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Cloning,tissue distribution and effects of fasting on pituitary adenylate cyclase-activating polypeptide in largemouth bass

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Chinese Journal of Oceanology and Limnology 2015年第2期33卷 328-338页

作者：李胜杰韩林强白俊杰马冬梅全迎春樊佳佳姜鹏于凌云 Pearl River fisheries Research Institute Chinese Academy of Fisheries SciencesKey Laboratory of Tropical & Subtropical Fishery Resource Application & CultivationChina Ministry of Agriculture

Pituitary adenylate cyclase activating polypeptide （PACAP） has a wide range of biological functions. We cloned the full-length cDNAs encoding PACAP and PACAP-related peptide （PRP） from the brain of largemouth bass （Micropterus salmoides） and used real-time quantitative PCR to detect PRP- PACAP mRNA expression. The PRP-PACAP cDNA has two variants expressed via alternative splicing： a long form, which encodes both PRP and PACAP, and a short form, which encodes only PACAR Sequence analysis results are consistent with a higher conservation of PACAP than PRP peptide sequences. The expression of PACAP-Iong and PACAP-short transcripts was highest in the forebrain, followed by the medulla, midbrain, pituitary, stomach, cerebellum, intestine, and kidney; however, these transcripts were either absent or were weakly expressed in the muscle, spleen, gill, heart, fatty tissue, and liver. The level of PACAP-short transcript expression was significantly higher than expression of the long transcript in the forebrain, cerebella, pituitary and intestine, but lower than that of the long transcript in the stomach. PA CAP- long and PACAP-short transcripts were first detected at the blastula stage of embryogenesis, and the level of expression increased markedly between the muscular contraction stage and 3 d post hatch （dph）. The expression of PACAP-long and PACAP-short transcripts decreased significantly in the brain following 4 d fasting compared with the control diet group. The down-regulation effect was enhanced as fasting continued. Conversely, expression levels increased significantly after 3 d of re-feeding. Our results suggest that PRP- PA CAP acts as an important factor in appetite regulation in largemouth bass.

关键词： pituitary adenylate cyclase activating polypeptide (PACAP) PACAP-related peptide largemouth bass gene expression fasting

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Chromosome-level genome assembly of the glass catfish(Kryptopterus vitreolus)reveals molecular clues to its transparent phenotype

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Zoological Research 2024年第5期45卷 1027-1036页

作者： Chao Bian Rui-Han Li Zhi-Qiang Ruan Wei-Ting Chen Yu Huang Li-Yue Liu Hong-Ling Zhou Cheong-Meng Chong Xi-Dong Mu Qiong Shi laboratory of Aquatic Genomics College of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdong 518057China key laboratory of Prevention and Control for Aquatic Invasive Alien Species Ministry of Agriculture and Rural AffairsGuangdong Modern.Recreational Fisheries Engineering Technology CenterPearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouGuangdong 510380China Shenzhen key Lab of Marine Genomics Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic AnimalsBGI Academy of Marine SciencesBGI MarineShenzhenGuangdong 518081China CAS key laboratory of Mountain Ecological Restoration and Bioresource Utilization&Ecological Restoration and Biodiversity Conservation key laboratory of Sichuan Province Chengdu Institute of BiologyChinese Academy of SciencesChengduSichuan 610041China School of Life Sciences Jiaying UniversityMeizhouGuangdong 514015China China Zebrafish resource Center National Aquatic Biological Resource CenterState Key Laboratory of Freshwater Ecology and BiotechnologyInstitute of HydrobiologyChinese Academy of ScienceWuhanHubei 430072China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518116China State key laboratory of Quality Research in Chinese Medicine Institute of Chinese Medical SciencesUniversity of MacaoMacaoMacao 999078China Center for Aquatic Genomics College of Life SciencesNeijiang Normal UniversityNeijiangSichuan 641100China

