Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): Applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis
Shao C.,Chinese Academy of Fishery Sciences |
Shao C.,Function Laboratory for Marine Fisheries Science and Food Production Processes |
Shao C.,Tokyo University of Marine Science and Technology |
Niu Y.,BGI Shenzhen |
And 14 more authors.
DNA Research | Year: 2015
High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome. Of these SNPs, 12,712 high-confidence SNPs were subjected to high-throughput genotyping and assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 3,497.29 cM with an average distance of 0.47 cM between loci, thereby representing the densest genetic map currently reported for Japanese flounder. Nine positive quantitative trait loci (QTLs) forming two main clusters for Vibrio anguillarum disease resistance were detected. All QTLs could explain 5.1-8.38% of the total phenotypic variation. Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance. In addition, 246 genome assembly scaffolds with an average size of 21.79 Mb were anchored onto the LGs; these scaffolds, comprising 522.99 Mb, represented 95.78% of assembled genomic sequences. The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes). Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence. The newly developed high-resolution genetic map, which will facilitate QTL mapping, scaffold assembly, and genome synteny analysis of Japanese flounder, marks a milestone in the ongoing genome project for this species. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.
Shan X.,Chinese Academy of Fishery Sciences |
Shan X.,Function Laboratory for Marine Fisheries Science and Food Production Processes |
Quan H.,Fisheries Institute of Mindong |
Dou S.,CAS Qingdao Institute of Oceanology
Fish Physiology and Biochemistry | Year: 2015
A histological method was used to describe the ontogenetic development of the digestive tract of laboratory-reared miiuy croaker (Miichthys miiuy) and to evaluate the effects of short-term food deprivation on the morphology and histology of the digestive tract. Larvae and juveniles were maintained at 24 °C in a thermostatically controlled system. Three starvation experiments were conducted during different developmental stages: 1–7 days after hatching (dah; prior to benthic swimming); 26–35 dah (during settling); and 42–53 dah (after benthic swimming). According to the structural changes in the ontogenetic development of the digestive tract, three stages were observed. The first stage was from hatching to 3 dah; the digestive tract was undifferentiated in newly hatched larvae and then showed remarkable morphological changes and differentiation. During this period, larvae depended on endogenous nutrition. The second stage (4–20 dah) was a critical period in which larvae transitioned from endogenous feeding to exogenous feeding and the digestive tract fully differentiated into the buccopharynx, oesophagus, stomach, anterior intestine and posterior intestine. Goblet cells and vacuoles appeared in the digestive tract, and pharyngeal teeth and taste buds developed. During the third stage (20–36 dah), the gastric glands developed and the stomach differentiated into the fundic, cardiac and pyloric regions. At 25 dah, pyloric caeca developed and mucosal folds and spiral valves were clearly distinguishable. After 30 dah, the digestive tract did not undergo any noticeable differentiation, indicating the complete development of the digestive system. The wet weight and SGR (specific growth rate) of miiuy croaker larvae and juveniles greatly decreased when they were deprived of food, and compensatory growth was observed in re-feeding juveniles. The livers of starved larvae and juveniles were atrophied and dark coloured, the intestines were transparent and thin, and the stomach cubages were reduced. The histological effects of starvation were mainly evident in the degeneration of cells in digestive organs, as seen in the shrinkage and separation of cells and the loss of intercellular substances in the liver, pancreas, intestine and stomach. These changes became more severe with increased duration of starvation. In addition, the histological structure of the digestive tracts of starved larvae and juveniles partly recovered after re-feeding, and the effects of starvation on miiuy croaker were age dependent. © 2015 Springer Science+Business Media Dordrecht
Bai C.,Chinese Academy of Fishery Sciences |
Bai C.,Function Laboratory for Marine Fisheries Science and Food Production Processes |
Wang C.,Chinese Academy of Fishery Sciences |
Wang C.,Function Laboratory for Marine Fisheries Science and Food Production Processes |
And 5 more authors.
Journal of Invertebrate Pathology | Year: 2015
Viral infection caused by Ostreid herpesvirus 1 (OsHV-1) is one of the proximate causes of mass mortalities of cultivated bivalves around the world. The emergence and spread of different variants of OsHV-1 accompanied by different epidemiological characteristics have been reported frequently in different countries around the world. In this paper, we present a study of the detection of OsHV-1 DNA and their variations from 1599 samples over 18 species collected in 27 aquaculture sites and two food markets during 2001-2013 in China. All of the samples were examined by a nested PCR assay targeting the C2/C6 fragment of OsHV-1 followed by sequencing. Our results showed 338 individuals (21.1%) of seven species sampled from 14 (14/27 = 51.9%) sites and the two food markets were positive for viral DNA. Sequencing of 289 PCR products revealed 24 virus types. No shared virus type was found among different countries with 47 types (23 in Japan, 16 in France, 2 in South Korea and 1 in each country of Australia, USA, Ireland, New Zealand, Mexico and China) identified in previous studies. As previously reported, two main phylogenetic groups were identified by phylogenetic analysis based on the 71 virus types; within which 6 separate clades were identified. Our results also demonstrated that two clades were associated with abnormal mortalities of the scallop, Chlamys farrier and the calm, Scapharca broughtonii in China. These findings indicated that cultivated bivalves may face potential threats from OsHV-1 types found in our study. © 2014 Elsevier Inc.
