JaRicFlor1
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB60730 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Ricordea florida (Florida false coral) genome assembly, jaRicFlor1, alternate haplotype
| PRJEB60729 | ENA
Project description:Ricordea florida (Florida false coral), genomic and transcriptomic data
| PRJEB52858 | ENA
Project description:Publication Abstract: As climate changes, sea surface temperature anomalies that negatively impact coral reef organisms continue to increase in frequency and intensity. Yet, despite widespread coral mortality, genetic diversity remains high even in those coral species listed as threatened. While this is good news in many ways it presents a challenge for the development of biomarkers that can identify resilient or vulnerable genotypes. Taking advantage of three coral restoration nurseries in Florida that serve as long-term common garden experiments, we exposed over thirty genetically distinct Acropora cervicornis colonies to hot and cold temperature shocks seasonally and measured pooled gene expression responses using RNAseq. Targeting a subset of twenty genes, we designed a high-throughput qPCR array to quantify expression in all individuals separately under each treatment with the goal of identifying predictive and/or diagnostic thermal stress biomarkers. We observed extensive transcriptional variation in the population, suggesting abundant raw material is available for adaptation via natural selection. However, this high variation made it difficult to correlate gene expression changes with colony performance metrics such as growth, mortality, and bleaching susceptibility. Nevertheless, we identified several promising diagnostic biomarkers for acute thermal stress that may improve coral restoration and climate change mitigation efforts in the future.
2017-12-21 | GSE108338 | GEO
Project description:The potential to adapt to a changing climate depends in part upon the standing genetic variation present in wild populations. In corals, the dispersive larval phase is particularly vulnerable to the effects of environmental stress. Larval survival and response to stress during dispersal and settlement will play a key role in the persistence of coral populations. To test the hypothesis that larval transcription profiles reflect population specific responses to thermal stress, symbiont-free gametes of the scleractinian coral Montastraea faveolata were collected from Florida and Mexico and raised under normal and elevated temperatures. These populations have been shown to exchange larvae frequently enough to prevent significant differentiation of neutral loci. Differences among thousands of genes were simultaneously characterized using microarrays, allowing investigation of gene expression patterns among wild populations under stressful environmental conditions. Results show site-specific signatures of gene expression in larvae of a reef-building coral from different parts of its range (despite low genetic divergence), and reveal both local and general components of stress response during later stages of larval development. These results provide evidence of site-specific variation in the face of gene flow, which may represent functional genetic variation in different subpopulations, and support the idea that coral host genomes may indeed house the adaptive potential needed to deal with changing environmental conditions. The experimental setup followed a reference design, i.e. all samples were hybridized against the same pool made up of equal amounts of RNA from all samples collected in Mexico. For samples from Mexico we used three technical replicates for each treatment temperature, for samples from Florida three biological replicates were used for each treatment temperature, except for the high temperature samples at day two where only two replicates were available due to high larval mortality at that temperature. Common reference samples were labeled with Cy3, temperature treatment samples with Cy5. Microarrays for M. faveolata contained 1,314 coding sequences, of which 43% had functional annotations as determined by homology to known genes.
2010-06-23 | E-GEOD-19998 | biostudies-arrayexpress
Project description:The potential to adapt to a changing climate depends in part upon the standing genetic variation present in wild populations. In corals, the dispersive larval phase is particularly vulnerable to the effects of environmental stress. Larval survival and response to stress during dispersal and settlement will play a key role in the persistence of coral populations. To test the hypothesis that larval transcription profiles reflect population specific responses to thermal stress, symbiont-free gametes of the scleractinian coral Montastraea faveolata were collected from Florida and Mexico and raised under normal and elevated temperatures. These populations have been shown to exchange larvae frequently enough to prevent significant differentiation of neutral loci. Differences among thousands of genes were simultaneously characterized using microarrays, allowing investigation of gene expression patterns among wild populations under stressful environmental conditions. Results show site-specific signatures of gene expression in larvae of a reef-building coral from different parts of its range (despite low genetic divergence), and reveal both local and general components of stress response during later stages of larval development. These results provide evidence of site-specific variation in the face of gene flow, which may represent functional genetic variation in different subpopulations, and support the idea that coral host genomes may indeed house the adaptive potential needed to deal with changing environmental conditions.
