Dataset Information

Whole-genome sequencing of leopard coral grouper ( Plectropomus leopardus) and exploration of regulation mechanism of skin color and adaptive evolution.

ABSTRACT: Leopard coral groupers belong to the Plectropomus genus of the Epinephelidae family and are important fish for coral reef ecosystems and the marine aquaculture industry. To promote future research of this species, a high-quality chromosome-level genome was assembled using PacBio sequencing and Hi-C technology. A 787.06 Mb genome was assembled, with 99.7% (784.57 Mb) of bases anchored to 24 chromosomes. The leopard coral grouper genome size was smaller than that of other groupers, which may be related to its ancient status among grouper species. A total of 22 317 protein-coding genes were predicted. This high-quality genome of the leopard coral grouper is the first genomic resource for Plectropomus and should provide a pivotal genetic foundation for further research. Phylogenetic analysis of the leopard coral grouper and 12 other fish species showed that this fish is closely related to the brown-marbled grouper. Expanded genes in the leopard coral grouper genome were mainly associated with immune response and movement ability, which may be related to the adaptive evolution of this species to its habitat. In addition, we also identified differentially expressed genes (DEGs) associated with carotenoid metabolism between red and brown-colored leopard coral groupers. These genes may play roles in skin color decision by regulating carotenoid content in these groupers.

SUBMITTER: Yang Y

PROVIDER: S-EPMC7231471 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:An 8-week feeding trial was conducted to evaluate the effects of dietary lysine level on growth performance and protein metabolism of juvenile leopard coral grouper (Plectropomus leopardus) and thereby obtained the optimal dietary lysine requirement of P. leopardus. Six isoproteic and isolipidic experimental diets were formulated to contain 1.10%, 1.69%, 2.30%, 3.08%, 3.56%, and 4.36% lysine of diets, respectively. Each diet was assigned at random to triplicate groups of 25 juveniles (initial mean weight is 10.57 g) per tank in a flow-through mariculture system maintained at 27-30°C. Dietary inclusion of 2.30-3.08% lysine improved the weight gain rate (WGR) and specific growth rate and decreased the feed conversion ratio (FCR) of juveniles (P < 0.05). The intestinal digestive enzyme (trypsin, amylase, and lipase) activities were overall enhanced by dietary inclusion of 3.08-3.56% lysine (P < 0.05). The mammalian target of rapamycin (mTOR) signaling pathway was activated in fish fed diets with 1.69-2.30% lysine by upregulating the relative expression levels of hepatic TOR and S6K1 (p70 ribosomal protein S6 kinase 1) but downregulating the relative expression level of hepatic 4E-BP2 (eIF4E-binding protein 2). Conversely, the amino acid response signaling pathway was inhibited in fish fed diet with 2.30% lysine by downregulating the relative expression levels of hepatic GCN2 (general control nondepressible 2), ATF3 (activating transcription factor 3), ATF4a (activating transcription factor 4a), and ATF4b (activating transcription factor 4b). Additionally, dietary 1.69-3.08% lysine enhanced the plasma total protein level and hepatic lysine α-ketoglutarate reductase activity but depressed the blood urea nitrogen level and hepatic adenosine monophosphate deaminase activity (P < 0.05). Moreover, dietary 3.08% lysine increased the contents of whole-body crude protein and total amino acids, while 1.69%-4.36% lysine depressed the whole-body lipid content (P < 0.05). These results indicated that optimal dietary lysine increased the digestive enzyme activities, promoted protein synthesis but depressed protein degradation, and thereby improved the growth performance of P. leopardus. Based on the second-order polynomial model, the optimal lysine requirement of juvenile P. leopardus for WGR, FCR, and lysine deposition was 2.60%-2.97% of diets (4.91%-5.60% of dietary protein).

Project description:Published data were used to model the transfer of ciguatoxins (CTX) across three trophic levels of a marine food chain on the Great Barrier Reef (GBR), Australia, to produce a mildly toxic common coral trout (Plectropomus leopardus), one of the most targeted food fishes on the GBR. Our model generated a 1.6 kg grouper with a flesh concentration of 0.1 µg/kg of Pacific-ciguatoxin-1 (P-CTX-1 = CTX1B) from 1.1 to 4.3 µg of P-CTX-1 equivalents (eq.) entering the food chain from 0.7 to 2.7 million benthic dinoflagellates (Gambierdiscus sp.) producing 1.6 pg/cell of the P-CTX-1 precursor, P-CTX-4B (CTX4B). We simulated the food chain transfer of ciguatoxins via surgeonfishes by modelling Ctenochaetus striatus feeding on turf algae. A C. striatus feeding on ≥1000 Gambierdiscus/cm2 of turf algae accumulates sufficient toxin in <2 days that when preyed on, produces a 1.6 kg common coral trout with a flesh concentration of 0.1 µg/kg P-CTX-1. Our model shows that even transient blooms of highly ciguatoxic Gambierdiscus can generate ciguateric fishes. In contrast, sparse cell densities of ≤10 Gambierdiscus/cm2 are unlikely to pose a significant risk, at least in areas where the P-CTX-1 family of ciguatoxins predominate. The ciguatera risk from intermediate Gambierdiscus densities (~100 cells/cm2) is more difficult to assess, as it requires feeding times for surgeonfish (~4-14 days) that overlap with turnover rates of turf algae that are grazed by herbivorous fishes, at least in regions such as the GBR, where stocks of herbivorous fishes are not impacted by fishing. We use our model to explore how the duration of ciguatoxic Gambierdiscus blooms, the type of ciguatoxins they produce, and fish feeding behaviours can produce differences in relative toxicities between trophic levels. Our simple model indicates thresholds for the design of risk and mitigation strategies for ciguatera and the variables that can be manipulated to explore alternate scenarios for the accumulation and transfer of P-CTX-1 analogues through marine food chains and, potentially, for other ciguatoxins in other regions, as more data become available.

Dataset Information

Whole-genome sequencing of leopard coral grouper ( Plectropomus leopardus) and exploration of regulation mechanism of skin color and adaptive evolution.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets