| Title: |
De novo genome assembly of the marine teleost, bluefin trevally ( Caranx melampygus) |
| Authors: |
Pickett, Brandon D; Glass, Jessica R; Ridge, Perry G; Kauwe, John S K |
| Contributors: |
Whitehead, A |
| Source: |
G3 Genes|Genomes|Genetics ; volume 11, issue 10 ; ISSN 2160-1836 |
| Publisher Information: |
Oxford University Press (OUP) |
| Publication Year: |
2021 |
| 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. |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| DOI: |
10.1093/g3journal/jkab229 |
| DOI: |
10.1093/g3journal/jkab229/39721299/jkab229.pdf |
| Availability: |
https://doi.org/10.1093/g3journal/jkab229; http://academic.oup.com/g3journal/advance-article-pdf/doi/10.1093/g3journal/jkab229/39721299/jkab229.pdf; http://academic.oup.com/g3journal/article-pdf/11/10/jkab229/40520271/jkab229.pdf |
| Rights: |
http://creativecommons.org/licenses/by/4.0/ |
| Accession Number: |
edsbas.4D70E150 |
| Database: |
BASE |