Xia J.,Ocean University of China |
Xia J.,Chinese Academy of Fishery Sciences |
Bai C.,Chinese Academy of Fishery Sciences |
Bai C.,Function Laboratory for Marine Fisheries Science and Food Production Processes |
And 6 more authors.
Virology Journal | Year: 2015
Background: Ostreid herpesvirus-1 (OsHV-1) is the major bivalve pathogen associated with severe mortality events in a wide host range. In the early summer of 2012 and 2013, mass mortalities of blood clam (Scapharca broughtonii) broodstocks associated with a newly described variant of OsHV-1 (OsHV-1-SB) were reported. Methods: In this study, the complete genome sequence of the newly described variant was determined through the primer walking approach, and compared with those of the other two OsHV-1 variants. Results: OsHV-1-SB genome was found to contain 199, 354 bp nucleotides with 38.5 % G/C content, which is highly similar to those of acute viral necrosis virus (AVNV) and OsHV-1 reference type. A total of 123 open reading frames (ORFs) putatively encoding functional proteins were identified; eight of which were duplicated in the major repeat elements of the genome. The genomic organization of OsHV-1-SB could be represented as TRL-UL-IRL-IRS-US-TRS, which is different from that of OsHV-1 reference type and AVNV due to the deletion of a unique region (X, 1.5Kb) between IRL and IRS. The DNA sequence of OsHV-1-SB is 95.2 % and 97.3 % identical to that of OsHV-1 reference type and AVNV respectively. On the basis of nucleotide sequences of 32 ORFs in OsHV-1-SB and the other nine OsHV-1 variants, results from phylogenetic analysis also demonstrated that OsHV-1-SB is most closely related to AVNV. Conclusions: The determination of the genome of OsHV-1 with distinguished epidemiological features will aid in our better understanding of OsHV-1 diversity, and facilitate further research on the origin, evolution, and epidemiology of the virus. © 2015 Xia et al.
Ren X.,Chinese Academy of Fishery Sciences |
Cui Y.,Chinese Academy of Fishery Sciences |
Gao B.,Chinese Academy of Fishery Sciences |
Liu P.,Function Laboratory for Marine Fisheries Science and Food Production Processes |
Li J.,Function Laboratory for Marine Fisheries Science and Food Production Processes
Marine Genomics | Year: 2016
MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that regulate gene expression by post-transcriptional repression of mRNAs. The swimming crab Portunus trituberculatus is one of the most important crustacean species for aquaculture in China. However, to date no miRNAs have been reported to for modulating growth in P. trituberculatus. To investigate miRNAs involved in the growth of this species, we constructed six small RNA libraries for big individuals (BIs) and small individuals (SIs) from a highly inbred family. Six mixed RNA pools of five tissues (eyestalk, gill, heart, hepatopancreas, and muscle) were obtained. By aligning sequencing data with those for known miRNAs, a total of 404 miRNAs, including 339 known and 65 novel miRNAs, were identified from the six libraries. MiR-100 and miR-276a-3p were among the most prominent miRNA species. We identified seven differentially expressed miRNAs between the BIs and SIs, which were validated using real-time PCR. Preliminary analyzes of their putative target genes and GO and KEGG pathway analyzes showed that these differentially expressed miRNAs could play important roles in global transcriptional depression and cell differentiation of P. trituberculatus. This study reveals the first miRNA profile related to the body growth of P. trituberculatus, which would be particularly useful for crab breeding programs. © 2016 Elsevier B.V.
Dietary supplementation of probiotic Bacillus PC465 isolated from the gut of Fenneropenaeus chinensis improves the health status and resistance of Litopenaeus vannamei against white spot syndrome virus
Chai P.-C.,Chinese Academy of Fishery Sciences |
Song X.-L.,Chinese Academy of Fishery Sciences |
Chen G.-F.,Harbin Institute of Technology |
Xu H.,Chinese Academy of Fishery Sciences |
And 2 more authors.
