Fine-tuning the tuna genome

Updated: Feb 22

Yellowfin tuna Thunnus albacares is a popular recreational and commercial species that has a vital role in global food security. This high value species is more than just seafood. It is a top predator and plays an important role in the marine food chain maintaining an ecosystem balance in the ocean environment.

Photo Description: Yellowfin (Thunnus albacares). Photo Copyright: CSIRO O&A, Australia. Drawing by Roger Swainston.

Also known as ahi, yellowfin are named such because of their – well, you guessed it – yellow fins. Aside from their yellow fins and finlets, they also have yellow to silver belly and metallic dark-blue back. Their bodies are shaped like torpedoes, allowing them to swim fast and continuously. Yellowfin tuna are medium sized yet they are bigger than Albacore and skipjack. The average size of the yellowfin tuna varies but in general they are a big fish. The world record yellowfin tuna was 224cm long and weighed close to 194kg.


Yellowfin tuna are a “highly migratory species”, crossing many national jurisdictions in their life time and being harvested by a range of industrial, artisanal and recreational fisheries. As a result, they require careful consideration, international collaboration and innovative science to support sustainable management. Molecular genetics plays an important role in providing key information to guide sustainable management practices by informing on stock structure of this important species (1, 2).


To help with the population structure, chain of custody and new methods for estimating abundance, such as Close-kin Mark Recapture (3) towards monitoring and management of these globally important fisheries DNA Zoo has been working with Dr. Pierre Feutry and Dr. Peter Grewe, CSIRO Oceans and Atmosphere, Hobart, Australia, to get a chromosome-length assembly genome.

The assembly we share today is based on a draft published by Malmstrøm et al 2017. The draft was scaffolded to 24 chromosomes (see interactive map below) with 132, 467, 299M Hi-C reads generated by DNA Zoo labs using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details!

We gratefully acknowledge the yellowfin tissue sample provided by Gary Heilmann, De Brett Seafood, Mooloolaba, Queensland. The Hi-C work was supported by resources provided by DNA Zoo Australia, The University of Western Australia (UWA), DNA Zoo and CSIRO Oceans and Atmosphere, Hobart, Australia with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.


This genome will facilitate projects examining population genetics of this species providing critical information on population connectivity and stock structure to help guide sustainable management of the species.


The following people contributed to the Hi-C chromosome-length upgrade of the project: Erez Aiden, Olga Dudchenko, Ashling Charles & Parwinder Kaur.


Blog by: Parwinder Kaur, Peter Grewe, Pierre Feutry, Chris Gerbing and Campbell Davies.


Citations

1. Grewe, P. M. and Feutry, P. and Hill, P. L. and Gunasekera, R. M. and Schaefer, K. M. and Itano, D. G. and Fuller, D. W. and Foster, S. D. and Davies, C. R. (2015) Evidence of discrete yellowfin tuna (Thunnus albacores) populations demands rethink of management for this globally important resource. Scientific Reports 5:16916. DOI: 10.1038/srep16916


2. Moorehead, Anne, (2015). Next gen sequencing means a brighter future for yellowfin tuna. ECOS: https://ecos.csiro.au/a-brighter-future-for-yellowfin-tuna/


3. Bravington, Mark V., Peter M. Grewe, and Campbell R. Davies. "Absolute abundance of southern bluefin tuna estimated by close-kin mark-recapture." Nature Communications 7.1 (2016): 1-8.

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