15 research outputs found
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Species and Population Specific Gene Expression in Blood Transcriptomes of Marine Turtles
Background: Transcriptomic data has demonstrated utility to advance the study of physiological diversity and organisms\u27 responses to environmental stressors. However, a lack of genomic resources and challenges associated with collecting high-quality RNA can limit its application for many wild populations. Minimally invasive blood sampling combined with de novo transcriptomic approaches has great potential to alleviate these barriers. Here, we advance these goals for marine turtles by generating high quality de novo blood transcriptome assemblies to characterize functional diversity and compare global transcriptional profiles between tissues, species, and foraging aggregations.ResultsWe generated high quality blood transcriptome assemblies for hawksbill (Eretmochelys imbricata), loggerhead (Caretta caretta), green (Chelonia mydas), and leatherback (Dermochelys coriacea) turtles. The functional diversity in assembled blood transcriptomes was comparable to those from more traditionally sampled tissues. A total of 31.3% of orthogroups identified were present in all four species, representing a core set of conserved genes expressed in blood and shared across marine turtle species. We observed strong species-specific expression of these genes, as well as distinct transcriptomic profiles between green turtle foraging aggregations that inhabit areas of greater or lesser anthropogenic disturbance.ConclusionsObtaining global gene expression data through non-lethal, minimally invasive sampling can greatly expand the applications of RNA-sequencing in protected long-lived species such as marine turtles. The distinct differences in gene expression signatures between species and foraging aggregations provide insight into the functional genomics underlying the diversity in this ancient vertebrate lineage. The transcriptomic resources generated here can be used in further studies examining the evolutionary ecology and anthropogenic impacts on marine turtles
Species and population specific gene expression in blood transcriptomes of marine turtles
Background: Transcriptomic data has demonstrated utility to advance the study of physiological diversity and organisms’ responses to environmental stressors. However, a lack of genomic resources and challenges associated with collecting high-quality RNA can limit its application for many wild populations. Minimally invasive blood sampling combined with de novo transcriptomic approaches has great potential to alleviate these barriers. Here, we advance these goals for marine turtles by generating high quality de novo blood transcriptome assemblies to characterize functional diversity and compare global transcriptional profiles between tissues, species, and foraging aggregations. Results: We generated high quality blood transcriptome assemblies for hawksbill (Eretmochelys imbricata), loggerhead (Caretta caretta), green (Chelonia mydas), and leatherback (Dermochelys coriacea) turtles. The functional diversity in assembled blood transcriptomes was comparable to those from more traditionally sampled tissues. A total of 31.3% of orthogroups identified were present in all four species, representing a core set of conserved genes expressed in blood and shared across marine turtle species. We observed strong species-specific expression of these genes, as well as distinct transcriptomic profiles between green turtle foraging aggregations that inhabit areas of greater or lesser anthropogenic disturbance. Conclusions: Obtaining global gene expression data through non-lethal, minimally invasive sampling can greatly expand the applications of RNA-sequencing in protected long-lived species such as marine turtles. The distinct differences in gene expression signatures between species and foraging aggregations provide insight into the functional genomics underlying the diversity in this ancient vertebrate lineage. The transcriptomic resources generated here can be used in further studies examining the evolutionary ecology and anthropogenic impacts on marine turtles
Additional file 9 of Species and population specific gene expression in blood transcriptomes of marine turtles
Additional file 9: Table S9. Functional enrichment analysis results. Functional enrichment analysis results for contrasts between green turtle foraging aggregations
Additional file 8 of Species and population specific gene expression in blood transcriptomes of marine turtles
Additional file 8: Table S8. Differential gene expression analyses results for comparisons between green turtle foraging aggregations. Log fold change and adjusted p-values are listed for the California and Hawai’i, California and the Commonwealth of the Northern Mariana Islands (CNMI), and Hawai’i and CNMI Islands comparisons
Additional file 5 of Species and population specific gene expression in blood transcriptomes of marine turtles
Additional file 5: Table S5. Species-specific orthogroups. Orthogroups and the transcripts that belong to each orthogroup from each species-specific blood transcriptome
Additional file 1 of Species and population specific gene expression in blood transcriptomes of marine turtles
Additional file 1: Table S1. Sample metadata. Detailed metadata, raw read count, and the percent of reads that map to green (Chelonia mydas) turtle hemoglobin genes for each individual (n = 43) included in this study. Individuals without straight carapace length (SCL) denoted were not measured for these parameters
Additional file 11 of Species and population specific gene expression in blood transcriptomes of marine turtles
Additional file 11: Figure S2. Leatherback GO slim plots. Bar plots representing the number of genes in each Gene Ontology (GO) slim functional category from the multi-tissue (brain, lung, and ovary) leatherback turtle transcriptome
Additional file 6 of Species and population specific gene expression in blood transcriptomes of marine turtles
Additional file 6: Table S6. Tissue-specific orthogroups. Orthogroups and the transcripts that belong to each orthogroup from each individual tissue-type leatherback transcriptome
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Species and population specific gene expression in blood transcriptomes of marine turtles
BackgroundTranscriptomic data has demonstrated utility to advance the study of physiological diversity and organisms' responses to environmental stressors. However, a lack of genomic resources and challenges associated with collecting high-quality RNA can limit its application for many wild populations. Minimally invasive blood sampling combined with de novo transcriptomic approaches has great potential to alleviate these barriers. Here, we advance these goals for marine turtles by generating high quality de novo blood transcriptome assemblies to characterize functional diversity and compare global transcriptional profiles between tissues, species, and foraging aggregations.ResultsWe generated high quality blood transcriptome assemblies for hawksbill (Eretmochelys imbricata), loggerhead (Caretta caretta), green (Chelonia mydas), and leatherback (Dermochelys coriacea) turtles. The functional diversity in assembled blood transcriptomes was comparable to those from more traditionally sampled tissues. A total of 31.3% of orthogroups identified were present in all four species, representing a core set of conserved genes expressed in blood and shared across marine turtle species. We observed strong species-specific expression of these genes, as well as distinct transcriptomic profiles between green turtle foraging aggregations that inhabit areas of greater or lesser anthropogenic disturbance.ConclusionsObtaining global gene expression data through non-lethal, minimally invasive sampling can greatly expand the applications of RNA-sequencing in protected long-lived species such as marine turtles. The distinct differences in gene expression signatures between species and foraging aggregations provide insight into the functional genomics underlying the diversity in this ancient vertebrate lineage. The transcriptomic resources generated here can be used in further studies examining the evolutionary ecology and anthropogenic impacts on marine turtles
Additional file 7 of Species and population specific gene expression in blood transcriptomes of marine turtles
Additional file 7: Table S7. Differential orthogroup expression analyses results for comparisons between marine turtle species. Log fold change and adjusted p-values are listed for the green v. leatherback, green v. hawksbill, and leatherback v. hawksbill turtle comparisons