The complete mitochondrial DNA of the silky shark (
            <i>Carcharhinus falciformis</i>
            )

Galván‐Tirado, Carolina; Hinojosa-Álvarez, Silvia; Díaz‐Jaimes, Píndaro; Marcet‐Houben, Marina; León, Francisco J. Garcı́a de

doi:10.3109/19401736.2013.878922

Cited by 7 publications

(14 citation statements)

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“…3A , Genbank accession #MK092088), a genome size similar to mitochondrial genomes reported for Carcharhinus spp., (eg. Carcharhinus sorrah (16,707 bp), Carcharhinus brevipinna (16,706 bp), Carcharhinus melanopterus (16,706 bp), Carcharhinus plumbeus (16,706 bp), and Carcharhinus obscurus (16,706 bp) 26 , but significantly different than the published mitogenome for Carcharhinus falciformis at 17,639 bp 27 . Mean coverage for the complete mitochondrial genome was 19.4 × ± 2 × (Fig.…”

Section: Resultsmentioning

confidence: 72%

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‘Genome skimming’ with the MinION hand-held sequencer identifies CITES-listed shark species in India’s exports market

Johri

Solanki

Cantu

et al. 2019

Sci Rep

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Chondrichthyes - sharks, rays, skates, and chimeras, are among the most threatened and data deficient vertebrate species. Global demand for shark and ray derived products, drives unregulated and exploitative fishing practices, which are in turn facilitated by the lack of ecological data required for effective conservation of these species. Here, we describe a Next Generation Sequencing method (using the MinION, a hand-held portable sequencing device from Oxford Nanopore Technologies), and analyses pipeline for molecular ecological studies in Chondrichthyes. Using this method, the complete mitochondrial genome and nuclear intergenic and protein-coding sequences were obtained by direct sequencing of genomic DNA obtained from shark fin tissue. Recovered loci include mitochondrial barcode sequences- Cytochrome oxidase I, NADH2, 16S rRNA and 12S rRNA- and nuclear genetic loci such as 5.8S rRNA, Internal Transcribed Spacer 2, and 28S rRNA regions, which are commonly used for taxonomic identification. Other loci recovered were the nuclear protein-coding genes for antithrombin or SerpinC, Immunoglobulin lambda light chain, Preprogehrelin, selenium binding protein 1(SBP1), Interleukin-1 beta (IL-1β) and Recombination-Activating Gene 1 (RAG1). The median coverage across all genetic loci was 20x and sequence accuracy was ≥99.8% compared to reference sequences. Analyses of the nuclear ITS2 region and the mitochondrial protein-encoding loci allowed accurate taxonomic identification of the shark specimen as Carcharhinus falciformis, a CITES Appendix II species. MinION sequencing provided 1,152,211 bp of new shark genome, increasing the number of sequenced shark genomes to five. Phylogenetic analyses using both mitochondrial and nuclear loci provided evidence that Prionace glauca is nested within Carcharhinus, suggesting the need for taxonomic reassignment of P. glauca. We increased genomic information about a shark species for ecological and population genetic studies, enabled accurate identification of the shark tissue for biodiversity indexing and resolved phylogenetic relationships among multiple taxa. The method was independent of amplification bias, and adaptable for field assessments of other Chondrichthyes and wildlife species in the future.

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Section: Resultsmentioning

confidence: 72%

“…A single complete mitochondrial genome sequence of 17,639 bp for Carcharhinus falciformis has been published 27 . A suspicious insertion of ~939 bp is evident when the sequence 27 is compared to all Carcharinus spp. mitogenomes, which are at ~16,700 bp.…”

Section: Discussionmentioning

confidence: 99%

‘Genome skimming’ with the MinION hand-held sequencer identifies CITES-listed shark species in India’s exports market

Johri

Solanki

Cantu

et al. 2019

Sci Rep

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“…Mitogenome size and gene annotations showed concordance with those of other Carcharhiniformes (e.g. C. amblyrhynchoides (Feutry et al 2014) , C. falciformis (Galvan-Tirado et al 2016), C.…”

Section: G3 Supplementary Resourcessupporting

confidence: 60%

Estimating contemporary abundance, demography, and vulnerability to change for long-lived species with effective population size and population simulation

