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The utility of reptile blood transcriptomes in molecular ecology.

Authors
  • Waits, Damien S1
  • Simpson, Dasia Y1
  • Sparkman, Amanda M2
  • Bronikowski, Anne M3
  • Schwartz, Tonia S1
  • 1 Department of Biological Sciences, Auburn University, Auburn, AL, USA.
  • 2 Biology Department, Westmont College, Santa Barbara, CA, USA.
  • 3 Ecology, Evolution and Organismal Biology Department, Iowa State University, Ames, IA, USA.
Type
Published Article
Journal
Molecular Ecology Resources
Publisher
Wiley (Blackwell Publishing)
Publication Date
Oct 29, 2019
Identifiers
DOI: 10.1111/1755-0998.13110
PMID: 31660689
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Reptiles and other nonmammalian vertebrates have transcriptionally active nucleated red blood cells. If blood transcriptomes can provide quantitative data to address questions relevant to molecular ecology, this could circumvent the need to euthanize animals to assay tissues. This would allow longitudinal sampling of animals' responses to treatments, as well as sampling of protected taxa. We developed and annotated blood transcriptomes from six reptile species and found on average 25,000 proteins are being transcribed in the blood, and there is a CORE group of 9,282 orthogroups that are found in at least four of six species. In comparison to liver transcriptomes from the same taxa, approximately two-thirds of the orthogroups were found in both blood and liver; and a similar percentage of ecologically relevant gene groups (insulin and insulin-like signalling, electron transport chain, oxidative stress, glucocorticoid receptors) were found transcribed in both blood and liver. As a resource, we provide a user-friendly database of gene ids identified in each blood transcriptome. Although on average 37% of reads mapped to haemoglobin, importantly, the majority of nonhaemoglobin transcripts had sufficient depth (e.g., 97% at ≥10 reads) to be included in differential gene expression analysis. Thus, we demonstrate that RNAseq blood transcriptomes from a very small blood sample (<10 μl) is a minimally invasive option in nonmammalian vertebrates for quantifying expression of a large number of ecologically relevant genes that would allow longitudinal sampling and sampling of protected populations. © 2019 John Wiley & Sons Ltd.

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