Browse
Submit Data
Databases
API
Help

Dataset Information

31 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete mitochondrial genome of the three Colombian Caribbean loggerhead sea turtles, using next-generation sequencing.

ABSTRACT: The loggerhead turtle, Caretta caretta (Linnaeus, 1758), is an endangered sea turtle in Colombian Caribbean beach. In the present study was sequenced the complete mitochondrial DNA of three loggerhead turtles using Illumina next-generation sequencing (NGS). The average nucleotide frequency was A: 35% T: 26%, C: 27% and G: 12%. This genome provides knowledge to the study of genetic variations and evolution of mitochondrial genomes of C. caretta. The sequences were deposited at the GenBank database under the accession number MF554690.1, MF579504.1 and MF579505.1.

SUBMITTER: Hernandez-Fernandez J

PROVIDER: S-EPMC7800953 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Complete mitochondrial genome of the three Colombian Caribbean loggerhead sea turtles, using next-generation sequencing.

Hernández-Fernández Javier J Delgado Cano David Arley DA

Mitochondrial DNA. Part B, Resources 20180521 2

The loggerhead turtle, <i>Caretta caretta</i> (Linnaeus, 1758), is an endangered sea turtle in Colombian Caribbean beach. In the present study was sequenced the complete mitochondrial DNA of three loggerhead turtles using Illumina next-generation sequencing (NGS). The average nucleotide frequency was A: 35% T: 26%, C: 27% and G: 12%. This genome provides knowledge to the study of genetic variations and evolution of mitochondrial genomes of <i>C. caretta</i>. The sequences were deposited at the G ...[more]

PMID: 33474265

Similar Datasets

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

Project description: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 tRNATyr 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.

| S-EPMC8179041 | biostudies-literature

De novo transcriptome assembly of loggerhead sea turtle nesting of the Colombian Caribbean.

Project description:Loggerhead sea turtle Caretta caretta is widely distributed in the oceans of tropical and subtropical latitude. This turtle is an endangered species due to anthropic and natural factors that have decreased their population levels. In this study, RNA sequencing and de-novo assembly of genes expressed in blood were performed. The raw FASTQ files have been deposited on NCBI's SRA database with accession number SRX2629512. A total of 5.4 Gb raw sequence data were obtained, corresponding to 48,257,019 raw reads. Trinity pipeline was used to perform a de-novo assembly, we were able to identify 64,930 transcripts for female loggerhead turtle transcriptome with an N50 of 1131 bp. The obtained transcriptome data will be useful for further studies of the physiology, biochemistry and evolution in this species.

| S-EPMC5472237 | biostudies-literature

A biphasic navigational strategy in loggerhead sea turtles.

Project description:The homing journeys of nine loggerhead turtles translocated from their nesting beach to offshore release sites, were reconstructed through Argos and GPS telemetry while their water-related orientation was simultaneously recorded at high temporal resolution by multi-sensor data loggers featuring a three-axis magnetic sensor. All turtles managed to return to the nesting beach area, although with indirect routes encompassing an initial straight leg not precisely oriented towards home, and a successive homebound segment carried out along the coast. Logger data revealed that, after an initial period of disorientation, turtles were able to precisely maintain a consistent direction for several hours while moving in the open sea, even during night-time. Their water-related headings were in accordance with the orientation of the resulting route, showing little or no effect of current drift. This study reveals a biphasic homing strategy of displaced turtles involving an initial orientation weakly related to home and a successive shift to coastal navigation, which is in line with the modern conceptual framework of animal migratory navigation as deriving from sequential mechanisms acting at different spatial scales.

| S-EPMC7581759 | biostudies-literature

Complete mitochondrial genome of the nesting Colombian Caribbean Hawksbill Turtle.

Project description: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.

| S-EPMC6200328 | biostudies-literature

Data on heteroplasmic mutations in mitochondrial genomes of loggerhead and hawksbill sea turtles: First approach.