Blower¹

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The measure of effective population size (Ne) captures the effects of contemporary demographic and genetic processes and the future evolutionary potential of a population. In a Wright-Fisher ideal population with discrete generations in which all adults breed, Ne simply equals the adult population size (Nc). However, due to their longevity, most vertebrate species have concurrent mature generations that interbreed (overlap when mating). Such iteroparous overlapping-generation (OG) species do not conform to Ne theory, and often have vulnerable populations due to life-history traits that slow population increase: long life, slow maturation, low fecundity, protracted gestation, lengthy reproductive pauses, and complex mating behaviours. These traits, along with demographic processes (e.g. birth and mortality) and genetic circumstances (e.g. genetic diversity gain and loss), collectively influence the relationship of Ne to Nc for a population, termed the Ne /Nc ratio or relationship. Furthermore, the magnitude and accuracy of genetic Ne estimates are influenced by the sampling regimen and quantities of samples and loci. Accordingly, Ne /Nc relationships are difficult to estimate for natural populations but are much needed for geneticbased population assessment of vulnerable OG species.To facilitate population assessments, an easy-to-use simulator has been developed in this thesis to estimate Ne /Nc relationships. The simulator incorporates OG species' life-history traits known to influence Ne, and produces populations of known Nc that can be sampled flexibly to accurately estimate Ne. I use sharks as an example OG species, as sharks mature slowly, have a long life and low fecundity, combined with low natural mortality, all factors that simplify the Ne /Nc relationship. Furthermore, these characteristics make shark populations vulnerable to depletion, and they are frequently harvested with little understanding of their demographic or genetic vulnerabilities to depletion.In chapter two, I detail the development and validation of the OG species simulator. The design incorporates OG species' life-history traits that influence Ne, along with demographic (AgeNe method) and genetic (LDNe method; Ne.LD ) methods to estimate Ne and Nb (number of breeders in a given mating season). The simulator produces populations of a known size that can be sampled flexibly to determine the Ne /Nc relationship for a wide range of OG species' life-histories.Validation of the simulator satisfied general demographic and genetic theoretical expectations and compared well with independently simulated estimates of Ne and Nc for OG species.In chapter three, I reconfigure the simulator as an easy-to-use software tool, NeOGen, that simplifies the planning and execution of Ne-based population assessments. Empirical estimates of Ne.LD often suffer from low accuracy or precision. NeOGen provides a power analysis to determine Publications included in this thesisChapter 3 -Blower DC, Riginos C, Ovenden JR (2019) NeOGen: a tool to predict genetic effectiv...

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“…This method allowed access to previously unexplored parts of the silky shark nuclear genome which encode developmental and immune function proteins, among others. The entire mitochondrial genome of C. falciformis was also obtained which provided a correct version of the mitogenome, compared to the previously published genome which had a ~1000 bp insertion from errors introduced during sequencing or analyses [77]. Last, access to the nuclear and mitochondrial genomes also allowed assignment of accurate taxonomic identity to a market specimen based on multigenic analyses and provided strong evidence for inclusion of the blue shark (P. Glauca) in the Carcharhinus genus.…”

Section: Genome Skimming: a Non-targeted Approach To Sub-sampling Chondrichthyan Genomesmentioning

confidence: 99%

Taking Advantage of the Genomics Revolution for Monitoring and Conservation of Chondrichthyan Populations

et al. 2019

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Chondrichthyes (sharks, rays, skates and chimaeras) are among the oldest extant predators and are vital to top-down regulation of oceanic ecosystems. They are an ecologically diverse group occupying a wide range of habitats and are thus, exploited by coastal, pelagic and deep-water fishing industries. Chondrichthyes are among the most data deficient vertebrate species groups making design and implementation of regulatory and conservation measures challenging. High-throughput sequencing technologies have significantly propelled ecological investigations and understanding of marine and terrestrial species’ populations, but there remains a paucity of NGS based research on chondrichthyan populations. We present a brief review of current methods to access genomic and metagenomic data from Chondrichthyes and discuss applications of these datasets to increase our understanding of chondrichthyan taxonomy, evolution, ecology and population structures. Last, we consider opportunities and challenges offered by genomic studies for conservation and management of chondrichthyan populations.

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The complete mitochondrial DNA of the silky shark ( Carcharhinus falciformis )

Cited by 7 publications

References 4 publications

‘Genome skimming’ with the MinION hand-held sequencer identifies CITES-listed shark species in India’s exports market

‘Genome skimming’ with the MinION hand-held sequencer identifies CITES-listed shark species in India’s exports market

Estimating contemporary abundance, demography, and vulnerability to change for long-lived species with effective population size and population simulation

Taking Advantage of the Genomics Revolution for Monitoring and Conservation of Chondrichthyan Populations

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