Caranx ignobilis, commonly known as the kingfish or giant trevally, is a large, reef-associated apex predator. It is a prized sportfish, targeted heavily throughout its tropical and subtropical range in the Indian and Pacific Oceans, and it has drawn significant interest in aquaculture due to an unusual tolerance for freshwater. In this study, we present a high-quality nuclear genome assembly of a C. ignobilis individual from Hawaiian waters, which have recently been shown to host a genetically distinct population. The assembly has a contig NG50 of 7.3Mbp and scaffold NG50 of 46.3Mbp. Twenty-five of the 203 scaffolds contain 90% of the genome. We also present the raw Pacific Biosciences continuous long-reads from which the assembly was created. A Hi-C dataset (Dovetail Genomics Omni-C) and Illumina-based RNA-seq from eight tissues are also presented; the latter of which can be particularly useful for annotation and studies of freshwater tolerance. Overall, this genome assembly and supporting data is a valuable tool for ecological and comparative genomics studies of kingfish and other carangoid fishes.
The aim to sequence, catalog, and characterize the genomes of all of Earth’s eukaryotic biodiversity is the shared mission of many ongoing large-scale biodiversity genomics initiatives. Reference genomes of global flora and fauna have the potential to inform a broad range of major issues facing both biodiversity and humanity, such as the impact of climate change, the conservation of endangered species and ecosystems, public health crises, and the preservation and enhancement of ecosystem services. Biodiversity is dramatically declining: 28% of species being assessed by the IUCN are threatened with extinction, and recent reports suggest that a transformative change is needed to conserve and protect what remains. To provide a collective and global genomic response to the biodiversity crisis, many biodiversity genomics initiatives have come together, creating a network of networks under the Earth BioGenome Project. This network seeks to expedite the creation of an openly available, “public good” encyclopedia of high-quality eukaryotic reference genomes, in the hope that by advancing our basic understanding of nature, it can lead to the transformational scientific developments needed to conserve and protect global biodiversity. Key to completing this ambitious encyclopedia of reference genomes, is the ability to responsibly, ethically, legally, and equitably access and use samples from all of the eukaryotic species across the planet, including those that are under the custodianship of Indigenous Peoples and Local Communities. Here, the biodiversity genomics community is subject to the provisions codified in international, national, and local legislations and customary community norms, principles, and protocols. We propose a framework to support biodiversity genomic researchers, projects, and initiatives in building trustworthy and sustainable partnerships with communities, providing minimum recommendations on how to access, utilize, preserve, handle, share, analyze, and communicate samples, genomics data, and associated Traditional Knowledge obtained from, and in partnership with, Indigenous Peoples and Local Communities across the data-lifecycle.
The Republic of Seychelles is one of six African Small Island Developing States (SIDS) and has a marine-based economy reliant on fisheries and international tourism. Seychelles has been flagged by the United Nations as highly vulnerable to climate change. Climatic threats are compounded with population declines of key fishery species. A progressive national stance towards ocean sustainability and an emerging economy partially driven by tourists are two of several factors that make Seychelles a good candidate for a sustainable seafood labelling and consumption programme, which would provide market-based incentives for fishery harvesters, regulators, buyers and consumers to improve sustainable practices. To address the feasibility of such a programme, we conducted a pilot study, surveying 33 artisanal fishers and mapping supply chain structure to examine incentives and challenges. Questions addressed fishers’ years of experience, reliance on fishing for income, and flexibility in gear type and species targeted. Of the total number of respondents, 64% would like to see a programme implemented but only 34% thought it would be successful. Participants identified several barriers and benefits that primarily spanned socioeconomic and regulatory themes. Our pilot results indicate the sociocultural and economic impacts of sustainability programmes in Seychelles are as important as environmental considerations, a finding pertinent to anyone undertaking similar research efforts in other SIDS. We advocate for the necessity of thorough, location-based research and in-depth stakeholder consultation to elucidate economic, societal, behavioural and cultural factors that will affect the success of designing and implementing seafood labelling programmes in SIDS.
