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PROVIDER: PRJNA716105 | ENA |
REPOSITORIES: ENA
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Project description:The formation of new species is often a consequence of genetic incompatibilities accumulated between populations during allopatric divergence. When divergent taxa interbreed, these incompatibilities impact physiology and have a direct cost resulting in reduced hybrid fitness. Recent surveys of gene regulation in interspecific hybrids have revealed anomalous expression across large proportions of the genome, with 30-70% of all genes apparently misexpressed, mostly in the direction of down-regulation. However, since most of these studies have focused on pairs of species exhibiting high degrees of reproductive isolation, the association between regulatory disruption and reduced hybrid fitness prior to species formation remains unclear. Within the copepod species Tigriopus californicus, interpopulation hybrids show reduced fitness associated with mitochondrial dysfunction. Here we show that in contrast to studies of interspecific hybrids, only 1.2% of the transcriptome was misexpressed in interpopulation hybrids of T. californicus, and nearly 80% of misexpressed genes were overexpressed rather than underexpressed. Moreover, many of the misexpressed genes were components of functional pathways impacted by mitonuclear incompatibilities in hybrid T. californicus (e.g., oxidative phosphorylation and antioxidant response). We also show that the magnitude of hybrid misregulation is not dependent on levels of protein sequence divergence, even though the latter is correlated with expression divergence between parental populations. Our results suggest that hybrid breakdown at early stages of speciation may result from initial incompatibilities amplified by the cost of compensatory physiological responses.
2015-01-05 | GSE62672 | GEO
Project description:Chromatin accessibility is an important functional genomics phenotype that influences transcription factor binding and gene expression. Genome-scale technologies allow chromatin accessibility to be mapped with high-resolution, facilitating detailed analyses into the genetic architecture and evolution of chromatin structure within and between species. We performed Formaldehyde-Assisted Isolation of Regulatory Elements sequencing (FAIRE-Seq) to map chromatin accessibility in two parental haploid yeast species, Saccharomyces cerevisiae and Saccharomyces paradoxus and their diploid hybrid. We show that although broad-scale characteristics of the chromatin landscape are well conserved between these species, accessibility is significantly different for 947 regions upstream of genes that are enriched for GO terms such as intracellular transport and protein localization exhibit. We also develop new statistical methods to investigate the genetic architecture of variation in chromatin accessibility between species, and find that cis effects are more common and of greater magnitude than trans effects. Interestingly, we find that cis and trans effects at individual genes are often negatively correlated, suggesting widespread compensatory evolution to stabilize levels of chromatin accessibility. Finally, we demonstrate that the relationship between chromatin accessibility and gene expression levels is complex, and a significant proportion of differences in chromatin accessibility might be functionally benign. There are 20 samples in total. These consist of 10 FAIRE-seq samples, specifically 6 haploid samples, S. cerevisiae strain UWOPS05_217_3 replicates 1 and 2, S. cerevisiae strain DBVPG1373 replicates 1 and 2, and S. paradoxus strain CBS432 replicates 1 and 2. There are also 4 diploid hybrid samples, hybrid between S. cerevisiae strain UWOPS05_217_3 and S. paradoxus strain CBS432 replicates 1 and 2, and the hybrid between S. cerevisiae strain DBVPG1373 and S. paradoxus strain CBS432 replicates 1 and 2. There are also RNA-seq samples for each of these 10 samples.
