Dataset Information

Complete mitochondrial genome of the nesting Colombian Caribbean Hawksbill Turtle.

ABSTRACT: The hawksbill turtle, Eretmochelis imbricata (Linnaeus, 1766), is an endangered sea turtle in Colombian Caribbean beach. In this study, we report the complete mitochondrial DNA sequences of hawksbill turtle. The entire genome comprised 16,386 base pairs, and a nucleotide frequency of T: 25.6%, C: 26.9%, A: G 35.4% and 12.1%. The mitogenome sequence of hawksbill turtle would contribute to better understand population genetics, and evolution of sea turtles. Molecule was deposited at the GenBank database under the accession number KP221806.

SUBMITTER: Hernandez-Fernandez J

PROVIDER: S-EPMC6200328 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Complete mitochondrial genome of the nesting Colombian Caribbean Hawksbill Turtle.

Hernández-Fernández Javier J Beltrán-Torres Gerson G Mariño-Ramírez Leonardo L

Mitochondrial DNA. Part B, Resources 20170223 1

The hawksbill turtle, <i>Eretmochelis imbricata</i> (Linnaeus, 1766), is an endangered sea turtle in Colombian Caribbean beach. In this study, we report the complete mitochondrial DNA sequences of hawksbill turtle. The entire genome comprised 16,386 base pairs, and a nucleotide frequency of T: 25.6%, C: 26.9%, A: G 35.4% and 12.1%. The mitogenome sequence of hawksbill turtle would contribute to better understand population genetics, and evolution of sea turtles. Molecule was deposited at the Gen ...[more]

PMID: 30370335

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Project description:The understanding of the functional properties of mitochondrial transfer RNA (mt tRNAs) depend on the knowledge of its structure. tRNA acts as an interface between polynucleotides and polypeptides thus, they are key molecules in protein biosynthesis. The tRNA molecule has a functional design and, given its importance in the translation of mitochondrial genes, it is plausible that modifications of the structure can affect the synthesis of proteins and the functional properties of the mitochondria. In a previous work, the mitochondrial genome of an individual of the nesting Caretta caretta of the Colombian Caribbean was obtained, where specific mutations were identified in the only tRNALeu (CUN), tRNATrp and tRNALys genes. In order to analyze the effect of these mutations on these three mt tRNAs, the prediction of 2D and 3D structures was performed. Genes were sequenced in 11 nesting loggerhead turtles from the Colombian Caribbean. Two-dimensional structures were inferred using the ARWEN program, and three-dimensional structures were obtained with the RNA Composer 3D program. Two polymorphisms were identified in tRNATrp and another one was located in tRNALys, both specific to C. caretta. The thymine substitution in nucleotide position 14 of tRNATrp could constitute an endemic polymorphism of the nesting colony of the Colombian Caribbean. Two 2D and three 3D patterns were obtained for tRNATrp. In the case of tRNALys and tRNALeu 2D and 3D structures were obtained respectively, which showed compliance to canonical structures, with 4 bp in the D-arm, 4-5 bp in the T-arm, and 5 bp in the anticodon arm. Moderate deviations were found, such as a change in the number of nucleotides, elongation in loops or stems and non-Watson-Crick base pairing: adenine-adenine in stem D of tRNATrp, uracil-uracil and adenine-cytosine in the acceptor arm of the tRNALys and cytosine-cytosine in the anticodon stem of the tRNALeu. In addition, distortions or lack of typical interactions in 3D structures gave them unique characteristics. According to the size of the variable region (4-5 nt), the three analyzed tRNAs belong to class I. The interactions in the three studied tRNAs occur mainly between D loop-variable region, and between spacer bases-variable region, which classifies them as tRNA of typology II. The polymorphisms and structural changes described can, apparently, be post-transcriptionally stabilized. It will be crucial to perform studies at the population and functional levels to elucidate the synthetic pathways affected by these genes. This article analyses for the first time the 1D, 2D and 3D structures of the mitochondrial tRNALys, tRNATrp and tRNALeu in the loggerhead turtle.

Project description:Prior to 2008 and the discovery of several important hawksbill turtle (Eretmochelys imbricata) nesting colonies in the EP (Eastern Pacific), the species was considered virtually absent from the region. Research since that time has yielded new insights into EP hawksbills, salient among them being the use of mangrove estuaries for nesting. These recent revelations have raised interest in the genetic characterization of hawksbills in the EP, studies of which have remained lacking to date. Between 2008 and 2014, we collected tissue samples from 269 nesting hawksbills at nine rookeries across the EP and used mitochondrial DNA sequences (766 bp) to generate the first genetic characterization of rookeries in the region. Our results inform genetic diversity, population differentiation, and phylogeography of the species. Hawksbills in the EP demonstrate low genetic diversity: We identified a total of only seven haplotypes across the region, including five new and two previously identified nesting haplotypes (pooled frequencies of 58.4% and 41.6%, respectively), the former only evident in Central American rookeries. Despite low genetic diversity, we found strong stock structure between the four principal rookeries, suggesting the existence of multiple populations and warranting their recognition as distinct management units. Furthermore, haplotypes EiIP106 and EiIP108 are unique to hawksbills that nest in mangrove estuaries, a behavior found only in hawksbills along Pacific Central America. The detected genetic differentiation supports the existence of a novel mangrove estuary "reproductive ecotype" that may warrant additional conservation attention. From a phylogeographic perspective, our research indicates hawksbills colonized the EP via the Indo-Pacific, and do not represent relict populations isolated from the Atlantic by the rising of the Panama Isthmus. Low overall genetic diversity in the EP is likely the combined result of few rookeries, extremely small reproductive populations and evolutionarily recent colonization events. Additional research with larger sample sizes and variable markers will help further genetic understanding of hawksbill turtles in the EP.

Dataset Information

Complete mitochondrial genome of the nesting Colombian Caribbean Hawksbill Turtle.

Publications

Complete mitochondrial genome of the nesting Colombian Caribbean Hawksbill Turtle.

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