The Roundjaw Bonefish (Albula glossodonta) genome assembly was annotated following the MAKER pipeline. The steps we took are outlined here, but this process assumes you have successfully installed MAKER in advance. The following versions of tools were used (in alphabetical order): AUGUSTUS v3.3.2, BEDTools v2.28.0, BUSCO v4.0.6 with OrthoDB v10, EVidenceModeler v1.1.1, GeneMark-ES v4.38, gFACs v1.1.1, InterProScan v5.45-80.0, MAKER v3.01.02-beta, NCBI BLAST+ Suite v2.9.0, SNAP commit #daf76ba (3 June 2019), and tRNAscan-SE v1.3.1.
Background: Bonefishes are cryptic species indiscriminately targeted by subsistence and recreational fisheries worldwide. The roundjaw bonefish, Albula glossodonta is the most widespread bonefish species in the Indo-Pacific and is listed as vulnerable to extinction by the IUCN's Red List due to anthropogenic activities. Whole-genome datasets allow for improved population and species delimitation, which – prior to this study – were lacking for Albula species. Results: We generated a high-quality genome assembly of an A. glossodonta individual from Hawai'i, USA. The assembled contigs had an NG50 of 4.75 Mbp and a maximum length of 28.2 Mbp. Scaffolding yielded an NG50 of 14.49 Mbp, with the longest scaffold reaching 42.29 Mbp. Half the genome was contained in 20 scaffolds. The genome was annotated with 28.3 K protein-coding genes. We then analyzed 66 A. glossodonta individuals and 38,355 SNP loci to evaluate population genetic connectivity between six atolls in Seychelles and Mauritius in the Western Indian Ocean. We observed genetic homogeneity between atolls in Seychelles and evidence of reduced gene flow between Seychelles and Mauritius. The South Equatorial Current could be one mechanism limiting gene flow of A. glossodonta populations between Seychelles and Mauritius. Conclusions: Quantifying the spatial population structure of widespread fishery species such as bonefishes is necessary for effective transboundary management and conservation. This population genomic dataset mapped to a high-quality genome assembly allowed us to discern shallow population structure in a widespread species in the Western Indian Ocean. The genome assembly will be useful for addressing the taxonomic uncertainties of bonefishes globally.
The aim to sequence, catalog, and characterize the genomes of all of Earth’s eukaryotic biodiversity is the shared mission of many ongoing large scale biodiversity genomics initiatives. Reference genomes of our global flora and fauna have the potential to inform a broad range of major issues facing both biodiversity and humanity, such as the impact of climate change, the conservation of endangered species and ecosystems, public health crises, and the preservation and enhancement of ecosystem services. Biodiversity is dramatically declining: 28% of species being assessed by IUCN are threatened with extinction and recent reports suggest that a transformative change is needed to conserve and protect what remains. To provide a collective and global genomic response to the biodiversity crisis, many biodiversity genomics initiatives have come together, creating a network of networks under the Earth BioGenome Project. This network seeks to expedite the creation of an openly available, “public good” encyclopedia of high-quality eukaryotic reference genomes, in hope that by advancing our basic understanding of nature it can lead to the transformational scientific developments needed to conserve and protect global biodiversity. Key to completing this ambitious encyclopedia of reference genomes, is the ability to responsibly, ethically, legally, and equitably access and use samples from all of the eukaryotic species across the planet, including those that are under the custodianship of Indigenous Peoples and Local Communities. Here, the biodiversity genomics community is subject to the provisions codified in international, national, and local legislations but also customary community policies and protocols. We propose a framework to support biodiversity genomic researchers, projects, and initiatives in building trustworthy and sustainable partnerships with communities, providing minimum recommendations on how to access, utilize, preserve, handle, share, analyze and communicate samples, genomics data and associated Traditional Knowledge obtained from, and in partnership with, Indigenous Peoples and Local Communities across the data-lifecycle.
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