Species and population specific gene expression in blood transcriptomes of marine turtles

Shreya M Banerjee; Jamie Adkins Stoll; Camryn D Allen; Jennifer M Lynch; Heather S Harris; Lauren Kenyon; Richard E Connon; Eleanor J Sterling; Eugenia Naro-Maciel; Kathryn McFadden; Margaret M Lamont; James Benge; Nadia B Fernandez; Jeffrey A Seminoff; Scott R Benson; Rebecca L Lewison; Tomoharu Eguchi; Tammy M Summers; Jessy R Hapdei; Marc R Rice; Summer Martin; T Todd Jones; Peter H Dutton; George H Balazs; Lisa M Komoroske

doi:10.1186/s12864-021-07656-5

Species and population specific gene expression in blood transcriptomes of marine turtles

BMC Genomics. 2021 May 13;22(1):346. doi: 10.1186/s12864-021-07656-5.

Authors

Shreya M Banerjee¹, Jamie Adkins Stoll¹, Camryn D Allen^{2

3}, Jennifer M Lynch⁴, Heather S Harris³, Lauren Kenyon¹, Richard E Connon⁵, Eleanor J Sterling⁶, Eugenia Naro-Maciel⁷, Kathryn McFadden⁸, Margaret M Lamont⁹, James Benge¹⁰, Nadia B Fernandez¹, Jeffrey A Seminoff³, Scott R Benson^{11

12}, Rebecca L Lewison¹³, Tomoharu Eguchi³, Tammy M Summers¹⁴, Jessy R Hapdei¹⁵, Marc R Rice¹⁶, Summer Martin², T Todd Jones², Peter H Dutton³, George H Balazs¹⁷, Lisa M Komoroske^{18

19}

Affiliations

¹ Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA.
² Marine Turtle Biology and Assessment Program, Protected Species Division, Pacific Islands Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Honolulu, HI, USA.
³ Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA.
⁴ Chemical Sciences Division, National Institute of Standards and Technology, Hawai'i Pacific University, Waimanalo, HI, USA.
⁵ Department of Anatomy, Physiology and Cell Biology, University of California, Davis, Davis, CA, USA.
⁶ Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY, USA.
⁷ New York University, New York, NY, USA.
⁸ School of Agricultural, Forest, and Environmental Sciences, Clemson University, Clemson, SC, USA.
⁹ United States Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, USA.
¹⁰ Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
¹¹ Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Moss Landing, CA, 95039, USA.
¹² Moss Landing Marine Laboratories, San Jose State University, Moss Landing, CA, 95039, USA.
¹³ Department of Biology, San Diego State University, San Diego, CA, USA.
¹⁴ Rainbow Connection Research, Guam, USA.
¹⁵ Jessy's Tag Services, Saipan, Commonwealth of the Northern Mariana Islands, USA.
¹⁶ Hawai'i Preparatory Academy, Kamuela, HI, USA.
¹⁷ Golden Honu Services of Oceania, Honolulu, HI, USA.
¹⁸ Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA. lkomoroske@umass.edu.
¹⁹ Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA. lkomoroske@umass.edu.

Abstract

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.

Keywords: Comparative transcriptomics; Conservation physiology; Minimally invasive sampling; Ortholog; RNA-sequencing; Sea turtle.

MeSH terms

Animals
Base Sequence
Species Specificity
Transcriptome
Turtles* / genetics