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De novo genome assembly of the marine teleost, bluefin trevally (Caranx melampygus)

The bluefin trevally, Caranx melampygus, also known as the bluefin kingfish or bluefin jack, is known for its remarkable, bright-blue fins. This marine teleost is a widely prized sportfish, but few resources have been devoted to the genomics and conservation of this species because it is not targete...

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Autores principales: Pickett, Brandon D, Glass, Jessica R, Ridge, Perry G, Kauwe, John S K
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8473972/
https://www.ncbi.nlm.nih.gov/pubmed/34568914
http://dx.doi.org/10.1093/g3journal/jkab229
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author Pickett, Brandon D
Glass, Jessica R
Ridge, Perry G
Kauwe, John S K
author_facet Pickett, Brandon D
Glass, Jessica R
Ridge, Perry G
Kauwe, John S K
author_sort Pickett, Brandon D
collection PubMed
description The bluefin trevally, Caranx melampygus, also known as the bluefin kingfish or bluefin jack, is known for its remarkable, bright-blue fins. This marine teleost is a widely prized sportfish, but few resources have been devoted to the genomics and conservation of this species because it is not targeted by large-scale commercial fisheries. Population declines from recreational and artisanal overfishing have been observed in Hawai‘i, USA, resulting in both an interest in aquaculture and concerns about the long-term conservation of this species. Most research to-date has been performed in Hawai‘i, raising questions about the status of bluefin trevally populations across its Indo-Pacific range. Genomic resources allow for expanded research on stock status, genetic diversity, and population demography. We present a high quality, 711 Mb nuclear genome assembly of a Hawaiian bluefin trevally from noisy long-reads with a contig NG50 of 1.2 Mb and longest contig length of 8.9 Mb. As measured by single-copy orthologs, the assembly was 95% complete, and the genome is comprised of 16.9% repetitive elements. The assembly was annotated with 33.1 K protein-coding genes, 71.4% of which were assigned putative functions, using RNA-seq data from eight tissues from the same individual. This is the first whole-genome assembly published for the carangoid genus Caranx. Using this assembled genome, a multiple sequentially Markovian coalescent model was implemented to assess population demography. Estimates of effective population size suggest population expansion has occurred since the Late Pleistocene. This genome will be a valuable resource for comparative phylogenomic studies of carangoid fishes and will help elucidate demographic history and delineate stock structure for bluefin trevally populations throughout the Indo-Pacific.
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spelling pubmed-84739722021-09-27 De novo genome assembly of the marine teleost, bluefin trevally (Caranx melampygus) Pickett, Brandon D Glass, Jessica R Ridge, Perry G Kauwe, John S K G3 (Bethesda) Genome Report The bluefin trevally, Caranx melampygus, also known as the bluefin kingfish or bluefin jack, is known for its remarkable, bright-blue fins. This marine teleost is a widely prized sportfish, but few resources have been devoted to the genomics and conservation of this species because it is not targeted by large-scale commercial fisheries. Population declines from recreational and artisanal overfishing have been observed in Hawai‘i, USA, resulting in both an interest in aquaculture and concerns about the long-term conservation of this species. Most research to-date has been performed in Hawai‘i, raising questions about the status of bluefin trevally populations across its Indo-Pacific range. Genomic resources allow for expanded research on stock status, genetic diversity, and population demography. We present a high quality, 711 Mb nuclear genome assembly of a Hawaiian bluefin trevally from noisy long-reads with a contig NG50 of 1.2 Mb and longest contig length of 8.9 Mb. As measured by single-copy orthologs, the assembly was 95% complete, and the genome is comprised of 16.9% repetitive elements. The assembly was annotated with 33.1 K protein-coding genes, 71.4% of which were assigned putative functions, using RNA-seq data from eight tissues from the same individual. This is the first whole-genome assembly published for the carangoid genus Caranx. Using this assembled genome, a multiple sequentially Markovian coalescent model was implemented to assess population demography. Estimates of effective population size suggest population expansion has occurred since the Late Pleistocene. This genome will be a valuable resource for comparative phylogenomic studies of carangoid fishes and will help elucidate demographic history and delineate stock structure for bluefin trevally populations throughout the Indo-Pacific. Oxford University Press 2021-07-14 /pmc/articles/PMC8473972/ /pubmed/34568914 http://dx.doi.org/10.1093/g3journal/jkab229 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Genome Report
Pickett, Brandon D
Glass, Jessica R
Ridge, Perry G
Kauwe, John S K
De novo genome assembly of the marine teleost, bluefin trevally (Caranx melampygus)
title De novo genome assembly of the marine teleost, bluefin trevally (Caranx melampygus)
title_full De novo genome assembly of the marine teleost, bluefin trevally (Caranx melampygus)
title_fullStr De novo genome assembly of the marine teleost, bluefin trevally (Caranx melampygus)
title_full_unstemmed De novo genome assembly of the marine teleost, bluefin trevally (Caranx melampygus)
title_short De novo genome assembly of the marine teleost, bluefin trevally (Caranx melampygus)
title_sort de novo genome assembly of the marine teleost, bluefin trevally (caranx melampygus)
topic Genome Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8473972/
https://www.ncbi.nlm.nih.gov/pubmed/34568914
http://dx.doi.org/10.1093/g3journal/jkab229
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