2014-06-01 | E-GEOD-55717 | biostudies-arrayexpress
Project description:The formation of new species is often a consequence of genetic incompatibilities accumulated between populations during allopatric divergence. When divergent taxa interbreed, these incompatibilities impact physiology and have a direct cost resulting in reduced hybrid fitness. Recent surveys of gene regulation in interspecific hybrids have revealed anomalous expression across large proportions of the genome, with 30-70% of all genes apparently misexpressed, mostly in the direction of down-regulation. However, since most of these studies have focused on pairs of species exhibiting high degrees of reproductive isolation, the association between regulatory disruption and reduced hybrid fitness prior to species formation remains unclear. Within the copepod species Tigriopus californicus, interpopulation hybrids show reduced fitness associated with mitochondrial dysfunction. Here we show that in contrast to studies of interspecific hybrids, only 1.2% of the transcriptome was misexpressed in interpopulation hybrids of T. californicus, and nearly 80% of misexpressed genes were overexpressed rather than underexpressed. Moreover, many of the misexpressed genes were components of functional pathways impacted by mitonuclear incompatibilities in hybrid T. californicus (e.g., oxidative phosphorylation and antioxidant response). We also show that the magnitude of hybrid misregulation is not dependent on levels of protein sequence divergence, even though the latter is correlated with expression divergence between parental populations. Our results suggest that hybrid breakdown at early stages of speciation may result from initial incompatibilities amplified by the cost of compensatory physiological responses. Our experiment included nine RNA-seq samples: 3 San Diego, 2 Santa Cruz, and 4 hybrid samples. For each sample, 400-500 copepods across all developmental stages were collected from their stock cultures. They were transferred to fresh filtered seawater in a 50-mL Falcon tubes and immersed in a 20°C water bath for two hours. Water was then quickly removed, 4 mL of Tri-Reagent (Sigma) added, and tissue immediately disrupted using a tissue homogenizer. RNA was isolated following the manufacturer’s protocol. Re-suspended RNA pellets were further purified with RNeasy Mini columns (Qiagen), and final sample integrity and quantity were assessed with an Agilent 2100 BioAnalyzer. Please note that two samples (GSM1531288, GSM1531290) have been accessioned under BioProject PRJNA168170, SRA study SRP013608, while the remaining seven samples under BioProject PRJNA263967, SRA Study SRP048974. The current records including all 9 samples (PRJNA264820/SRP049247) were re-created for the convenient retrieval of the complete raw data from SRA
2015-01-05 | E-GEOD-62672 | biostudies-arrayexpress
Project description:Species of the genus Drosophila have served as favorite models in speciation studies, however genetic factors of the interspecific hybrid sterility are underinvestigated to date. Here we performed the analysis of reproductive incompatibilities of hybrid females in crossing Drosophila melanogaster females and Drosophila simulans males. Using transcriptomic data analysis, molecular, cellular and genetic approaches we analyzed differential gene expression, transposable element (TE) activity, piRNA biogenesis and functional defects of oogenesis in hybrids. A premature GSC loss was a most prominent defect of oogenesis in hybrid ovaries. Owing differential expression of genes encoding components of the piRNA pathway rhino and deadlock, functional RDCmel complex in hybrid ovaries was not assembled. At the same time the activity of RDCsim complex was maintained in hybrids, independently from the genomic origin of piRNA clusters. Despite identification of a cohort of overexpressed TEs in hybrid ovaries we found no evidences that their activity can be considered as the main cause of hybrid sterility. We revealed complex pattern of Vasa protein expression in hybrid germline, including partial AT-chX piRNA targeting of vasasim allele and significant developmental delay of vasamel expression. We came to the conclusions that complex multi-locus genetic changes between the species were responsible for hybrid sterility phenotype.
2024-05-30 | GSE263983 | GEO
Project description:The genetic architecture of hybrid fitness under environmental stress
| PRJEB33368 | ENA
Project description:Species of the genus Drosophila have served as favorite models in speciation studies, however genetic factors of the interspecific hybrid sterility are underinvestigated to date. Here we performed the analysis of reproductive incompatibilities of hybrid females in crossing Drosophila melanogaster females and Drosophila simulans males. Using transcriptomic data analysis, molecular, cellular and genetic approaches we analyzed differential gene expression, transposable element (TE) activity, piRNA biogenesis and functional defects of oogenesis in hybrids. A premature GSC loss was a most prominent defect of oogenesis in hybrid ovaries. Owing differential expression of genes encoding components of the piRNA pathway rhino and deadlock, functional RDCmel complex in hybrid ovaries was not assembled. At the same time the activity of RDCsim complex was maintained in hybrids, independently from the genomic origin of piRNA clusters. Despite identification of a cohort of overexpressed TEs in hybrid ovaries we found no evidences that their activity can be considered as the main cause of hybrid sterility. We revealed complex pattern of Vasa protein expression in hybrid germline, including partial AT-chX piRNA targeting of vasasim allele and significant developmental delay of vasamel expression. We came to the conclusions that complex multi-locus genetic changes between the species were responsible for hybrid sterility phenotype.
