Complete Colombian Caribbean loggerhead turtle mitochondrial genome: tRNA structure analysis and revisited marine turtle phylogeny

Univ. Sci. 23 (3): 355-381, 2018. doi: 10.11144/Javeriana.SC23-3.cccl Bogotá original article Complete Colombian Caribbean loggerhead turtle mitochondrial genome: tRNA structure analysis and revisited marine turtle phylogeny Katherin Otálora1, Javier Hernández-Fernández1, * Edited by Juan Carlos Salcedo-Reyes () 1. Facultad de Ciencias Naturales e Ingeniería. Grupo de Investigación en Genética, Biología Molecular y Bioinformática – genbimol, Universidad Jorge Tadeo Lozano, Cra 4 No 22-61, Bogotá, Colombia, South America. * Received: 02-10-2017 Accepted: 16-04-2018 Published on line: 31-10-2018 Citation: Otálora K, Hernández-Fernández J. Complete Colombian Caribbean loggerhead turtle mitochondrial genome: tRNA structure analysis and revisited marine turtle phylogeny, Universitas Scientiarum, 23 (3): 355-381, 2018. doi: 10.11144/Javeriana.SC23-3.cccl Funding: Research, Creativity and Innovation Department at Universidad Jorge Tadeo Lozano. Electronic supplementary material: Supp. 1. Abstract The loggerhead marine turtle, Caretta caretta, is a widely distributed and endangered species that is facing critical population decline, especially in Colombian Caribbean rookeries. Mitochondrial DNA sequence data are of great importance for the description, monitoring, and phylogenetic analyses of migratory turtle populations. In this study, the first full mitochondrial genome of a loggerhead turtle nesting in the Colombian Caribbean was sequenced and analyzed. This mitochondrial genome consists of 16 362 bp with a nucleotide composition of T: 25.7 %, C: 27 %, A: 35 % and G: 12 %. Sequence annotation of the assembled molecule revealed an organization and number of coding and functional units as reported for other vertebrate mitogenomes. This Colombian loggerhead turtle (Cc-AO-C) showed a novel D-Loop haplotype consisting of thirteen new variable sites, sharing 99.2 % sequence identity with the previously reported Caribbean loggerhead CC-A1 D-Loop haplotype. All 13 protein-coding genes in the Cc-AO-C mitogenome were compared and aligned with those from four other loggerhead turtles from different locations (Florida, Greece, Peru, and Hawaii). Eleven of these genes presented moderate genetic diversity levels, and genes COII and ND5 showed the highest diversity, with average numbers of pair-wise differences of 16.6 and 25, respectively. In addition, the first approach related to t-RNAs 2D and 3D structure analysis in this mitogenome was conducted, leading to observed unique features in two tRNAs (tRNATrp and tRNALeu ). The marine turtle phylogeny was revisited with the newly generated data. The entire mitogenome provided phylogenetically informative data, as well as individual genes ND5, ND4, and 16S. In conclusion, this study highlights the importance of complete mitogenome data in revealing gene flow processes in natural loggerhead turtle populations, as well as in understanding the evolutionary history of marine turtles. Keywords: Mitogenome; Caretta caretta; Cheloniidae; coding genes; sea turtle phylogeny. Introduction Marine turtles (superfamily Chelonioidae) comprise seven existing species grouped into two families: Cheloniidae, including the flatback (Natator depressus), olive ridley (Lepidochelys olivacea), Kemp’s ridley (Lepidochelys Universitas Scientiarum, Journal of the Faculty of Sciences, Pontificia Universidad Javeriana, is licensed under the Creative Commons Attribution 4.0 International Public License 356 Mitochondrial genome of Caretta caretta kempii), loggerhead (C. caretta), hawksbill (Eretmochelys imbricata), and green turtle (Chelonia mydas) species (Pritchard & Mortimer, 1999); and Dermochelyidae which currently comprises a single species, the leatherback sea turtle (Dermochelys coriacea). The loggerhead turtle, Caretta caretta (Cc) is distributed around the oceans of the world in tropical and subtropical latitudes (Amorocho, 2003). Its main nesting locations have been reported in the coasts of the peninsula of Florida (FWC 2015), in the western Brazilian Atlantic Ocean, in the Eastern Mediterranean Sea, in the Omani Arabian Sea, in Madagascar, and in Japan (Dodd 1988, Lancheros & Hernández 2013, Hernández et al. 2017). Despite its wide global distribution, it is considered as an endangered species (IUCN 2016). Loggerhead populations are directly threatened by several anthropic activities including: fisheries bycatch, excessive fishing/hunting, and illegal trade of eggs and meat. In addition, Loggerhead turtle populations are affected by habitat deterioration, coastal development, pollution, pathogens and climate change (Eckert et al. 2000, Lancheros & Hernández, 2013, Machado & Bermejo, 2012). Loggerhead turtles reach their sexual maturity at around 20-30 years of age (Machado & Bermejo, 2012), which does not offset the rampant overall population decline of the species. The threat to Loggerhead turtles has been well documented the Colombian Caribbean (Amorocho, 2003, Ceballos-Fonseca, 2004), where the world’s second highest number of catches per year (approximately 600 turtles) has been reported (Humber et al. 2014). This, despite existing national laws and international agreements to protect the species from anthropic threats (SWOT 2012, IUCN 2016). In all vertebrate taxa, the mitochondrial genome (mitogenome) is arranged as a single, circular, and haploid DNA molecule that features a uniquely high mutation rate, is non-recombining, maternally inherited, and has a specific organization and expression mode (Avise, 1994). Stretches from the mitogenome constitute the most commonly used molecular markers for genetic analysis of loggerhead turtle populations (Drosopoulou et al. 2012, ^ et al. 2012). The loggerhead turtle mitogenome contains 37 coding Duchene units including two ribosomal RNAs (rRNAs) genes, 22 transfer RNAs (tRNAs) genes, 13 protein-coding genes, and one non-coding region of approximately 1 100 bp called the D-Loop or control region. This D-Loop contains the origin of the H replication strand and signals for mitochondrial ^ et al. 2012, replication and transcription (Drosopoulou et al. 2012, Duchene Chiari et al. 2012). In sea turtles, as well as in other vertebrates, point mutations in tRNA genes are likely to alter the 3D structure and function of this machinery, hence compromising peptide synthesis and possibly leading to systemic lifespan-threatening conditions. Despite the key role of mitochondrial Universitas Scientiarum Vol. 23 (3): 355-381 http://ciencias.javeriana.edu.co/investigacion/universitas-scientiarum 357 Otálora & Hernández-Fernández tRNAs, their study has almost exclusively been undertaken in humans (MITOMAP, 2018). But, the availability of large databases containing thousands of tRNA sequences from hundreds of complete genomes has promoted the development of the new field of “tRNAomics” (Marck & Grosjean, 2002). Furthermore, the understanding of sea turtle tRNA secondary and tertiary structures can benefit greatl (...truncated)