Abstract
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.
Highlights
Transcriptomic data has demonstrated utility to advance the study of physiological diversity and organisms’ responses to environmental stressors
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
Summary
Transcriptomic data has demonstrated utility to advance the study of physiological diversity and organisms’ responses to environmental stressors. Invasive blood sampling combined with de novo transcriptomic approaches has great potential to alleviate these barriers. 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. Combined with advances in bioinformatics approaches, high-throughput sequencing has enabled the completion of studies in wild populations with limited genomic resources that were previously not possible. De novo transcriptome assemblies paired with analyses to identify orthologs derived from common ancestral genes have facilitated comparisons of functional diversity and gene expression between closely-related species, especially when reference genomes are not available [2,3,4,5]. Transcriptomics has been used to identify differing physiological responses in urban and rural dwelling great tits (Parus major [8]) and for setting baselines and identifying potential cold adaptation mechanisms in dolphins (Tursiops truncatus [10]) and beluga whales (Delphinapterus leucas [11])
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