S. uvarum, then experimentally evolved them under continuous ammonium limitation. We discovered that a characteristic interspecific genome rearrangement arose multiple times in independently evolved populations. We uncovered nine different breakpoints, all occurring in a ~1 kb region of chromosome 14, and all producing an “interspecific fusion junction” within the MEP2 gene coding sequence, such that the 5’ portion derives from S. cerevisiae and the 3’ portion derives from S. uvarum. In most cases the rearrangements altered both chromosomes, resulting in what can be considered to be an introgression of a several-kb region of S. uvarum into an otherwise intact S. cerevisiae chromosome 14, while the S. uvarum chromosome 14 experienced an interspecific reciprocal translocation at the same breakpoint within MEP2, yielding a chimaeric chromosome. The net result is the presence in the cell of two MEP2 fusion genes having identical breakpoints. Given that MEP2 encodes for a high-affinity ammonium permease, that MEP2 fusion genes arise repeatedly under ammonium-limitation, and that three independent evolved isolates carrying MEP2 fusion genes are each more fit than their common ancestor, the novel MEP2 fusion genes are very likely adaptive under ammonium limitation. Our results suggest that when homoploid hybrids form, the admixture of two genomes enables swift and otherwise unlikely evolutionary innovations. Furthermore, the architecture of the MEP2 rearrangement suggests a model for rapid introgression, a phenomenon seen in numerous eukaryotic phyla, that does not invoke repeated backcrossing to one of the parental species. Nomenclature: GSY86 TimeZeroInoculum = ancestral interspecific hybrid used to inoculate ammonium-limited chemostats into 3 replicate vessels A, B, C. 150gen = various single-clone isolates from 150 generations of evolutions from vessels A, B or C. 200gen = various isolates from 200 generations of evolutions from vessels A, B or C. Logical Set: Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
2013-04-01 | E-GEOD-18060 | biostudies-arrayexpress