The yellowtail (Seriola quinqueradiata) genome and transcriptome atlas of the digestive tract

Morphological and Molecular Functional Evidence of the Pharyngeal Sac in the Digestive Tract of Silver Pomfret, Pampus argenteus

The pharyngeal sac is a comparatively rare organ in the digestive tract among teleost fishes. However, our understanding of this remarkable organ in the silver pomfret (Pampus argenteus) is limited. In the present study, we examined the various morphological and histological characteristics of the pharyngeal sac using histochemical techniques and electron microscopy. The pharyngeal sac showed unique characteristics such as well-developed muscular walls, weakly keratinized epithelium, numerous goblet cells, and needle-like processes on the papillae. The porous cavity of the papillae contained numerous adipocytes and was tightly enveloped by type I collagen fibers. These structures might provide mechanical protection and excellent biomechanical properties for grinding and shredding prey. A comparison of gene expression levels between the pharyngeal sac and esophagus using RNA-seq showed that phenotype-associated genes (epithelial genes and muscle genes) were upregulated, whereas genes related to nutrient digestion and absorption were downregulated in the pharyngeal sac. These results support the role of the pharyngeal sac in shredding and predigesting food. Overall, these findings provide a clearer understanding of the pharyngeal sac morphology and explain the morphological adaptations of the digestive tract for feeding on gelatinous prey. To our knowledge, this is the first report on pharyngeal sac gene expression in P. argenteus.

The genome of a giant (trevally): Caranx ignobilis

Caranx ignobilis, commonly known as giant kingfish or giant trevally, is a large, reef-associated apex predator. It is a prized sportfish, targeted throughout its tropical and subtropical range in the Indian and Pacific Oceans. It also gained significant interest in aquaculture due to its unusual freshwater tolerance. Here, we present a draft assembly of the estimated 625.92 Mbp nuclear genome of a C. ignobilis individual from Hawaiian waters, which host a genetically distinct population. Our 97.4% BUSCO-complete assembly has a contig NG50 of 7.3 Mbp and a scaffold NG50 of 46.3 Mbp. Twenty-five of the 203 scaffolds contain 90% of the genome. We also present noisy, long-read DNA, Hi-C, and RNA-seq datasets, the latter containing eight distinct tissues and can help with annotations and studies of freshwater tolerance. Our genome assembly and its supporting data are valuable tools for ecological and comparative genomics studies of kingfishes and other carangoid fishes.

The chromosome-level genome assembly of the Japanese yellowtail jack Seriola aureovittata provides insights into genome evolution and efficient oxygen transport

Fishes of the genus Seriola are widely farmed and highly valued in global aquaculture production. To further understand their economically important traits and help improve aquaculture product quality and sustainability, we performed a chromosome-level genome construction for Seriola aureovittata. Combining two technologies, PacBio and BGISEQ-500, we assembled 649.86 Mb S. aureovittata genome sequences with a contig N50 of 22.21 Mb, and 98% of BUSCO genes were detected in total. The initial assembly was then further scaffolded into 24 pseudochromosomes using Hi-C data, indicating the high quality of the genome. Genome evolution analysis showed that many genes related to fatty acid metabolism and oxygen binding, or transport were expanded, which provided insights into the metabolic characteristics of fatty acids and efficient oxygen transport. Based on the genome data, we confirmed the evolutionary relationship of S. aureovittata, S. dorsalis and S. lalandi and identified chr12 as the putative sex chromosome of S. aureovittata. Our chromosome-level genome assembly provides a genetic foundation for the phylogenetic and taxonomic investigation of different Seriola species. Moreover, the genome will provide an important genomic resource for further biological and aquaculture studies of S. aureovittata.

Linking Pedigree Information to the Gene Expression Phenotype to Understand Differential Family Survival Mechanisms in Highly Fecund Fish: A Case Study in the Larviculture of Pacific Bluefin Tuna

Mass spawning in fish culture often brings about a marked variance in family size, which can cause a reduction in effective population sizes in seed production for stock enhancement. This study reports an example of combined pedigree information and gene expression phenotypes to understand differential family survival mechanisms in early stages of Pacific bluefin tuna, Thunnus orientalis, in a mass culture tank. Initially, parentage was determined using the partial mitochondrial DNA control region sequence and 11 microsatellite loci at 1, 10, 15, and 40 days post-hatch (DPH). A dramatic proportional change in the families was observed at around 15 DPH; therefore, transcriptome analysis was conducted for the 15 DPH larvae using a previously developed oligonucleotide microarray. This analysis successfully addressed the family-specific gene expression phenotypes with 5739 differentially expressed genes and highlighted the importance of expression levels of gastric-function-related genes at the developmental stage for subsequent survival. This strategy demonstrated herein can be broadly applicable to species of interest in aquaculture to comprehend the molecular mechanism of parental effects on offspring survival, which will contribute to the optimization of breeding technologies.

