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

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...

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Autor principal: Javier Hernández-Fernández, Katherin Otálora
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Publicado: Pontificia Universidad Javeriana 2018
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spelling oai:doaj.org-article:27438ab2c1fa40d6a987683930b9c1e32021-11-16T13:53:17ZComplete Colombian Caribbean loggerhead turtle mitochondrial genome: tRNA structure analysis and revisited marine turtle phylogeny10.11144/Javeriana.SC23-3.cccl0122-74832027-1352https://doaj.org/article/27438ab2c1fa40d6a987683930b9c1e32018-11-01T00:00:00Zhttps://revistas.javeriana.edu.co/index.php/scientarium/article/view/18526https://doaj.org/toc/0122-7483https://doaj.org/toc/2027-1352The 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.Javier Hernández-Fernández, Katherin OtáloraPontificia Universidad Javerianaarticlemitogenome; caretta caretta; cheloniidae; coding genes; sea turtle phylogenyScience (General)Q1-390ENESUniversitas Scientiarum, Vol 23, Iss 3, Pp 355-381 (2018)
institution DOAJ
collection DOAJ
language EN
ES
topic mitogenome; caretta caretta; cheloniidae; coding genes; sea turtle phylogeny
Science (General)
Q1-390
spellingShingle mitogenome; caretta caretta; cheloniidae; coding genes; sea turtle phylogeny
Science (General)
Q1-390
Javier Hernández-Fernández, Katherin Otálora
Complete Colombian Caribbean loggerhead turtle mitochondrial genome: tRNA structure analysis and revisited marine turtle phylogeny
description 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.
format article
author Javier Hernández-Fernández, Katherin Otálora
author_facet Javier Hernández-Fernández, Katherin Otálora
author_sort Javier Hernández-Fernández, Katherin Otálora
title Complete Colombian Caribbean loggerhead turtle mitochondrial genome: tRNA structure analysis and revisited marine turtle phylogeny
title_short Complete Colombian Caribbean loggerhead turtle mitochondrial genome: tRNA structure analysis and revisited marine turtle phylogeny
title_full Complete Colombian Caribbean loggerhead turtle mitochondrial genome: tRNA structure analysis and revisited marine turtle phylogeny
title_fullStr Complete Colombian Caribbean loggerhead turtle mitochondrial genome: tRNA structure analysis and revisited marine turtle phylogeny
title_full_unstemmed Complete Colombian Caribbean loggerhead turtle mitochondrial genome: tRNA structure analysis and revisited marine turtle phylogeny
title_sort complete colombian caribbean loggerhead turtle mitochondrial genome: trna structure analysis and revisited marine turtle phylogeny
publisher Pontificia Universidad Javeriana
publishDate 2018
url https://doaj.org/article/27438ab2c1fa40d6a987683930b9c1e3
work_keys_str_mv AT javierhernandezfernandezkatherinotalora completecolombiancaribbeanloggerheadturtlemitochondrialgenometrnastructureanalysisandrevisitedmarineturtlephylogeny
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