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Genomic resources for the Yellowfin tuna Thunnus albacares

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Abstract

Background

The Yellowfin tuna (Thunnus albacares) is a large tuna exploited by major fisheries in tropical and subtropical waters of all oceans except the Mediterranean Sea. Genomic studies of population structure, adaptive variation or of the genetic basis of phenotypic traits are needed to inform fisheries management but are currently limited by the lack of a reference genome for this species. Here we report a draft genome assembly and a linkage map for use in genomic studies of T. albacares.

Methods and results

Illumina and PacBio SMRT sequencing were used in combination to generate a hybrid assembly that comprises 743,073,847 base pairs contained in 2,661 scaffolds. The assembly has a N50 of 351,587 and complete and partial BUSCO scores of 86.47% and 3.63%, respectively. Double-digest restriction associated DNA (ddRAD) was used to genotype the 2 parents and 164 of their F1 offspring resulting from a controlled breeding cross, retaining 19,469 biallelic single nucleotide polymorphism (SNP) loci. The SNP loci were used to construct a linkage map that features 24 linkage groups that represent the 24 chromosomes of yellowfin tuna. The male and female maps span 1,243.8 cM and 1,222.9 cM, respectively. The map was used to anchor the assembly in 24 super-scaffolds that contain 79% of the yellowfin tuna genome. Gene prediction identified 46,992 putative genes 20,203 of which could be annotated via gene ontology.

Conclusions

The draft reference will be valuable to interpret studies of genome wide variation in T. albacares and other Scombroid species.

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Data availability

The sequencing data obtained during this project (PacBio and Illumina sequences used in assembly, dd-RAD illumine sequencing reads) were uploaded in genbank (Bioproject PRJNA504596). Supplementary Materials (Supplementary Methods and Materials, Supplementary Figs. 1–3) are included as supplementary Materials published with this manuscript. Supplementary File 2 (GO annotations) is uploaded in the Aquila Repository of the University of Southern Mississippi ((https://aquila.usm.edu/datasets/7/).

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Funding

This work was supported by the National Oceanic and Atmospheric Administration Saltonstall-Kennedy program award #NA16NMF4270223.

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Authors and Affiliations

  1. School of Ocean Science and Engineering, The University of Southern Mississippi, Ocean Springs, MS, 39564, USA

    Pavel V. Dimens, Brooke McPeak, Tami E. Hildahl & Eric A. E. Saillant

  2. Bioinformatic Solutions LLC, Sheridan, WY, 82801, USA

    Kenneth L. Jones

  3. Inter-American Tropical Tuna Commission, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA

    Daniel Margulies, Vernon Scholey & Susana Cusatti

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  1. Pavel V. Dimens
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Contributions

Funding acquisition: ES; Study design: ES, PD; Sample acquisition: DM, SC, VS, ES; Data analysis and interpretations: PD, ES; Manuscript drafting: PD, ES; Manuscript reviewing: All authors. All authors read and approved the final manuscript.

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Correspondence to Eric A. E. Saillant.

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The authors have no relevant financial or non-financial interests to disclose.

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Protocols employed in this study were approved by the Institutional Animal Care and Use Committee at the University of Southern Mississippi (protocol #1710301).

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Dimens, P.V., Jones, K.L., Margulies, D. et al. Genomic resources for the Yellowfin tuna Thunnus albacares. Mol Biol Rep 51, 232 (2024). https://doi.org/10.1007/s11033-023-09117-6

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