Fish and Shellfish Immunology | Year: 2016
This study conducted a 30-day feeding trial and a subsequent 20-day anti-virus infection trial to determine the effects of probiotic Bacillus PC465 on the growth, health status, and disease resistance of Litopenaeus vannamei. Shrimp samples were fed with three practical diets prepared from shrimp feed containing varying probiotic doses [0 (control), 107, and 109 CFU g-1]. Probiotic supplementation significantly increased the weight gain and survival of L. vannamei (p < 0.05). The effect of 109 CFU g-1 on the growth rate was higher than that of 107 CFU g-1. Compared with those in the control group, the activities of digestive enzymes, such as amylase, protease, and lipase, in the shrimp mid-gut significantly increased in the probiotic-fed groups on days 15 and 30, except lipase on day 30. The influence of 109 CFU g-1 on enzyme activities was also greater than that of 107 CFU g-1. Scanning electron microscopy revealed folds and large ravines across the interior surface of the mid-gut, and the number of these folds and ravines increased significantly after the probiotic was administered. The probiotic treatment significantly (p < 0.05) enhanced the transcription of penaeidin 3a (Pen-3a), peroxinectin, C-type lectin 3 (Lec-3), and thioredoxin (Trx) in the hemocytes of L. vannamei. Likewise, probiotic treatment increased the transcription of hemocyanin in the hepatopancreas of L. vannamei. The probiotic treatment also significantly increased the transcription of prophenoloxidase (proPO) but decreased the transcription of crustin in hemocytes. By contrast, the same treatment failed to increase the transcription of Ras-related protein (Rab-6) in hemocytes. The number of species and biomass of Bacillus in the mid-gut were higher in the probiotic-fed group than in the control group. The total biomass of microbes was higher in the shrimp fed with 107 CFU g-1 than in the shrimp fed with 109 CFU g-1 and the control group on days 15 and 30 post-feeding. In two white spot syndrome virus (WSSV) infections, the weight gain, survival, and WSSV copies within the gills of the probiotic-treated shrimp significantly differed (p < 0.05) from those of the control group. Relatively efficient protection was associated with probiotic feeding. Results suggested that Bacillus PC465 feeding improves the growth performance, survival, digestion, and nutrient absorption of L. vannamei. Probiotic treatment also enhances the microbial structures in the gut, promotes the immune status of shrimp, and provides protection against viral infection. The supplementation with 109 CFU g-1 can also improve the growth and survival of L. vannamei. © 2016 Elsevier Ltd.
Duan Y.,CAS South China Sea Fisheries Research Institute |
Li J.,Chinese Academy of Fishery Sciences |
Li J.,Function Laboratory for Marine Fisheries Science and Food Production Processes |
Zhang Z.,CAS South China Sea Fisheries Research Institute |
And 2 more authors.
Fish and Shellfish Immunology | Year: 2016
ADP ribosylation factors (Arf), as highly conserved small guanosine triphosphate (GTP)-binding proteins, participates in intracellular trafficking and organelle structure. In this study, a full-length cDNA of Arf1 (designated EcArf1) was cloned from Exopalaemon carinicauda by using rapid amplification of cDNA ends (RACE) approaches. The full-length cDNA of EcArf1 was 1428 bp, which contains an open reading frame (ORF) of 549 bp, encoding a 182 amino-acid polypeptide with the predicted molecular weight of 20.69 kDa and estimated isoelectric point was 7.24. Sequence analysis revealed that the conserved Arf protein family signatures were identified in EcArf1. The deduced amino acid sequence of EcArf1 shared high identity (95%-98%) with that of other species and clustered together with Arf1 of other shrimp in the NJ phylogenetic tree, indicating that EcArf1 should be a member of the Arf1 family. Quantitative real-time RT-qPCR analysis indicated that EcArf1 was expressed in hemocytes, hepatopancreas, gills, muscle, ovary, intestine, stomach and heart, and the most abundant level was in hemocytes and gills, which were also the two main target tissues of pathogen infection and environmental stress. After Vibrio parahaemolyticus challenge, EcArf1 transcripts level significantly increased in hemocytes and hepatopancreas at 3 h and 6 h, respectively. The expression of EcArf1 in hemocytes and hepatopancreas significantly up-regulated at 12 h and 6 h respectively, and down-regulated at 72 h and 48 h, respectively. EcArf1 expression in hepatopancreas and gills both significantly increased at 6 h and decreased at 24 h under ammonia-N stress. The results suggested that EcArf1 might be involved in immune responses to pathogens (V. parahaemolyticus and WSSV) challenge and ammonia-N stress in E. carinicauda. © 2016 Elsevier Ltd.
Du Y.,Ocean University of China |
Tang X.,Ocean University of China |
Zhan W.,Ocean University of China |
Zhan W.,Function Laboratory for Marine Fisheries Science and Food Production Processes |
And 2 more authors.
