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.

Population structure of blackfin tuna (Thunnus atlanticus) in the western Atlantic Ocean inferred from microsatellite loci.

The blackfin tuna, Thunnus atlanticus, is a small tropical tuna exploited by recreational and commercial fisheries in various parts of its range. Information on stock structure is needed to develop management plans for this species but is currently lacking. In this work, 470 blackfin tuna from nine geographic populations were assayed at 13 homologous microsatellite markers to provide a first assessment of stock structure across the species range. The overall divergence among locality samples was very low (overall FST = 0.0004) indicating high connectivity of blackfin tuna across their range. No clear grouping of localities in differentiated units was inferred but structuring followed a weak isolation by distance pattern (r = 0.16, P = 0.032). Pairwise exact tests and spatial analysis of molecular variance suggested divergence of the sample collected offshore Baía Formosa (Brazil) possibly reflecting reproductive isolation of Brazilian populations from those in the Caribbean region and further north. Further study of the status of Brazilian populations and the transition between this region and the Caribbean is warranted. Cryptic subdivision within the Northern Hemisphere part of the range is possible and should be evaluated using increased marker density and a more comprehensive geographic coverage.

Community composition and antibiotic resistance of bacteria in bottlenose dolphins Tursiops truncatus - Potential impact of 2010 BP Oil Spill.

Aquatic contamination, oil spills in particular, could lead to the accumulation of antibiotic resistance by promoting selection for and/or transfer of resistance genes. However, there have been few studies on antibiotic resistance in marine mammals in relation to environmental disturbances, specifically oil contaminations. Here we initiated a study on antibiotic resistance bacteria in bottlenose dolphins Tursiops truncatus in relation to oil contamination following the 2010 BP Oil Spill in the northern Gulf of Mexico. Bacterial communities and antibiotic resistance prevalence one year after the 2010 BP Oil Spill were compared between Barataria Bay (BB) and Sarasota Bay (SB) by applying the rarefaction curve method, and (generalized) linear mixed models. The results showed that the most common bacteria included Vibrio, Shewanella, Bacillus and Pseudomonas. The prevalence of antibiotic resistance was high in the bacterial isolates at both bays. Though bacterial diversity did not differ significantly among water or dolphin samples, and antibiotic resistance did not differ significantly among water samples between the two bays, antibiotic resistance and multi-drug resistance in dolphin samples was significantly higher in the BB than in the SB, mainly attributed to the resistance to E, CF, FEP and SXT. We also found sulfamethoxazole-trimethoprim-resistant Stenotrophomonas maltophilia the first time in the natural aquatic environment. The higher antibiotic resistance in the dolphins in BB is likely attributed to 2010 BP Oil Spill as we expected SB, a more urbanized bay area, would have had higher antibiotic resistance based on the previous studies. The antibiotic resistance data gathered in this research will fill in the important data gaps and contributes to the broader spatial-scale emerging studies on antibiotic resistance in aquatic environments.

Development and characterization of genomic resources for a non-model marine teleost, the red snapper (Lutjanus campechanus, Lutjanidae): Construction of a high-density linkage map, anchoring of genome contigs and comparative genomic analysis.

The red snapper Lutjanus campechanus is an exploited reef fish of major economic importance in the Gulf of Mexico region. Studies of genome wide genetic variation are needed to understand the structure of wild populations and develop breeding programs for aquaculture but interpretation of these genome scans is limited by the absence of reference genome. In this work, the first draft of a reference genome was developed and characterized for the red snapper. P-454 and Illumina sequencing were conducted to produce paired-end reads that were assembled into reference contigs and scaffolds. The current assembly spans over 770 Mb, representing an estimated 69% of the red snapper genome in 67,254 scaffolds (N50 = 16,803 bp). The genome contigs were applied to map double digest Restriction-Site Associated DNA Tags and characterize Single Nucleotide Polymorphisms (SNPs) in five outbred full-sib families. The identified SNPs and 97 microsatellite loci were used to generate a high-density linkage map that includes 7,420 markers distributed across 24 linkage groups and spans 1,346.64 cM with an average inter-marker distance of 0.18 cM. Sex-specific maps revealed a 1.10:1 female to male map length ratio. A total of 4,422 genome contigs (10.5% of the assembly) were anchored to the map and used in a comparative genomic analysis of the red snapper and two model teleosts. Red snapper showed a high degree of chromosome level syntenic conservation with both medaka and spotted green puffer and a near one to one correspondence between the 24 red snapper linkage groups and corresponding medaka chromosomes was observed. This work established the first draft of a reference genome for a lutjanid fish. The obtained genomic resources will serve as a framework for the interpretation of genome scans during studies of wild populations and captive breeding programs.