Ontology highlight
ABSTRACT:
PROVIDER: PRJNA840866 | 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: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:Intergenerational genomic DNA methylation patterns in mouse hybrid strains Reduced representation bisulfite sequencing from mouse liver, using MspI restriction enzyme, and selecting ~100-300bp size fraction.
2013-12-30 | E-GEOD-53714 | biostudies-arrayexpress
Project description:Oxidative phosphorylation (OXPHOS) complexes consist of nuclear- and mitochondrial- encoded subunits, forcing cross-compartment synchronization of gene expression to achieve mitonuclear balance. To characterize how human cells coordinate OXPHOS gene expression, we establish a mitoribosome profiling approach that resolves features of the mitochondrial translatome, including the synthesis of a four amino acid mitopeptide. Strikingly, average mitochondrial and cytoplasmic synthesis rates correspond precisely across OXPHOS complexes. Coordinated mitochondrial and cytosolic synthesis does not require rapid feedback between the two translation systems. By contrast, we find that the Leigh syndrome gene, LRPPRC, maintains correlated mitochondrial and cytosolic translatomes. Our results lead to a model of human mitonuclear balance that requires tightly balanced cross-compartment protein synthesis, representing a vulnerability for cellular proteostasis.
2021-05-30 | GSE173283 | GEO
Project description:DNA methylation is a conserved epigenetic mark in plants and many animals. How parental alleles interact in progeny to influence the epigenome is poorly understood. We analyzed the DNA methylomes of Arabidopsis Col and C24 ecotypes, and their hybrid progeny. Hy- brids displayed nonadditive DNA methylation levels, termed meth- ylation interactions, throughout the genome. Approximately 2,500 methylation interactions occurred at regions where parental DNA methylation levels are similar, whereas almost 1,000 were at differ- entially methylated regions in parents. Methylation interactions were characterized by an abundance of 24-nt small interfering RNAs. Furthermore, dysfunction of the RNA-directed DNA methylation pathway abolished methylation interactions but did not affect the increased biomass observed in hybrid progeny. Methylation interac- tions correlated with altered genetic variation within the genome, suggesting that they may play a role in genome evolution. Whole genome bisulfite sequencing and small RNA sequencing of the wild type and nrpd1nrpe1 double mutant background of parent Col ,C24, the hybrid ColXC24 and C24XCol to explore the role of the RdDM pathway in DNA methylation interactions.
2016-06-15 | E-GEOD-72993 | biostudies-arrayexpress
Project description:we demonstrate that 3' end tag profiling vi deep sequencing is a powerful approach to mesure allele-specific expression genome-wide. examination of gene expression in A. thaliana, A. lyrata and the F1 hybrid
2014-03-28 | E-GEOD-28211 | biostudies-arrayexpress
Project description:This experiment aims at analyzing crossover distribution in male and female meiosis, in the Arabidopsis. Wild-type Col plant was crossed with Ler plant to produce F1 hybrid. Then, the F1 hybrid was crossed as female or as male with wild-type Col to generate two BC1 populations. Leaf samples from plants of the obtained BC1 populations were used for DNA purification and library preparation for Illumina sequencing (HiSeq 3000 2x150 bp), performed by the Max Planck-Genome-centre Cologne, Germany (https://mpgc.mpipz.mpg.de/home/) and Novogene.
2022-06-14 | E-MTAB-11254 | biostudies-arrayexpress