Project description:The populations of loggerhead (Caretta caretta) and hawksbill (Eretmochelys imbricata) sea turtles are suffering an exponential decline due to anthropic and environmental actions that threaten their survival. In these turtle populations, the degree of heteroplasmic mutations commonly related with pathologies, has not been studied. In this data report, the specifications of each heteroplasmic site (region, mutation, length) and the percentage of heteroplasmy of each gene for four mitochondrial genomes of turtles (loggerhead: Cc1, Cc2, Cc3 and hawksbill: Ei1) are presented. The highest value of heteroplasmy in tRNA was of 83.33% for the Cc2 turtle (tRNASer gene), in protein coding genes was 38.62% for Cc2 (ND5), and in rRNA genes of 0.74% for Ei1 turtle (rRNA-16S). The variability data obtained will be useful for further conservation projects, evolution studies and population health of these species. This is the first study of heteroplasmy in complete mitogenomes of loggerhead and hawksbill turtles.

| S-EPMC6906639 | biostudies-literature

Identifying global favourable habitat for early juvenile loggerhead sea turtles.

Project description:Loggerhead sea turtles (Caretta caretta) nest globally on sandy beaches, with hatchlings dispersing into the open ocean. Where these juveniles go and what habitat they rely on remains a critical research question for informing conservation priorities. Here a high-resolution Earth system model is used to determine the biophysical geography of favourable ocean habitat for loggerhead sea turtles globally during their first year of life on the basis of ocean current transport, thermal constraints and food availability (defined here as the summed lower trophic level carbon biomass). Dispersal is simulated from eight major nesting sites distributed across the globe in four representative years using particle tracking. Dispersal densities are identified for all turtles, and for the top 15% 'best-fed' turtles that have not encountered metabolically unfavourable temperatures. We find that, globally, rookeries are positioned to disperse to regions where the lower trophic biomass is greatest within loggerheads' thermal range. Six out of the eight nesting sites are associated with strong coastal boundary currents that rapidly transport hatchlings to subtropical-subpolar gyre boundaries; narrow spatial migratory corridors exist for 'best-fed' turtles associated with these sites. Two other rookeries are located in exceptionally high-biomass tropical regions fuelled by natural iron fertilization. 'Best-fed' turtles tend to be associated with lower temperatures, highlighting the inverse relationship between temperature and lower trophic biomass. The annual mean isotherms between 20°C and the thermal tolerance of juvenile loggerheads are a rough proxy for favourable habitat for loggerheads from rookeries associated with boundary currents. Our results can be used to constrain regions for conservation efforts for each subpopulation, and better identify foraging habitat for this critical early life stage.

| S-EPMC8086883 | biostudies-literature

Female loggerhead sea turtles (Caretta caretta L.) rarely remate during nesting season.

Project description:The goal of this study was to assess the consequences of single versus multiple paternity by identifying paternity of clutches per female to identify whether there were detectable costs or benefits. Multiple mating can occur when the benefits of mating outweigh the costs, but if costs and benefits are equal, no pattern is expected. Previous research on loggerhead sea turtle (Caretta caretta) populations found male-biased breeding sex ratios and multiple mating by many females nesting in southwestern Florida. A sample of nesting loggerhead females who laid more than one nest over the course of the season and a subset of their hatchlings were examined from 36 clutches in 2016 on Sanibel Island, Florida. Males that fathered hatchlings in the first clutch sampled were identified in subsequent clutches. Interestingly, 75% of the females analyzed had mated singly. No male was represented in more than one female's clutches. The results suggest that females likely mate at the beginning of the season and use stored sperm for multiple clutches. Evidence for mating between laying events was limited. There was no consistent pattern across the subsequent multiple paternity clutches, suggesting benefits to loggerhead females likely equal their costs and subsequent mating is likely determined by female preference.

| S-EPMC6972835 | biostudies-literature

Active dispersal in loggerhead sea turtles (Caretta caretta) during the 'lost years'.