Glass catfish(Kryptopterus vitreolus)are notable in the aquarium trade for their highly transparent body *** transparency is due to the loss of most reflective iridophores and light-absorbing melanophores in the main body,although certain black and silver pigments remain in the face and *** date,however,the molecular mechanisms underlying this transparent phenotype remain largely *** explore the genetic basis of this transparency,we constructed a chromosome-level haplotypic genome assembly for the glass catfish,encompassing 32 chromosomes and 23344 protein-coding genes,using PacBio and Hi-C sequencing technologies and standard assembly and annotation *** revealed a premature stop codon in the putative albinism-related tyrp1b gene,encoding tyrosinase-related protein 1,rendering it a nonfunctional ***,a synteny comparison with over 30 other fish species identified the loss of the endothelin-3(edn3b)gene in the glass catfish *** investigate the role of edn3b,we generated edn3b^(−/−)mutant zebrafish,which exhibited a remarkable reduction in black pigments in body surface stripes compared to wild-type *** findings indicate that edn3b loss contributes to the transparent phenotype of the glass *** high-quality chromosome-scale genome assembly and identification of key genes provide important molecular insights into the transparent phenotype of glass *** findings not only enhance our understanding of the molecular mechanisms underlying transparency in glass catfish,but also offer a valuable genetic resource for further research on pigmentation in various animal species.

关键词： Glass catfish Whole-genome sequencing edn3b−/−mutant Transparent phenotype

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Molecular Characterization and Expression Analysis of Matrix Metalloproteinase 3 in the Asian Yellow Pond Turtle Mauremys mutica

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Asian Herpetological Research 2014年第1期5卷 38-48页

作者： Mi ZHAO Yan SHI Jian ZHAO Xinping ZHU Kunci CHEN Debo PAN Chengqing WEI key laboratory of tropical and subtropical Fishery resource application and cultivation Ministry of AgriculturePearl River Fishery Research Institute Chinese Academic of Fishery Science

Matrix metallopeptidase 3 is a zinc-containing proteinase that participates in tissue remodeling and immune responses. In this study, a cDNA encoding matrix metallopeptidase 3 was isolated and characterized from the Asian yellow pond turtle Mauremys mutica（designated as MaMMP3）. The MaMMP3 cDNA is 1805 bp and consists of a 5＇-untranslated region（UTR） of 56 bp, a 3＇-UTR of 243 bp, and an open reading frame（ORF） of 1506 bp encoding 481 amino acids. Homology analysis of MaMMP3 revealed that the MaMMP3 shared 25%–63% similarity to other known MMP3 sequences. The genomic sequence covers 6007 bp. Comparative analysis of the cDNA sequence revealed that the Asian yellow pond turtle MMP3 has eight exons and seven introns. The phylogenetic tree showed that the MaMMP3 is closely related to Gallus gallus MMP3 and Taeniopygia guttata MMP3. The mRNA expression of the MaMMP3 in normal group without any bacterial challenge could be detected in all studied tissues including kidney, heart, live and spleen, with the highest level in the spleen. The results of immune challenge showed that the expression level of MaMMP3 was up-regulated in the spleen and liver. These results provided an important information for studying the roles of Asian yellow pond turtle MMP3 in immunity further.

关键词： Asian yellow pond turtle Mauremys mutica Serratia marcescens Matrix metallopeptidase 3 Immune responses

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Denitrification potential evaluation of a newly indigenous aerobic denitrifier isolated from largemouth bass Micropterus salmoides culture pond

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Journal of Oceanology and Limnology 2018年第3期36卷 913-925页

作者： WANG Cuicui ZHANG Kai XIE Jun LIU Qigen YU Deguang WANG auangjun YU Ermeng GONG Wangbao LI Zhifei key laboratory of tropical and subtropical Fishery resource application and cultivation Ministry of AgriculturePearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhou 510380China College of fisheries and Life Sciences Shanghai Ocean UniversityShanghai 201306China

This work evaluates the application potential of a new indigenous aerobic denitrifi er, strain Pseudomonas CW-2, isolated from a largemouth bass culture pond. The rate of ammonium-N removal by strain CW-2 was approximately 97% at a DO concentration of 5.2 mg/L. Furthermore, when nitrate and ammonia coexisted, the strain gave priority to assimilating ammonia, and thereafter to denitrifi cation. Under optimal cultivation conditions, citrate and acetate were the carbon resources, C/N was 8, dissolved oxygen was 5.2 mg/L, and pH was 7; the removal rate of ammonium reached nearly 90%. The changing patterns of different bacteria in strain CW-2-treated and the control pond water were also compared. Lower levels of ammonia, nitrite, and phosphates were observed in the treated water as compared with the controls. Meanwhile, phylum-level distributions of the bacterial OTUs revealed that P roteobacteria, Bacteroidetes, Planctomycetes, and N itrospirae continuously changed their relative abundances in relation to carbon and the addition of strain CW-2; this finding implies that the conventional denitrifi cation process was weakened under the ef fects of carbon or the presence of strain CW-2. We propose that strain CW-2 is a promising organism for the removal of ammonium in intensive fish culture systems, according to our evaluations of its denitrifi cation performance.

