Prediction of the Sex-Associated Genomic Region in Tunas (Thunnus Fishes)

Fish species have a variety of sex determination systems. Tunas (genus Thunnus) have an XY genetic sex determination system. However, the Y chromosome or responsible locus has not yet been identified in males. In a previous study, a female genome of Pacific bluefin tuna (T. orientalis) was sequenced, and candidates for sex-associated DNA polymorphisms were identified by a genome-wide association study using resequencing data. In the present study, we sequenced a male genome of Pacific bluefin tuna by long-read and linked-read sequencing technologies and explored male-specific loci through a comparison with the female genome. As a result, we found a unique region carrying the male-specific haplotype, where a homolog of estrogen sulfotransferase gene was predicted to be encoded. The genome-wide mapping of previously resequenced data indicated that, among the functionally annotated genes, only this gene, named sult1st6y, was paternally inherited in the males of Pacific bluefin tuna. We reviewed the RNA-seq data of southern bluefin tuna (T. maccoyii) in the public database and found that sult1st6y of southern bluefin tuna was expressed in all male testes, but absent or suppressed in the female ovary. Since estrogen sulfotransferase is responsible for the inactivation of estrogens, it is reasonable to assume that the expression of sult1st6y in gonad cells may inhibit female development, thereby inducing the individuals to become males. Thus, our results raise a promising hypothesis that sult1st6y is the sex determination gene in Thunnus fishes or at least functions at a crucial point in the sex-differentiation cascade.

Small scale tuna fisheries profiles in the Indonesia archipelagic waters

Indonesia is one of the largest tuna producers in the world, which contributes 16% to world tuna production. The dominant tuna species catched in Indonesia are Albacore Tuna (Thunnus alalunga), Madidihang/Yellowfin Tuna (T. albacares), Big Eye Tuna (T. obesus) dan Southern Bluefin Tuna (T. maccoyii). The tuna fisheries have contributed significant jobs or livelihood to the coastal communities. Profit and revenue sharing is a common remuneration system found on tuna fisheries though out Indonesia. However, these fishers are vulnerable given their economic and welfare conditions and of usually limited options of others livelihood. Small fishers have limited access to livelihoods, access to finance and access to skills or fishing technology. Therefore, the inclusion of socio-economic performance or indicators into the tuna fisheries management is crucial in Indonesia.

Prevalence and Intensity of Cardicola spp. Infection in Ranched Southern Bluefin Tuna and a Comparison of Diagnostic Methods

The parasitic blood flukes Cardicola forsteri and C. orientalis are an ongoing health concern for Southern Bluefin Tuna Thunnus maccoyii (SBT) ranched in Australia. In this study we compared the effect of treatment, company, and ranching year on blood fluke infections in ranched SBT. SBT were sampled during the 2018 and 2019 ranching seasons from praziquantel (PZQ) treated pontoons and untreated pontoons managed by two companies. Severity of infection was diagnosed by several criteria including adult fluke counts from hearts, egg counts from gill filaments and the use of specific quantitative polymerase chain reaction (qPCR) for detection of C. forsteri and C. orientalis ITS-2 DNA in SBT hearts and gills. PZQ treatment remains highly effective against C. forsteri infection. Prevalence and intensity of Cardicola spp. infection was lower in 2019 than 2018 for Company A in treated pontoons at week 12 and week 17 of ranching, and lower for Company A than Company B in untreated pontoons at month 5 of ranching. Results indicate re-infection may be less likely in the environment near Company A pontoons, and consistent years of treatment may have lowered the parasite load in the environment. qPCR demonstrated higher sensitivity when comparing diagnostic methods for C. forsteri in heart, and higher specificity when comparing diagnostic methods for Cardicola spp. in gills. Continuing to monitor blood fluke infections in ranched SBT can help to detect changes in drug efficacy over time and help industry to develop a best practice for treatment.

Age and Growth of Southern Bluefin Tuna, Thunnus maccoyii, Based on Otolith Microstructure

Age and growth of southern bluefin tuna (SBT, Thunnus maccoyii) were estimated based on otoliths collected by Korean tuna longline vessels in the Atlantic and Indian Oceans from 2015 to 2019. A total of 739 specimens were used to estimate age and growth of SBT, with sizes ranging from 66 to 181 cm in fork length. It was confirmed that the otolith is a suitable aging characteristic for determining SBT age, and otolith annuli can be used as an annual ring. The relationship between fork length (FL) and total weight (W) was W = 7.7e − 05FL2.722 (R2 = 0.874). The von Bertalanffy’s growth parameters estimated from the non-linear method using length-at-age data were L∞ = 170.0 cm, K = 0.200/year, t0 = − 1.615 years, with 95% confidence intervals between 166 and 175 cm for L∞, 0.17–0.23/year for K, and − 2.27 to − 1.09 years for t0 from bootstrapping. The Kimura’s likelihood ratio test results of the models under assumptions of common and different parameters between female and male concluded that the growth of SBT has no difference between genders.

