Dataset Information

Mitochondrial genome of an Atlantic white shark (Carcharodon carcharias).

ABSTRACT: Here we report the first full mitochondrial genome sequence for a white shark caught in the Atlantic Ocean. The mitochondrial genome is 16,745?bp in length and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region. The base composition of this mtDNA lineage is A: 30.7%, C: 26.9%, G: 13.8%, and T: 28.6%. In concordance with previous population genetic studies, the Atlantic caught individual forms a separate lineage from individuals caught on either side of the Pacific Ocean.

SUBMITTER: Marra NJ

PROVIDER: S-EPMC7799651 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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Publications

Mitochondrial genome of an Atlantic white shark (<i>Carcharodon carcharias</i>).

Marra Nicholas J NJ Wang Minghui M Sun Qi Q Pavinski Bitar Paulina D PD Stanhope Michael J MJ Shivji Mahmood S MS

Mitochondrial DNA. Part B, Resources 20161122 1

Here we report the first full mitochondrial genome sequence for a white shark caught in the Atlantic Ocean. The mitochondrial genome is 16,745 bp in length and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region. The base composition of this mtDNA lineage is A: 30.7%, C: 26.9%, G: 13.8%, and T: 28.6%. In concordance with previous population genetic studies, the Atlantic caught individual forms a separate lineage from individuals caught on either side of ...[more]

PMID: 33473604

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Project description:BACKGROUND: The white shark (Carcharodon carcharias) is a globally distributed, apex predator possessing physical, physiological, and behavioral traits that have garnered it significant public attention. In addition to interest in the genetic basis of its form and function, as a representative of the oldest extant jawed vertebrate lineage, white sharks are also of conservation concern due to their small population size and threat from overfishing. Despite this, surprisingly little is known about the biology of white sharks, and genomic resources are unavailable. To address this deficit, we combined Roche-454 and Illumina sequencing technologies to characterize the first transciptome of any tissue for this species. RESULTS: From white shark heart cDNA we generated 665,399 Roche 454 reads (median length 387-bp) that were assembled into 141,626 contigs (mean length 503-bp). We also generated 78,566,588 Illumina reads, which we aligned to the 454 contigs producing 105,014 454/Illumina consensus sequences. To these, we added 3,432 non-singleton 454 contigs. By comparing these sequences to the UniProtKB/Swiss-Prot database we were able to annotate 21,019 translated open reading frames (ORFs) of ? 20 amino acids. Of these, 19,277 were additionally assigned Gene Ontology (GO) functional annotations. While acknowledging the limitations of our single tissue transcriptome, Fisher tests showed the white shark transcriptome to be significantly enriched for numerous metabolic GO terms compared to the zebra fish and human transcriptomes, with white shark showing more similarity to human than to zebra fish (i.e. fewer terms were significantly different). We also compared the transcriptome to other available elasmobranch sequences, for signatures of positive selection and identified several genes of putative adaptive significance on the white shark lineage. The white shark transcriptome also contained 8,404 microsatellites (dinucleotide, trinucleotide, or tetranucleotide motifs ? five perfect repeats). Detailed characterization of these microsatellites showed that ORFs with trinucleotide repeats, were significantly enriched for transcription regulatory roles and that trinucleotide frequency within ORFs was lower than for a wide range of taxonomic groups including other vertebrates. CONCLUSION: The white shark heart transcriptome represents a valuable resource for future elasmobranch functional and comparative genomic studies, as well as for population and other biological studies vital for effective conservation of this globally vulnerable species.

Project description:Increases in the number of shark bites, along with increased media attention on shark-human interactions has led to growing interest in preventing injuries from shark bites through the use of personal mitigation measures. The leading cause of fatality from shark bite victims is blood loss; thus reducing haemorrhaging may provide additional time for a shark bite victim to be attended to by emergency services. Despite previous shark-proof suits being bulky and cumbersome, new technological advances in fabric has allowed the development of lightweight alternatives that can be incorporated onto traditional wetsuits. The ability for these fabrics to withstand shark bites has not been scientifically tested. In this report, we compared two types of recently developed protective fabrics that incorporated ultra-high molecular weight polyethylene (UHMWPE) fibre onto neoprene (SharkStop and ActionTX) and compared them to standard neoprene alternatives. We tested nine different fabric variants using three different tests, laboratory-based puncture and laceration tests, along with field-based trials involving white sharks Carcharodon carcharias. Field-based trials consisted of measuring C. carcharias bite force and quantifying damages to the new fabrics following a bite from 3-4 m total length C. carcharias. We found that SharkStop and ActionTX fabric variants were more resistant to puncture, laceration, and bites from C. carcharias. More force was required to puncture the new fabrics compared to control fabrics (laboratory-based tests), and cuts made to the new fabrics were smaller and shallower than those on standard neoprene for both types of test, i.e. laboratory and field tests. Our results showed that UHMWPE fibre increased the resistance of neoprene to shark bites. Although the use of UHMWPE fibre (e.g. SharkStop and ActionTX) may therefore reduce blood loss resulting from a shark bite, research is needed to assess if the reduction in damages to the fabrics extends to human tissues and decreased injuries.

Project description:White sharks are highly migratory apex predators, globally distributed in temperate, sub-tropical, and tropical waters. Knowledge of white shark biology and ecology has increased recently based on research at known aggregation sites in the Indian, Atlantic, and Northeast Pacific Oceans; however, few data are available for the Northwest Pacific Ocean. This study provides a meta-analysis of 240 observations of white sharks from the Northwest Pacific Ocean between 1951 and 2012. Records comprise reports of bycatch in commercial fisheries, media accounts, personal communications, and documentation of shark-human interactions from Russia (n = 8), Republic of Korea (22), Japan (129), China (32), Taiwan (45), Philippines (1) and Vietnam (3). Observations occurred in all months, excluding October-January in the north (Russia and Republic of Korea) and July-August in the south (China, Taiwan, Philippines, and Vietnam). Population trend analysis indicated that the relative abundance of white sharks in the region has remained relatively stable, but parameterization of a 75% increase in observer effort found evidence of a minor decline since 2002. Reliably measured sharks ranged from 126-602 cm total length (TL) and 16-2530 kg total weight. The largest shark in this study (602 cm TL) represents the largest measured shark on record worldwide. For all countries combined the sex ratio was non-significantly biased towards females (1∶1.1; n = 113). Of 60 females examined, 11 were confirmed pregnant ranging from the beginning stages of pregnancy (egg cases) to near term (140 cm TL embryos). On average, 6.0±2.2 embryos were found per litter (maximum of 10) and gestation period was estimated to be 20 months. These observations confirm that white sharks are present in the Northwest Pacific Ocean year-round. While acknowledging the difficulties of studying little known populations of a naturally low abundance species, these results highlight the need for dedicated research to inform regional conservation and management planning.

Dataset Information

Mitochondrial genome of an Atlantic white shark (Carcharodon carcharias).

Publications

Mitochondrial genome of an Atlantic white shark (<i>Carcharodon carcharias</i>).

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