Detection of high heteroplasmy in complete loggerhead and hawksbill sea turtles mitochondrial genomes using RNAseq

Abstract

Sea turtle populations around the world face rapid decline due to the effect of anthropogenic and environmental factors. Among the affected populations are those of hawksbill turtles (Eretmochelys imbricata) and loggerhead turtles (Caretta caretta), which is why a greater effort is currently being made in their monitoring and tracing. The intragenic degree of heteroplasmic mutations, commonly associated with diseases of variable symptoms, has not been analyzed in these species. In this study, heteroplasmy in the complete mitogenome (mtDNA) of three loggerhead turtles and one hawksbill turtle was identified from data obtained by RNAseq. Individuals Cc3, Ei1, Cc1 and Cc2 presented 0.3, 1.7, 1.8 and 7.1% of heteroplasmic mutations in all their mtDNA, respectively. The protein-coding genes that presented the highest percentage of heteroplasmy were ND4 and ND5 in individual Cc2 with 16 and 38.6%, respectively. Of the tRNA genes, only tRNA^Tyr was heteroplasmic in the four individuals with 5.63% (Cc1), 25.35% (Ei1 and Cc2) and 49.3% (Cc3). In this study, we identified the critical sites of heteroplasmy in each individual and the genetic variability of their mitogenomes. The data obtained represents the baseline for future projects that evaluate the population status of these species.

Keywords:

• Eretmochelys imbricata
• Caretta caretta
• RNA-seq
• mitochondrial genome
• heteroplasmy

Acknowledgments

The authors are grateful to CEINER Oceanarium on the island of St. Martin Pajares for their collaboration in obtaining and providing samples of C. caretta and E. imbricata for the development of this study. Samples were obtained under a research permit that was granted by the Ministry of Environment and Territorial Development (#24 of June 22, 2012) Contract for Access to Genetic Resources (#64 of April 23, 2013), and permit for the collection of samples of Colombian biodiversity, issued to the Jorge Tadeo Lozano University (Resolution 1271 of October 23, 2014, IDB040I File).

Disclosure statement

The authors declare that they have no known competing financial interests or personal relationships that could have influenced the results reported in this article.

Additional information

Funding

This work was supported by the Office of Research, Creation and Innovation of the Universidad Jorge Tadeo Lozano (340-07-10). Additional funding came from the Intramural Research Program of the National Institutes of Health (NIH, USA), National Library of Medicine (USA), National Center for Biotechnology Information (NCBI) ZIA LM082713–06. There was no additional external funding received for this study.