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

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 proteincoding 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.

Marker-assisted selection of YY supermales from a genetically improved farmed tilapia-derived strain

DEAR EDITOR, Genetically improved farmed tilapia (GIFT)and GIFT-derived strains account for the majority of farmed tilapia worldwide.As male tilapias grow much faster than females,they are often considered more desirable in the aquacultural industry.Sex reversal of females to males using the male sex hormone 17-α-methyltestosterone (MT)is generally used to induce phenotypic males during large-scale production of all male fingerlings.However,the widespread use of large quantities of sex reversal hormone in hatcheries may pose a health risk to workers and ecological threats to surrounding environments. Breeding procedures to produce genetically all-male tilapia with limited or no use of sex hormones are therefore urgently needed.

Role of epithelial-to-mesenchymal transition in the pulmonary fi brosis induced by paraquat in rats

BACKGROUND:This study aims to explore the characteristics of the epithelial-to-mesenchymal transition(EMT)process and its underlying molecular mechanisms in the period of paraquat(PQ)-induced pulmonary fi brosis(PF).METHODS:Picrosirius red staining and collagen volume fraction were utilized to evaluate the pathological changes of PQ-induced PF in rats.Immunohistochemistry,Western blot,and real-time reverse transcriptase-polymerase chain reaction(RT-PCR)were used to measure the protein and gene expression of EMT markers,EMT-associated transcription factors,and regulators of EMT-related pathways,respectively.RESULTS:The collagen deposition in the alveolar septum and increased PF markers were characteristics of pathological changes in PQ-induced PF,reached a peak on day 14 after PQ poisoning,and then decreased on day 21.The protein and gene expression of the fibrosis marker,EMT markers,transcription factors,and regulators of EMT-related signaling pathways signifi cantly increased at diff erent time points after PQ poisoning compared with corresponding controls(P<0.05),and most of them reached a peak on day 14,followed by a decrease on day 21.The gene expression of EMT markers was significantly correlated with PF markers,transcription factors,and regulators of EMT-related signaling pathways(P<0.05).The mRNA expression of transcription factors was signifi cantly correlated with that of TGF-β1 and Smad2(P<0.05 or P<0.01),instead of Wnt2 andβ-catenin(P>0.05).CONCLUSIONS:EMT process plays a role in the PQ-induced PF,in which most PF and EMT markers have a peak phenomenon,and its underlying molecular mechanisms might be determined by further studies.

First identification of two co-existing genome-wide significant sex quantitative trait loci(QTL) in red tilapia using integrative QTL mapping

Red tilapia(Oreochromis spp.)is one of the most popular fish in China due to its bright red appearance,fast growth rate,and strong adaptability.Understanding the sex determination mechanisms is of vital importance for the selection of all-male lines to increase aquacultural production of red tilapia.In this research,the genetic architecture for sex from four mapping populations(n=1090)of red tilapia was analyzed by quantitative trait loci(QTL)-seq,linkage-based QTL mapping,and linkage disequilibrium(LD)-based genome-wide association studies.Two genome-wide significant QTL intervals associated with sex were identified on ChrLG1(22.4-23.9 Mb)and ChrLG23(32.0-35.9 Mb),respectively.The QTL on ChrLG1 was detected in family 1(FAM1),FAM2,and FAM4,and the other QTL on ChrLG23 was detected in FAM3 and FAM4.Four microsatellite markers located within the QTL were successfully developed for marker-assisted selection.Interestingly,three(Ipp,sox14,and amh)of the 12 candidate genes located near or on the two QTL intervals were abundantly expressed in males,while the remaining genes were more highly expressed in females.Seven genes(scly,ube3a,Ipp,gpr17,oca2,cog4,and atp10a)were significantly differentially expressed between the male and female groups.Furthermore,LD block analysis suggested that a cluster of genes on ChrLG23 may participate in regulating sex development in red tilapia.Our study provides important information on the genetic architecture of sex in red tilapia and should facilitate further exploration of sex determination mechanisms in this species.

A genome-wide association study on growth traits in orangespotted grouper(Epinephelus coioides) with RAD-seq genotyping

The orange-spotted grouper, Epinephelus coioides, is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of orange-spotted grouper has never been fully understood. Herein, we performed a genome-wide association study （GWAS） on a natural population of 198 individuals aiming to screen the whole genome of orange-spotted grouper for identification of growth-related loci by restriction-site associated DNA sequencing. In this research, 261,366 single nucleotide polymorphisms （SNPs） were developed, in which 110 SNPs were identified to be correlated with growth and 20 SNPs were further confirmed to be associated with both body weight and total length. From these identified SNPs, we annotated a total of 34 genes, including adgrb2, csnkzal, cers5, co122al, creb5, dndl, dzankl, dnail, npy2r, fat3, lrrk2, lrp5, map3k9, and so on. Among these candidate genes, npy2r （neuropeptide Y receptor Y2） was reported to play a critical role in growth of the orange-spotted grouper. In addition, population structure, principal component analysis, kinship matrix and linkage disequilibrium were examined to verify the accuracy and reliability of our GWAS results. Our data will also provide a valuable genetic resource for further marker-assisted selection program to improve growth quality in groupers.