关键词： aerobic denitrification ammonium removal Micropterus salmoides Pseudomonas CW-2

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Effects of dietary probiotic supplementation on the growth,gut health and disease resistance of juvenile Nile tilapia(Oreochromis niloticus)

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Animal Nutrition 2020年第1期6卷 69-79页

作者： Yun Xia Miao Wang Fengying Gao Maixin Lu Gang Chen key laboratory of tropical&subtropical Fishery resource application&cultivation Ministry of AgriculturePearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhou 510380China College of fisheries Guangdong Ocean UniversityZhanjiang 524025China

This study investigated the effects of the Streptococcus agalactiae antagonizing probiotics Bacillus cereu NY5 and Bacillus subtilis as feed additives for Nile tilapia in terms of growth performance,intestinz health and re sistance to ***.A total of 720 apparently healthy juvenile Nile tilapia(0.20±0.05 g were randomly divided into 4 equal groups with 3 replicates for each *** were fed a basal die(control check group,CK group)supplemented with ***(1 x 108 CFU/g feed,BS group),*** NY5(1 x 10~8 CFU/g feed,BC group),and ***+*** NY5(0.5 x 10~8 CFU/g feed of each probioti BS+BC group)for 6 wk,and the probiotic supplementation groups were then fed the basal diet for 1 w to investigate the gut microbial *** results of this study showed that BS+BC and B treatments significantly increased weight gain(WG),feed conversion ratio(FCR)and *** resistance in Nile tilapia(P<0.05).Gut microvilli length and density and c-type lysozyme(lyzc)gen expression were significantly increased by probiotic supplementation(P<0.05).The results of high throughput sequencing showed that the *** NY5 and ***+*** NY5-supplementei feed resulted in a significant improvement in tilapia autochthonous gut bacterial communities ani had a stimulation effect on a variety of potential probiotics after 6 wk of *** cessation c probiotic administration for 1 wk,the gut bacteria of the fish in the BS+BC and BC groups had mino changes and maintained a stable ***,it was inferred that,as a feed supplement,*** NY5 and the mixture of *** and *** NY5 at 1 x 10~8 CFU/g feed were able to promote growtl and disease resistance,which may be associated with the supplement’s effects on gut immune statu intestinal morphology,and intestinal microbial community composition.

关键词： Tilapia Bacillus subtilis Bacillus cereus Intestinal microbiota Probiotic

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Evidence for the paternal mitochondrial DNA in the crucian carp-like fish lineage with hybrid origin

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Science China(Life Sciences) 2020年第1期63卷 102-115页

作者： Shi Wang Ni Jiao Lu Zhao Meiwen Zhang Pei Zhou Xuexue Huang Fangzhou Hu Conghui Yang Yuqin Shu Wuhui Li Chun Zhang Min Tao Bo Chen Ming Ma Shaojun Liu State key laboratory of Developmental Biology of Freshwater Fish Hunan Normal UniversityChangsha 410081China College of Life Sciences Hunan Normal UniversityChangsha 410081China College of Chemistry and Chemical Engineering Hunan Normal UniversityChangsha 410081China key laboratory of tropical and subtropical fisheries resource application and cultivation Ministry of AgriculturePearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhou 510380China

In terms of taxonomic status,common carp(Cyprinus carpio,Cyprininae)and crucian carp(Carassius auratus,Cyprininae)are different species;however,in this study,a newborn homodiploid crucian carp-like fish(2n=100)(2nNCRC)lineage(F1–F3)was established from the interspecific hybridization of female common carp(2n=100)×male blunt snout bream(Megalobrama amblycephala,Cultrinae,2n=48).The phenotypes and genotypes of 2 n NCRC differed from those of its parents but were closely related to those of the existing diploid crucian *** further sequenced the whole mitochondrial(mt)genomes of the 2n NCRC lineage from F1 to *** paternal mt DNA fragments were stably embedded in the mt-genomes of F1–F3 generations of 2n NCRC to form chimeric DNA *** with this chimeric process,numerous base sites of F1–F3 generations of 2 n NCRC underwent *** of these mutation sites were consistent with the existing diploid crucian ***,the mt DNA organization and nucleotide composition of 2n NCRC were more similar to those of the existing diploid crucian carp than those of the *** inheritable chimeric DNA fragments and mutant loci in the mt-genomes of different generations of 2nNCRC provided important evidence of the mt DNA change process in the newborn lineage derived from hybridization of different *** findings demonstrated for the first time that the paternal mt DNA were transmitted into the mt-genomes of homodiploid lineage,which provided new insights into the existence of paternal mt DNA in the mt DNA inheritance.