International Journal of Molecular Sciences | Year: 2016
Immunoglobulin tau (IgT) is a new teleost immunoglobulin isotype, and its potential function in adaptive immunity is not very clear. In the present study, the membrane-bound and secreted IgT (mIgT and sIgT) heavy chain genes were cloned for the first time and characterized in flounder (Paralichthys olivaceus), and found the nucleic acid sequence were exactly same in the Cτ1-Cτ4 constant domains of mIgT and sIgT, but different in variable regions and the C-terminus. The amino acid sequence of mIgT shared higher similarity with Bovichtus diacanthus (51.2%) and Dicentrarchus labrax (45.0%). Amino acid of flounder IgT, IgM, and IgD heavy chain was compared and the highest similarity was found between IgT Cτ1 and IgM Cµ1 (38%). In healthy flounder, the transcript levels of IgT mRNA were the highest in gill, spleen, and liver, and higher in peripheral blood leucocytes, skin, and hindgut. After infection and vaccination with Edwardsiella tarda via intraperitoneal injection and immersion, the qRT-PCR analysis demonstrated that the IgT mRNA level was significantly upregulated in all tested tissues, with similar dynamic tendency that increased firstly and then decreased, and higher in gill, skin, hindgut, liver, and stomach in immersion than in the injection group, but no significant difference existed in spleen and head kidney between immersion and injection groups. These results revealed that IgT responses could be simultaneously induced in both mucosal and systemic tissues after infection/vaccination via injection and immersion route, but IgT might play a more important role in mucosal immunity than in systemic immunity. © 2016 by the authors; licensee MDPI, Basel, Switzerland.
Li Z.,Ocean University of China |
Ye Z.,Ocean University of China |
Wan R.,Ocean University of China |
Wan R.,Function Laboratory for Marine Fisheries Science and Food Production Processes
Journal of Ocean University of China | Year: 2015
Surveys were conducted in five voyages in Haizhou Bay and its adjacent coastal area from March to December 2011 during full moon spring tides. The ichthyoplankton assemblages and the environmental factors that affect their spatial and seasonal patterns were determined. Totally 35 and 12 fish egg and larvae taxa were identified, respectively. Over the past several decades, the egg and larval species composition has significantly changed in Haizhou Bay and its adjacent waters, most likely corresponding with the alteration of fishery resources, which are strongly affected by anthropogenic activities and climate change. The Bray-Curtis dissimilarity index identified four assemblages: near-shore bay assemblage, middle bay assemblage and two closely related assemblages (near-shore/middle bay assemblage and middle/edge of bay assemblage). The primary species of each assemblage principally reflected the spawning strategies of adult fish. The near-shore bay assemblage generally occurred in near-shore bay, with depths measuring <20 m, and the middle bay assemblage generally occurred in the middle of bay, with depths measuring 20 to 40 m. Spatial and seasonal variations in ichthyoplankton in each assemblage were determined by interactions between biological behavioral traits and oceanographic features, particularly the variation of local conditions within the constraint of a general reproductive strategy. The results of Spearman’s rank correlation analysis indicated that both fish egg and larval abundance were positively correlated with depth, which is critical to the oceanographic features in Haizhou Bay. © 2015, Science Press, Ocean University of China and Springer-Verlag Berlin Heidelberg.
Wu R.-H.,Ocean University of China |
Tang X.-Q.,Ocean University of China |
Sheng X.-Z.,Ocean University of China |
Zhan W.-B.,Ocean University of China |
Zhan W.-B.,Function Laboratory for Marine Fisheries Science and Food Production Processes
Journal of Comparative Pathology | Year: 2015
Lymphocystis disease virus (LCDV) enters and infects the gill cells of flounder (. Paralichthys olivaceus) via a 27.8 kDa membrane protein receptor. In the present study, immunohistochemistry was performed to locate the tissue distribution of this molecule in healthy flounder and showed that it was widely distributed in the tissues tested. Indirect enzyme-linked immunosorbent assay (ELISA) showed that the expression of the receptor in healthy flounder was highest in the gills and stomach, then in the skin, intestine and liver, followed by the spleen, head kidney, heart, ovary and brain and finally the kidney. On LCDV infection, ELISA indicated that the expression of the receptor, as determined by ELISA, was significantly upregulated in all tissues of LCDV-infected flounder compared with controls, but this expression decreased over the 4 weeks post infection. In contrast, real-time quantitative polymerase chain reaction demonstrated that the copy number of the LCDV gene in the tissues increased with time post infection, and that viral loads were higher in the tissues with higher expressions of the receptor. These results point to a correlation between high expression of the 27.8 kDa receptor and efficient LCDV propagation. The wide tissue distribution of the receptor might be one reason why LCDV can infect various tissues leading to systemic infection. © 2015 Elsevier Ltd.