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

ABSTRACT: 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-1?) 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.

SUBMITTER: Johri S

PROVIDER: S-EPMC6418218 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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

Johri Shaili S Solanki Jitesh J Cantu Vito Adrian VA Fellows Sam R SR Edwards Robert A RA Moreno Isabel I Vyas Asit A Dinsdale Elizabeth A EA

Scientific reports 20190314 1

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 analys ...[more]

PMID: 30872700

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Project description:The international wildlife trade presents severe conservation and environmental security risks, yet no international regulatory framework exists to monitor the trade of species not listed in the appendices of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). We explored the composition and dynamics of internationally regulated versus nonregulated trade, with a focus on importations of wild-caught terrestrial vertebrates entering the United States from 2009 to 2018. We used 10 years of species-level trade records of the numbers of live, wild-caught animals imported to the United States and data on International Union for the Conservation of Nature (IUCN) estimates of extinction risk to determine whether there were differences in the diversity, abundance, and risk to extinction among imports of CITES-listed versus unlisted species. We found 3.6 times the number of unlisted species in U.S. imports compared with CITES-listed species (1366 vs. 378 species). The CITES-listed species were more likely to face reported conservation threats relative to unlisted species (71.7% vs. 27.5%). However, 376 unlisted species faced conversation threats, 297 species had unknown population trends, and 139 species were without an evaluation by the IUCN. Unlisted species appearing for the first time in records were imported 5.5 times more often relative to CITES-listed species. Unlisted reptiles had the largest rate of entry, averaging 53 unique species appearing in imports for the first time per year. Overall trade quantities were approximately 11 times larger for imports of unlisted species relative to imports of CITES-listed species. Countries that were top exporters of CITES-listed species were mostly different from exporters of unlisted species. Because of the vulnerabilities of unlisted, traded species entering the United States and increasing global demand, we strongly recommend governments adapt their policies to monitor and report on the trade of all wildlife.

Project description:BackgroundCITES is an international agreement between governments to ensure that international trade in specimens of wild animals and plants does not threaten their survival. Regarding spiders, all species listed in CITES are tarantulas. They are included in Appendix II, meaning that they are species that are not necessarily now threatened with extinction but that they may become so unless trade is closely controlled.Many tarantulas are legally and illegally traded in the pet market and they are one of the most traded invertebrate groups. Originally, the CITES list published in 1995 included all the current species of the genus Brachypelma Simon, 1891 plus Aphonopelma pallidum (F. O. Pickard-Cambridge, 1897) and the so-called Aphonopelma albiceps (Pocock, 1903). After that, some taxonomic changes were done, as well as descriptions of new species in the genus Brachypelma. The objective of this paper is to assess the 21 taxonomically valid spider species listed on CITES according to the IUCN criteria, study the general patterns and trends and advise on possible future conservation actions critical for the survival of endangered species.New informationAmongst all 21 species assessed, 16 had sufficient data on their distribution, ecology and threats to properly understand their current status and suggest possible conservation measures. A decline in the area of occupancy (AOO) and extent of occurrence (EOO) was inferred to almost all species, caused mostly by human activities (urbanisation, roads, agricultural and touristic activities), which often lead to the complete loss of subpopulations across their range. Hurricanes and frequent rising water, which are increasing in frequency due to climate change, can cause decline in habitat quality and consequent change in EOO and AOO of some species and should also be considered when planning conservation actions. Severe fragmentation was detected in 13 species and is therefore one of the most relevant threats to the most endangered Brachypelma species and should be made a priority aspect to deal with when proposing conservation actions for the group. Regarding the loss of individuals in wild populations, the main cause seems to be the overharvesting to meet the illegal trade.The most important conservation actions identified across species include preserving their natural habitat through protected areas, establishing management plans for both the species and their habitats and undertaking systematic monitoring to provide information about population recovery and species re-introduction programmes. In general, we propose to prioritise and support research on the population trends and distribution, as well as on the impact of land use and habitat degradation. Special attention regarding conservation actions and research plans has to be given to the central Pacific coastal area of Mexico, particularly around Guerrero State where five species of Brachypelma occur. Critically, for some of the most endangered species, such as B. baumgarteni and B. hamorii, there is no official protected area in their range of occurrence. It would therefore be highly recommended to establish at least one conservation unit which focuses on protecting each of these species in situ. In some cases, basic taxonomic research is needed before development of any appropriate conservation action can be proposed.

Dataset Information

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

Publications

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

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