关键词： hybridization homodiploid common carp blunt snout bream crucian carp mitochondrial genome genetic evolution

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Sex determination mechanisms and sex control approaches in aquaculture animals

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Science China(Life Sciences) 2022年第6期65卷 1091-1122页

作者： Xi-Yin Li Jie Mei Chu-Tian Ge Xiao-Li Liu Jian-Fang Gui State key laboratory of Freshwater Ecology and Biotechnology Hubei Hongshan LaboratoryThe Innovative Academy of Seed DesignInstitute of HydrobiologyChinese Academy of SciencesUniversity of Chinese Academy of SciencesWuhan 430072China College of fisheries Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China College of Biological and Environmental Sciences Zhejiang Wanli UniversityNingbo 315100China key laboratory of tropical&subtropical Fishery resource application&cultivation of Ministry of Agriculture and Rural Affairs Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhou 510380China

Aquaculture is one of the most efficient modes of animal protein production and plays an important role in global food *** animals exhibit extraordinarily diverse sexual phenotypes and underlying mechanisms,providing an ideal system to perform sex determination research,one of the important areas in life ***,sex is also one of the most valuable traits because sexual dimorphism in growth,size,and other economic characteristics commonly exist in aquaculture ***,we synthesize current knowledge of sex determination mechanisms,sex chromosome evolution,reproduction strategies,and sexual dimorphism,and also review several approaches for sex control in aquaculture animals,including artificial gynogenesis,application of sex-specific or sex chromosome-linked markers,artificial sex reversal,as well as gene *** anticipate that better understanding of sex determination mechanisms and innovation of sex control approaches will facilitate sustainable development of aquaculture.

关键词： sex determination sex control approach sexual dimorphism sex chromosome sex change reproduction strategy sex reversal

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Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass(Micropterus salmoides)

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Zoological Research 2023年第1期44卷 78-89页

作者： Cheng-Fei Sun Xin-Hui Zhang Jun-Jian Dong Xin-Xin You Yuan-Yuan Tian Feng-Ying Gao He-Tong Zhang Qiong Shi Xing Ye key laboratory of tropical and subtropical Fishery resources application and cultivation Ministry of Agriculture and Rural AffairsPearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouGuangdong 510380China Shenzhen key Lab of Marine Genomics Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic AnimalsBGI Academy of Marine SciencesBGI MarineShenzhenGuangdong 518081China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China

Largemouth bass(Micropterus salmoides) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In this study,we sequenced 149 largemouth bass fish, including protospecies(imported from the US) and improved breeds(four domestic breeding populations from China). We detected genomic regions harboring certain genes associated with improved traits, which may be useful molecular markers for practical domestication, breeding, and selection. Subsequent analyses of genetic diversity and population structure revealed that the improved breeds have undergone more rigorous genetic changes. Through selective signal analysis, we identified hundreds of putative selective sweep regions in each largemouth bass line. Interestingly, we predicted 103 putative candidate genes potentially subjected to selection,including several associated with growth(psst1 and grb10), early development(klf9, sp4, and sp8), and immune traits(pkn2, sept2, bcl6, and ripk2). These candidate genes represent potential genomic landmarks that could be used to improve important traits of biological and commercial interest. In summary, this study provides a genome-wide map of genetic variations and selection footprints in largemouth bass, which may benefit genetic studies and accelerate genetic improvement of this economically important fish.

