Genomic resources for the Yellowfin tuna Thunnus albacares.

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.

Effects of elevated CO2 on metabolic rate and nitrogenous waste handling in the early life stages of yellowfin tuna (Thunnus albacares).

Ocean acidification is predicted to have a wide range of impacts on fish, but there has been little focus on broad-ranging pelagic fish species. Early life stages of fish are thought to be particularly susceptible to CO2 exposure, since acid-base regulatory faculties may not be fully developed. We obtained yellowfin tuna (Thunnus albacares) from a captive spawning broodstock population and exposed them to control or 1900 µatm CO2 through the first three days of development as embryos transitioned into yolk sac larvae. Metabolic rate, yolk sac depletion, and oil globule depletion were measured to assess overall energy usage. To determine if CO2 altered protein catabolism, tissue nitrogen content and nitrogenous waste excretion were quantified. CO2 exposure did not significantly impact embryonic metabolic rate, yolk sac depletion, or oil globule depletion, however, there was a significant decrease in metabolic rate at the latest measured yolk sac larval stage (36 h post fertilization). CO2-exposure led to a significant increase in nitrogenous waste excretion in larvae, but there were no differences in nitrogen tissue accumulation. Nitrogenous waste accumulated in embryos as they developed but decreased after hatch, coinciding with a large increase in nitrogenous waste excretion and increased metabolic rate in newly hatched larvae. Our results provide insight into how yellowfin tuna are impacted by increases in CO2 in early development, but more research with higher levels of replication is needed to better understand long-term impacts and acid-base regulatory mechanisms in this important pelagic fish.

Ultraviolet avoidance by embryonic buoyancy control in three species of marine fish.

Pelagic fish embryos are thought to float in or near surface waters for the majority of their development and are presumed to have little to no control over their mobility, rendering these embryos at high risk for damages associated with surface stressors such as ultraviolet radiation (UVR). We recently challenged these long-standing paradigms by characterizing a potential mechanism of stressor avoidance in early-life stage mahi-mahi (Coryphaena hippurus) in which embryos sense external cues, such as UVR, and modify their buoyancy to reduce further exposure. It is unknown whether embryos of other marine fish with pelagic spawning strategies have similar capabilities. To fill this knowledge gap, we investigated buoyancy change in response to UVR in three additional species of marine fish that utilize a pelagic spawning strategy: yellowfin tuna (Thunnus albacares), red snapper (Lutjanus campechanus), and cobia (Rachycentron canadum). Embryos of all three species displayed increased specific gravity and loss of buoyancy after exposures to environmentally relevant doses of UVR, a response that may be ubiquitous to fish with pelagic embryos. To gain further insight into this response, we investigated recovery of buoyancy, oxygen consumption, energy depletion, and photolyase induction in response to UVR exposures in at least one of the three species listed above.

Gonadogenesis and slow proliferation of germ cells in juveniles of cultured yellowfin tuna, Thunnus albacares.

To develop techniques for seedling production of yellowfin tuna, the behavior of primordial germ cells (PGCs) and gonadogenesis were examined at 1-30 days post hatching (dph) using morphometric analysis, histological examination, and in situ hybridization. Immediately after hatching, PGCs were located on the dorsal side of the posterior end of the rectum under the peritoneum of the larvae, and at 3 dph they came into contact with stromal cells. PGCs and stromal cells gradually moved forward from the anus prior to 5 dph. At 7-10 dph, germ cells were surrounded by stromal cells and the gonadal primordia were formed. In individuals collected at 12 dph, PGCs were detected by in situ hybridization using a vasa mRNA probe that is a germ-cell-specific detection marker. The proliferation of germ cells in the gonadal primordia began at 7-10 dph. We observed double the number of germ cells at 30 dph (22 ± 3.2 cells), compared to that at 1 dph (11 ± 2.1 cells). Therefore, based on our data and previous reports, the initial germ cell proliferation of yellowfin tuna is relatively slower than that of other fish species.