Chromosome-Scale Genome Assembly and Transcriptome Assembly of Kawakawa Euthynnus affinis; A Tuna-Like Species.

Abstract

Kawakawa Euthynnus affinis, also known as eastern little tuna or mackerel tuna, is a species of tuna (Thunnini tribe, subgroup Pelagiaria clade) (Sanciangco et al., 2016). Tuna includes 15 species: eight of genus Thunnus (true tuna) and seven “tuna-like” of four genera: Allothunnus, Auxis, Euthynnus, and Katsuwonus. E. affinis is widely distributed throughout the tropical and subtropical waters of the continental shelf areas of the Indo-Pacific region (Collette, 2001). The fish reaches a length of 45–60 cm and matures at approximately 3 years of age. It inhabits almost exclusively the upper layers of the ocean (Bernal et al., 2017) and feeds mainly on small pelagic fish (Griffiths et al., 2009). E. affinis makes up a substantial proportion of the commercial and artisanal fishery in many countries of the Indo-Pacific region. The meat of E. affinis is of high quality (Mukundan et al., 1979) with a comparatively high level of docosahexaenoic acid (Saito et al., 1999), but deteriorates rapidly if not properly handled (Mukundan et al., 1979). E. affinis exhibits the swimming mechanics of true tunas (Donley and Dickson, 2000) but has no swim bladder and differs from true tunas in red muscle distribution, allometry, and vascular anatomy (Bernal et al., 2017). The ability to maintain an elevated temperature in eye, brain, and red muscle has been suggested for the genus Euthynnus (Dickson et al., 2000), but reports specific to E. affinis are lacking. Compared to true tunas, E. affinis has received scant attention from researchers, and little is known about its biology and physiology. This is likely to change, as E. affinis has recently become of interest in marine aquaculture. E. affinis is the second tuna species whose full-life cycle culture in captivity has been developed so far, including spawning, egg collection, incubation, larval rearing, and grow-out to marketable size (Yazawa et al., 2015, 2016). Aquaculture in general is currently facing significant challenges to increasing production while maintaining sustainability (Bridson et al., 2020). Genetic improvement, via selective breeding and genetic engineering, is a major focus of research and can yield rapid benefits to efficient production in fish farming (Lu and Luo, 2020). To these ends, a high-quality species genome assembly is critical. Despite recent advances in sequencing technologies and genomics that, in addition to basic fish science (Lien et al., 2016; Hughes et al., 2018; Yuan et al., 2018; Du et al., 2020), have applications to aquaculture practices (Lu and Luo, 2020) and fisheries (Benestan, 2020), genomic information of tuna species is limited. To date, the genomes of only three tuna species are available in the public repositories, none of which are assembled to chromosome level. This situation exists within the entire Pelagiaria clade that, along with tuna, includes the economically important mackerel (Scombrini tribe) and bonito (Sardini tribe). Here, we report the chromosome-level genome assembly of kawakawa E. affinis (NCBI:txid8227). To our knowledge, this is the first available chromosome-level assembly within the Pelagiaria clade. The reported genome assembly is accompanied by transcriptome assembly, genetic linkage map, annotation of transposons, repetitive elements, and 23,059 genes. The dataset provides a solid genome resource not only for further study of E. affinis basic biology and genome-scale selective breeding but also for enhancing both basic and applied research within the Pelagiaria clade.