De novo genome assembly of the marine teleost, bluefin trevally (Caranx melampygus)

The bluefin trevally, Caranx melampygus, also known as the bluefin kingfish or bluefin jack, is known for its remarkable, bright-blue fins. This marine teleost is a widely prized sportfish, but few resources have been devoted to the genomics and conservation of this species because it is not targeted by large-scale commercial fisheries. Population declines from recreational and artisanal overfishing have been observed in Hawai'i, USA, resulting in both an interest in aquaculture and concerns about the long-term conservation of this species. Most research to-date has been performed in Hawai'i, raising questions about the status of bluefin trevally populations across its Indo-Pacific range. Genomic resources allow for expanded research on stock status, genetic diversity, and population demography. We present a high quality, 711 Mb nuclear genome assembly of a Hawaiian bluefin trevally from noisy long-reads with a contig NG50 of 1.2 Mb and longest contig length of 8.9 Mb. As measured by single-copy orthologs, the assembly was 95% complete, and the genome is comprised of 16.9% repetitive elements. The assembly was annotated with 33.1 K protein-coding genes, 71.4% of which were assigned putative functions, using RNA-seq data from eight tissues from the same individual. This is the first whole-genome assembly published for the carangoid genus Caranx. Using this assembled genome, a multiple sequentially Markovian coalescent model was implemented to assess population demography. Estimates of effective population size suggest population expansion has occurred since the Late Pleistocene. This genome will be a valuable resource for comparative phylogenomic studies of carangoid fishes and will help elucidate demographic history and delineate stock structure for bluefin trevally populations throughout the Indo-Pacific.

Cross-species Exon Capture and Whole Exome Sequencing: Application, Utility and Challenges for Genomic Resource Development in Non-model Species

Comprehending the genetic architecture of complex traits has many applications in evolution, ecology, conservation biology and plant and animal production systems. Underlying research questions in these fields are diverse species that often have limited genetic information available. In aquaculture, for example, genetic progress has been slow in many species due to a lack in such genetic information. In this study, zebrafish (as a well-studied model species) was used in cross-species transfer to develop genomic resources and identify candidate genes underling growth differentials in dusky kob. Dusky kob is a Sciaenid finfish and an emerging aquaculture species. The zebrafish All Exon Predesigned Probe-set capture protocol was used to enrich fractionated DNA samples from kob, classified as either large or small, before massive parallel sequencing on the Ion Torrent platform. Although vast quantities of sequence data were generated, only about 30% of contigs could be identified as zebrafish homologues. There were numerous species-specific sequences and inconsistent coverage of sequencing products across samples, likely due to non-specific binding of the probe-set as a result of the evolutionary divergence between zebrafish and kob. Nonetheless, more than 55,000 SNPs could be reliably identified and genotyped to the individual level. Using SNP genotypic divergence estimates, between large and small cohorts, a number of candidate genes associated with growth was also identified for future investigation. These findings contribute to the growing body of evidence demonstrating the utility of a cross-species capture approach in the development of important genomic resources for understanding traits of interest in species without reference genomes.

Intestinal Transcriptome Analysis Highlights Key Differentially Expressed Genes Involved in Nutrient Metabolism and Digestion in Yellowtail Kingfish (Seriola lalandi) Fed Terrestrial Animal and Plant Proteins

This study investigated the effects of dietary terrestrial animal and plant proteins on the intestinal transcriptomes of yellowtail kingfish (YTK), Seriola lalandi, an ecologically and economically important marine species in Australia. Five diets containing fish meal (FM), poultry by-product meal (PBM), blood meal (BLM), faba bean meal (FBM) and corn gluten meal (CGM) were formulated and fed over a period of 4 weeks. The Illumina RNA-sequencing (RNA-Seq) results identified a suite of differentially expressed genes involved in nutrient metabolism and protein digestion pathways, reinforced by quantitative polymerase chain reaction (qPCR) results. These findings provide molecular support to the notion that PBM and FBM are useful raw materials in commercial diets for YTK. Using the same evidence, we have demonstrated that BLM and CGM may be less useful and their incorporation into commercial aquafeeds for this species should be done cautiously. The differentially expressed genes showed a subtle difference and high correlation with apparent nutrient digestibility of raw materials. Further, our results indicate that transcriptome profiling provides a useful tool to evaluate alternative protein sources for use in aquaculture feeds.

Effects of short-term exercise on food intake and the expression of appetite-regulating factors in goldfish

In mammals, growing evidence indicates that exercise affects food intake, metabolism and the expression and blood levels of appetite regulators. In this study, we examined the effects of short-term (30 min, at low and high water flow) exercise on food intake, glucose levels and the expressions of appetite regulators in goldfish hypothalamus (irisin, orexin, CART, leptin), intestine (CCK, PYY, proglucagon/GLP-1), muscle (irisin) and liver (leptin), of brain-derived neurotrophic factor (BDNF) in brain, interleukin-6 (IL6) in muscle and hypothalamus, and major metabolic enzymes, the glycolytic enzyme glucokinase (GCK) and its regulatory protein (GCKR) in liver, the lipolytic enzyme lipoprotein lipase in intestine and muscle, and trypsin in intestine. Fish submitted to high flow exercise had a lower post-exercise food intake compared to control fish but no differences were seen in glucose levels between groups. Exercise induced an increase in hypothalamic expression levels of CART, IL6 and BDNF, but not orexin, irisin, CRF, leptin and NPY. High flow exercise induced an increase in intestine CCK, PYY and GLP-1, and muscle irisin and IL-6 expression levels. Exercise had no effects on expression levels of hepatic leptin or any of the metabolic enzymes examined. Our results suggest that, in goldfish, short-term exercise might decrease feeding in part by affecting the expressions of myokines and peripheral, but not central appetite regulators or metabolic enzyme/hormones.