2024-05-30 | GSE263982 | GEO
Project description:Hybrid sterility is one of the earliest postzygotic isolating mechanisms to evolve between two recently diverged species. Uncovering the mechanisms of hybrid sterilitynot only provides insight into the origins of species but also potentially revealsnovel causes of intra-species infertility.Here we identify causes underlying hybrid infertilityofSchizosaccharomyces pombeand S. kambucha, two fission yeast species that are 99.5% identical at the nucleotide level.These yeasts mate to form viable diploids that efficiently complete meiosis. However,S. kambucha/S. pombe hybrids generate few viable gametes, most of which are either aneuploid or diploid.We find that chromosomal rearrangements and related recombination defectsare major causes of hybrid infertility. Surprisingly, using experiments in which we eliminate meiotic recombination, we find thatrecombination defects cannot completely explain the hybrid infertility. Instead, we find that a significant fraction of hybrid infertility is caused by the action of at least three distinct meiotic drive alleles, one on each S. kambucha chromosome,that M-bM-^@M-^\cheatM-bM-^@M-^] to be transmitted to more than half (up to 90%) of viable gametes.Two of these driving lociare linked by a chromosomal translocation and thus constitute a novel type of paired meiotic drive complex. We find that all three S. kambuchadrive loci independently contribute to hybrid infertility by causing nonrandom spore death. This study reveals how quickly multiple barriers to fertility can arise.In addition, it provides further support for models in which genetic conflicts, such as those caused by meiotic drive alleles, can drive speciation. Meiotic DNA double-strand break analysis of Schizosaccharomyces kambucha by immunoprecipitating accumulated Rec12-FLAG covalently linked to DNA (without exogenous crosslinking agent used) following nitrogen starvation .
2014-05-15 | E-GEOD-57039 | biostudies-arrayexpress
Project description:This experiment investigates the genetic architecture of gene expression (eQTL) in three different treatments in a N2xCB4856 RIL population of Caenorhabditis elegans. The goal is to identify genetic variation linked to differences in gene expression. We exposed 48 RILs per treatment to a control, heat-stress, and recovery treatment. More specifically these three conditions can be characterized as: (i) the control treatment was grown for 48 hours at 20C, (ii) the heat-stress treatment was grown for 46 hours at 20C followed by 2 hours at 35C, and (iii) the recovery treatment was grown for 46 hours at 20C, followed by 2 hours at 35C and thereafter 2 hours at 20C. Thereafter RNA was isolated, labelled and hybridized on microarray. The gene expression profiles were used for eQTL mapping.
2017-05-30 | E-MTAB-5779 | biostudies-arrayexpress
Project description:Whilst the hybrids of F1 generations usually experience heterosis for fitness-related traits (including the resistance to parasites), post-F1 generations, due to Dobzhansky–Muller genetic incompatibilities, express numerous disadvantageous traits (including susceptibility to parasites). Genetic disruption in hybrids may also result from the broken system of cyto-nuclear coadaptation. Maternal backcrosses (each parent having with the same mtDNA of parents) and paternal backcrosses (each parent having with different mtDNA of parents) have the same nuclear genetic compositions, but differ in cytoplasmic genetic elements, affecting their viability and survival. Spring viraemia of the carp virus (SVCV), a disease with a serious economic impact in aquacultures, affects almost exclusively cyprinids, primarily common carp, and causes high mortality, whilst gibel carp is a less susceptible species. Our study was focused on the transcriptome profile analysis of head kidney to reveal differential gene expression in highly susceptible common carp, weakly susceptible gibel carp, and hybrid lines, hypothetizing that the patterns of differential gene expression will reflect hybrid heterosis in F1 generations and hybrid breakdown in backcrosses and F2 generations. We expected the differences in differential gene expression between maternal and paternal backcrosses to be in line with the hypothesis of broken cyto-nuclear coadaptation.
2023-09-12 | GSE240031 | GEO