Analisis Filogenetik Ikan Tuna (Thunnus spp.) yang didaratkan di Pelabuhan Benoa, Bali

Tuna is one of the largest fisheries commodities in Indonesia after shrimp and demersal fish. The genus Thunnus is a type of tuna that dominates the international market. The genus Thunnus consisted of seven species of tuna. In some cases, the same morphological character has caused misidentification and data collection on tuna species. Therefore, this study aimed to identify tuna species that are landed at Benoa Harbor and analyzed their phylogenetic relationships. Species identification and phylogenetic analysed in this study used the mtDNA control region locus. The results of this study indicated that there are five tuna species landed at Benoa Harbor, namely yellowfin tuna (T. albacares), longtail tuna (T. tonggol), bigeye tuna (T. obesus), southern bluefin tuna (T. maccoyii), and albacore tuna (T. alalunga). Based on phylogenetic tree reconstruction, all samples were divided into five according to the number of tuna species resulted from molecular identification. Reconstruction of phylogenetic trees is supported by genetic distance between clades has a value of 0.075 - 0.212, with the closest kinship found in yellowfin tuna (T. albacares) with bigeye tuna (T. obesus) and the farthest found in yelowfin tuna (T. albacares) with albacore tuna (T. alalunga).

Fishing Quota and International Obligation: Why Has Indonesia been Indicated as a Non-Compliant State

Indonesia committed to conserving the tuna resources by participating in some RFMOs. From all regional organizations where Indonesia has been joined, the CCSBT is the unique one, due to it governs a single tuna species, which is called Southern Bluefin Tuna. This kind of tuna is essential for Indonesia because it is the world’s most expensive tuna and SBT migrates through Indonesian fisheries management zones and goes even further within the territorial waters, where the SBT spawning area is located. This natural characteristic distinguishes Indonesia from other Parties to CCSBT. Nevertheless, the Country has been dealing with its obligation to comply with national quota allocation. For some fishing season periods, the CCSBT indicated Indonesia as a non-compliant. By applying the qualitative approach, this study considers how Indonesia’s non-compliance has been addressed in fishing for shared fish stocks. The data collection was conducted through semi-structured interviews and legal analysis of law and policy instruments. This method leads the elaboration to reveal domestic factors affecting non-compliance by Indonesia. This study argues, the fisheries legislation should consider the provision concerning fishing for resources under quota system, hence, it will provide sufficient legal base to take enforcement measures towards non-compliance with fishing quota.

A candidate for the sex-determination gene in tunas (Thunnus fishes)

Fish species have a variety of sex determination systems. Tunas (genus Thunnus) have an XY genetic sex-determination system. However, the Y chromosome or responsible locus has not yet been identified in males. In a previous study, a female genome of Pacific bluefin tuna (T. orientalis) was sequenced, and candidates for sex-associated DNA polymorphisms were identified by a genome-wide association study using resequencing data. In the present study, we sequenced a male genome of Pacific bluefin tuna by long-read and linked-read sequencing technologies, and explored male-specific loci through a comparison with the female genome. As a result, we found a unique region carrying the male-specific haplotype, where a homolog of estrogen sulfotransferase gene was predicted to be encoded. The genome-wide mapping of previously resequenced data indicated that, among the functionally annotated genes, only this gene, named sult1st6y, was paternally inherited in the males of Pacific bluefin tuna. We reviewed the RNA-seq data of southern bluefin tuna (T. maccoyii) in the public database and found that sult1st6y of southern bluefin tuna was expressed in all male testes, but absent or suppressed in the female ovary. Since estrogen sulfotransferase is responsible for the inactivation of estrogens, it is reasonable to assume that the expression of sult1st6y in gonad cells may inhibit female development, thereby inducing the individuals to become males. Thus, our results raise a promising hypothesis that sult1st6y is the sex-determination gene in Thunnus fishes, or at least functions at a crucial point in the sex-differentiation cascade.