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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| Formato: | article |
| Lenguaje: | EN ES |
| Publicado: |
Pontificia Universidad Javeriana
2018
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| Acceso en línea: | https://doaj.org/article/27438ab2c1fa40d6a987683930b9c1e3 |
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| Sumario: | 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. |
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