关键词： Largemouth bass Whole-genome resequencing Signatures of selection Growth Immunity

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Comparative Analysis of Microsatellite DNA Polymorphism in Gold Grass Carp and Four Grass Carp Populations from China

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Animal Husbandry and Feed Science 2017年第6期9卷 379-383,397页

作者： Zhu Bing Fan Jiajia Bai Junjie Jiang Peng key Lab. of tropical & subtropical Fishery resource application & cultivation Ministry of Agriculture Pearl River fisheries Research Institute Chinese Academy of Fishery Sciences College of fisheries and Life Science Shanghai Ocean University

[ Objectives ] To analyze the genetic structure and genetic diversity of gold grass carp population. [ Methods ] A total of 15 microsatellite markers were used to examine gold grass carp population and four grass carp populations[ Yuanjiang （YJ）, Ningxiang （NX） , Honghu （HH） and Xijiang （XJ） ] from the Yangtze River and the Pearl River of China. [ Results] All the 15 microsatellite loei were highly polymorphic, with polymorphism information content （PIC） of 0.763 -0.939. The expected heterozygosity （HE ） of gold grass carp population was 0. 662, lower than those of the four Chinese grass carp populations （HE = 0.85 - 0. 885 ）. The genetic differentiation index （ FST ） between gold grass carp population and YJ, NX, HH, XJ populations were 0. 157 2, 0. 129 5, 0. 147 5 and 0. 114 4, respectively. This suggests that gold grass carp population is highly differentiated from YJ grass carp population （0.15 〈 FST 〈0.25）, while moderately differentiated from other three grass carp populations （0.05 〈 FST 〈 0.15 ）. Gold grass carp population had the closest genetic relationship with XJ population （DA = 0.476 3）, and it showed the farthest genetic relationship with YJ grass carp population （DA = 0. 810 7）. The NJ phylogenetic tree based on genetic distance indicated that four Chinese grass carp populations clustered together as one branch, while gold grass carp population as another. [ Conclusions] Genetic di- versity of gold grass carp population is lower than that of Chinese grass carp population, with relative distant genetic relationship.

关键词： Ctenopharyngodon idellus Genetic structure Microsatellite Genetic distance Heterozygosity

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SNP Detection of High Density Lipoprotein Binding Protein Gene (HBP) and Its Correlations with Growth Traits in Largemouth Bass(Micropterus salmoides)

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Agricultural Biotechnology 2015年第3期4卷 43-46,50页

作者： Chunlong ZHOU Junjie BAI Shengjie LI Jiajia FAN Dongmei MA key Lab of tropical & subtropical Fishery resource application & cultivation Ministry of Agriculture/Pearl River Fisheries Research InstituteChinese Academy of Fishery Sciences College of fisheries and Life Science Shanghai Ocean University

High density lipoprotein binding protein （HBP） plays an important role in lipid metabolism of animals. Lipids are indispensable energy materials for fi- shes, especially for carnivorous fishes with low utilization efficiency of carbohydrates. The single nucleotide polymorphism （SNP） of HBP gene may affect the fat metabolism, thereby exerting an effect on the growth traits of largemouth bass （Micropterus salmoides）. Investigating the correlations between SNP and growth traits can provide candidate markers for molecular marker-assisted selection. In this study, partial genomic fraganents of HBP gene （ GenBank accession number： KF652241 ） were amplified based on the sequences of an available contig in the EST-SNP database of largemouth bass. Three SNP mutation loci were identified in the 3＇ non-ceding region of HBP gene by direct sequencing, including H1 （G ＋ 2782T）, 142 （T ＋ 2817C） and H3 （G ＋ 2857A）. Three SNP loci of 165 randomly selected largemouth bass individuals were detected and genotyped by SnaPshot assay. Genetic structure was analyzed by POPGENE32 software. By using spssl7.0 software, a general linear model （GLM） was established for correlation analysis between different genotypes at SNP loci of HBP gene and various growth traits. The results showed that three SNP loci were in Hardy-Weinberg equilibrium state. To be specific, loci H1 and H2 formed two haplotypes （ A and B）, and three geno- types （AA, AB, and BB） were observed; loci H1, H2 and H3 formed six diplotypes （DI, I）2, D3, D4, D5 and D6）. According to the correlations between dif- ferent genotypes and various growth traits, the body weight and total length of largemouth bass individuals with genotype BB were significantly higher than those of individuals with genotype AB （ P 〈 0.05 ） ; the body weight and total length of largemouth bass individuals with diplotype D6 were significantly higher than those of individuals with diplotype D4 （P 〈0.05）. In this study, SNP markers correlated with growth trait

关键词： Largemouth bass (Micropterus sa/mo/des) Single nucleotide polymorphism (SNP) High density lipoprotein binding protein gene (HBP) Haplo- type Diplotype

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