Project description:Highly migratory marine species can travel long distances and across entire ocean basins to reach foraging and breeding grounds, yet gaps persist in our knowledge of oceanic dispersal and habitat use. This is especially true for sea turtles, whose complex life history and lengthy pelagic stage present unique conservation challenges. Few studies have explored how these young at-sea turtles navigate their environment, but advancements in satellite technology and numerical models have shown that active and passive movements are used in relation to open ocean features. Here, we provide the first study, to the best of our knowledge, to simultaneously combine a high-resolution physical forcing ocean circulation model with long-term multi-year tracking data of young, trans-oceanic North Pacific loggerhead sea turtles during their 'lost years' at sea. From 2010 to 2014, we compare simulated trajectories of passive transport with empirical data of 1-3 year old turtles released off Japan (29.7-37.5 straight carapace length cm). After several years, the at-sea distribution of simulated current-driven trajectories significantly differed from that of the observed turtle tracks. These results underscore current theories on active dispersal by young oceanic-stage sea turtles and give further weight to hypotheses of juvenile foraging strategies for this species. Such information can also provide critical geographical information for spatially explicit conservation approaches to this endangered population.

| S-EPMC4920322 | biostudies-literature

Mortality associated with ingestion of sea urchins in loggerhead sea turtles (Caretta caretta): A case series.

Project description:AimsThe aims of this study were: a) to describe the pathological and laboratory findings in a case series of stranding and mortality associated with ingestion of large amounts of sea urchins in loggerhead turtles (Caretta caretta), and b) to alert veterinarians and biologists involved in sea turtle conservation of this cause of stranding and/or death.MethodsThe six loggerheads studied were stranded on the coasts of Gran Canaria, Canary Islands, Spain, between 2008 and 2015. Post mortem studies included pathological, microbiological, and sea urchin species identification procedures.ResultsAll turtles showed severe intestinal impaction caused by large amounts of sea urchins, mainly affecting the colon and the caudal half of the small intestine. Histologically, severe focal fibrinonecrotic enteritis was diagnosed in two turtles. In the remaining turtles, lesions ranged from mild desquamation of the intestinal epithelium to severe congestion of the blood vessels of lamina propria, submucosa, muscular and serosa, and edema. Vibrio sp. was isolated from the spleen and intestinal mucosa of a loggerhead in which focal fibrinonecrotic enteritis had been diagnosed. In five turtles, all the remains were fragments from long-spined sea urchins (Diadema africanum); the last turtle contained a mixture of long-spined sea urchin (90%) and purple sea urchin (Sphaerechinus granularis) (10%) remains.ConclusionsAlthough the prevalence of this cause of stranding was low (< 1.6%) compared to other mortality causes, continued overfishing and anthropogenic climate change could increase its incidence. Intestinal impaction with large amounts of sea urchins should be included in the differential diagnosis of gastrointestinal diseases in sea turtles, and the possible toxic effect of some sea urchin species on sea turtles should also be investigated.

| S-EPMC6707556 | biostudies-literature

Evidence for transoceanic migrations by loggerhead sea turtles in the southern Pacific Ocean.

Project description:Post-hatchling loggerhead turtles (Caretta caretta) in the northern Pacific and northern Atlantic Oceans undertake transoceanic developmental migrations. Similar migratory behaviour is hypothesized in the South Pacific Ocean as post-hatchling loggerhead turtles are observed in Peruvian fisheries, yet no loggerhead rookeries occur along the coast of South America. This hypothesis was supported by analyses of the size-class distribution of 123 post-hatchling turtles in the South Pacific and genetic analysis of mtDNA haplotypes of 103 nesting females in the southwest Pacific, 19 post-hatchlings stranded on the southeastern Australian beaches and 22 post-hatchlings caught by Peruvian longline fisheries. Only two haplotypes (CCP1 93% and CCP5 7%) were observed across all samples, and there were no significant differences in haplotype frequencies between the southwest Pacific rookeries and the post-hatchlings. By contrast, the predominant CCP1 haplotype is rarely observed in North Pacific rookeries and haplotype frequencies were strongly differentiated between the two regions (F(st)=0.82; p=<0.00001). These results suggest that post-hatchling loggerhead turtles emerging from the southwest Pacific rookeries are undertaking transoceanic migrations to the southeastern Pacific Ocean, thus emphasizing the need for a broader focus on juvenile mortality throughout the South Pacific to develop effective conservation strategies.

| S-EPMC2677240 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data