2010-06-23 | GSE19998 | GEO
Project description:Branching coral species like the Caribbean Acroporids are long lived and reproduce asexually via breakage of branches. Fragmentation is the dominant mode of local population maintenance for these corals across much of their range. Thus, large genets with many member ramets (colonies) are common. Each of the ramets experiences different microenvironments, especially with respect to light and water flow. Here, we investigate whether colonies that are members of the same genet have different epigenomes because of differences in their microenvironments. The Florida Keys experienced a large- scale coral bleaching event in 2014-2015 caused by high water temperatures. During the event, ramets of the same coral genet bleached differently. Previous work had shown that this was unlikely to be due to their eukaryotic algal symbionts (Symbiodinium ‘fitti’) because each genet of this coral species typically harbors a single strain of S. ‘fitti’. Characterization of the microbiome via 16S tag sequencing did not provide evidence for a central role of microbiome variation in determining bleaching response. Instead, epigenetic changes were significantly correlated with the host’s genetic background, the position of the sampled polyps within the colonies (e.g. tip versus base of colony), and differences in the colonies’ condition during the bleaching event. We conclude that microenvironmental differences in growing conditions led to long-term changes in the way the ramets methylated their genomes and thus to a differential bleaching response.
2020-12-18 | GSE124256 | GEO
Project description:Branching coral species like the Caribbean Acroporids are long lived and reproduce asexually via breakage of branches. Fragmentation is the dominant mode of local population maintenance for these corals across much of their range. Thus, large genets with many member ramets (colonies) are common. Each of the ramets experiences different microenvironments, especially with respect to light and water flow. Here, we investigate whether colonies that are members of the same genet have different epigenomes because of differences in their microenvironments. The Florida Keys experienced a large- scale coral bleaching event in 2014-2015 caused by high water temperatures. During the event, ramets of the same coral genet bleached differently. Previous work had shown that this was unlikely to be due to their eukaryotic algal symbionts (Symbiodinium ‘fitti’) because each genet of this coral species typically harbors a single strain of S. ‘fitti’. Characterization of the microbiome via 16S tag sequencing did not provide evidence for a central role of microbiome variation in determining bleaching response. Instead, epigenetic changes were significantly correlated with the host’s genetic background, the position of the sampled polyps within the colonies (e.g. tip versus base of colony), and differences in the colonies’ condition during the bleaching event. We conclude that microenvironmental differences in growing conditions led to long-term changes in the way the ramets methylated their genomes and thus to a differential bleaching response.
2019-12-05 | GSE124246 | GEO
Project description:The surprising observation that virtually the entire human genome is transcribed means we know very little about the function of many emerging classes of RNAs, except their astounding diversity. Traditional RNA function prediction methods rely on sequence or alignment information, which are limited in their ability to classify classes of non-coding RNAs (ncRNAs). To address this, we developed CoRAL, a machine learning-based approach for classification of RNA molecules. CoRAL uses biologically interpretable features including fragment length, cleavage specificity, and antisense transcription to distinguish between different ncRNA classes. We evaluated CoRAL using genome-wide small RNA sequencing (smRNA-seq) datasets from two human tissue types (brain and skin [GSE31037]), and were able to classify six different types of RNA transcripts with 79~80% accuracy in cross-validation experiments, and with 71~73% accuracy when CoRAL uses one tissue type for training and the other as validation. Analysis by CoRAL revealed that long intergenic ncRNAs, small cytoplasmic RNAs, and small nuclear RNAs show more tissue specificity, while microRNAs, small nucleolar, and transposon-derived RNAs are highly discernible and consistent across the two tissue types. The ability to consistently annotate loci across tissue types demonstrates the potential of CoRAL to characterize ncRNAs using smRNA-seq data in less characterized organisms.
2013-07-07 | GSE43335 | GEO