Golden pompano (Trachinotus ovatus), a marine fish in the Carangidae family, has a wide geographical distribution and adapts to severe environmental rigours. It is also an economically valuable aquaculture fish. To understand the genetic mechanism of adaption to environmental rigours and improve the production in aquaculture, we assembled its genome. By combination of Illumina and Pacbio reads, the obtained genome sequence is 647.5 Mb with the contig N50 of 1.80 Mb and the scaffold N50 of 5.05 Mb. The assembly covers 98.9% of the estimated genome size (655 Mb). Based on Hi-C data, 99.4% of the assembled bases are anchored into 24 pseudo-chromosomes. The annotation includes 21,915 protein-coding genes, in which 95.7% of 2,586 BUSCO vertebrate conserved genes are complete. This genome is expected to contribute to the comparative analysis of the Carangidae family.

The nuclear peroxisome proliferator-activated receptors (PPARs) regulate the transcription of elongases of very long-chain fatty acids (Elovl), which are involved in polyunsaturated fatty acid (PUFA) biosynthesis in mammals. In the present study, we first characterized the function of Elovl5 elongase in Trachinotus ovatus. The functional study showed that ToElovl5 displayed high elongation activity toward C18 and C20 PUFA. To investigate whether PPARαb was a regulator of Elovl5, we also reported the sequence of T. ovatus PPARαb (ToPPARαb). The open reading frame (ORF) sequence encoded 469 amino acids possessing four typical characteristic domains, including an N-terminal hypervariable region, a DNA-binding domain (DBD), a flexible hinge domain and a ligand-binding domain (LBD). Thirdly, promoter activity experiments showed that the region from PGL3-basic-Elovl5-5 (-146 bp to +459 bp) was defined as the core promoter by progressive deletion mutation of Elovl5. Moreover, PPARαb overexpression led to a clear time-dependent enhancement of ToElovl5 promoter expression in HEK 293T cells. Fourth, the agonist of PPARαb prominently increased PPARαb and Elovl5 expression, while PPARαb depletion by RNAi or an inhibitor was correlated with a significant reduction of Elovl5 transcription in T. ovatus caudal fin cells (TOCF). In conclusion, the present study provides the first evidence of the positive regulation of Elovl5 transcription by PPARαb and contributes to a better understanding of the transcriptional mechanism of PPARαb in fish.

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The black tiger shrimp, Penaeus monodon , is important in both fishery and aquaculture and is the second-most widely cultured shrimp species in the world. However, the current strains cannot meet the market needs in various cultural environments, and the genome resources for P. monodon are still lacking. Restriction-site associated DNA sequencing (RADseq) has been widely used in genetic linkage map construction and in quantitative trait loci (QTL) mapping. We constructed a high-density genetic linkage map with RADseq in a full-sib family. This map contained 6524 single nucleotide polymorphisms (SNPs) and 2208 unique loci. The total length was 3275.4 cM, and the genetic distance was estimated to be 1.1 Mb/cM. The sex trait is a dichotomous phenotype, and the same interval was detected as a QTL using QTL mapping and genome-wide association analysis. The most significant locus explained 77.4% of the phenotype variance. The sex locus was speculated to be the same in this species based on the sequence alignments in Mozambique, India, and Hawaii populations. The constructed genetic linkage map provided a valuable resource for QTL mapping, genome assembly, and genome comparison for shrimp. The demonstrated common sex locus is a step closer to locating the underlying gene.

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The elongases of very long-chain fatty acids (Elovls) are responsible for the rate-limiting elongation process in long-chain polyunsaturated fatty acid (LC-PUFA) biosynthesis. The transcription factor, PPARα, regulates lipid metabolism in mammals; however, the detailed mechanism whereby PPARαb regulates Elovls remains largely unknown in fish. In the present study, we report the full length cDNA sequence of Trachinotus ovatus Elovl4a (ToElovl4a), which encodes a 320 amino acid polypeptide that possesses five putative membrane-spanning domains, a conserved HXXHH histidine motif and an ER retrieval signal. Phylogenetic analysis revealed that the deduced protein of ToElovl4a is highly conserved with the Oreochromis niloticus corresponding homologue. Moreover, functional characterization by heterologous expression in yeast indicated that ToElovl4a can elongate C18 up to C20 polyunsaturated fatty acids. A nutritional study showed that the protein expressions of ToElovl4a in the brain and liver were not significantly affected among the different treatments. The region from PGL3-basic-Elovl4a-5 (−148 bp to +258 bp) is defined as the core promoter via a progressive deletion mutation of ToElovl4a. The results from promoter activity assays suggest that ToElovl4a transcription is positively regulated by PPARαb. Mutation analyses indicated that the M2 binding site of PPARαb is functionally important for protein binding, and transcriptional activity of the ToElovl4a promoter significantly decreased after targeted mutation. Furthermore, PPARαb RNA interference reduced ToPPARαb and ToElovl4a expression at the protein levels in a time-dependent manner. In summary, PPARαb may promote the biosynthesis of LC-PUFA by regulating ToElovl4a expression in fish.

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