Genome-wide mining,characterization, and development of microsatellite markers in <Emphasis Type="Italic">Marsupenaeus japonicus</Emphasis> by genome survey sequencing

The kuruma prawn, Marsupenaeus japonicus, is one of the most cultivated and consumed species of shrimp. However, very few molecular genetic/genomic resources are publically available for it. Thus, the characterization and distribution of simple sequence repeats (SSRs) remains ambiguous and the use of SSR markers in genomic studies and marker-assisted selection is limited. The goal of this study is to characterize and develop genome-wide SSR markers in M. japonicus by genome survey sequencing for application in comparative genomics and breeding. A total of 326 945 perfect SSRs were identified, among which dinucleotide repeats were the most frequent class (44.08%), followed by mononucleotides (29.67%), trinucleotides (18.96%), tetranucleotides (5.66%), hexanucleotides (1.07%), and pentanucleotides (0.56%). In total, 151 541 SSR loci primers were successfully designed. A subset of 30 SSR primer pairs were synthesized and tested in 42 individuals from a wild population, of which 27 loci (90.0%) were successfully amplified with specific products and 24 (80.0%) were polymorphic. For the amplified polymorphic loci, the alleles ranged from 5 to 17 (with an average of 9.63), and the average PIC value was 0.796. A total of 58 256 SSR-containing sequences had significant Gene Ontology annotation; these are good functional molecular marker candidates for association studies and comparative genomic analysis. The newly identified SSRs significantly contribute to the M. japonicus genomic resources and will facilitate a number of genetic and genomic studies, including high density linkage mapping, genome-wide association analysis, marker-aided selection, comparative genomics analysis, population genetics, and evolution.     

Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance,distribution, and potential for marker development

Microsatellites are a ubiquitous component of the eukaryote genome and constitute one of the most popular sources of molecular markers for genetic studies. However, no data are currently available regarding microsatellites across the entire genome in oysters, despite their importance to the aquaculture industry. We present the fi rst genome-wide investigation of microsatellites in the Pacifi c oyster Crassostrea gigas by analysis of the complete genome, resequencing, and expression data. The Pacifi c oyster genome is rich in microsatellites. A total of 604 653 repeats were identifi ed, in average of one locus per 815 base pairs(bp). A total of 12 836 genes had coding repeats, and 7 332 were expressed normally, including genes with a wide range of molecular functions. Compared with 20 different species of animals, microsatellites in the oyster genome typically exhibited 1) an intermediate overall frequency; 2) relatively uniform contents of(A)n and(C)n repeats and abundant long(C)n repeats(≥24 bp); 3) large average length of(AG)n repeats; and 4) scarcity of trinucleotide repeats. The microsatellite-fl anking regions exhibited a high degree of polymorphism with a heterozygosity rate of around 2.0%, but there was no correlation between heterozygosity and microsatellite abundance. A total of 19 462 polymorphic microsatellites were discovered, and dinucleotide repeats were the most active, with over 26% of loci found to harbor allelic variations. In all, 7 451 loci with high potential for marker development were identifi ed. Better knowledge of the microsatellites in the oyster genome will provide information for the future design of a wide range of molecular markers and contribute to further advancements in the fi eld of oyster genetics, particularly for molecular-based selection and breeding.     

日本囊对虾的遗传育种研究进展

日本囊对虾是我国优质对虾资源。综述日本囊对虾(Marsupenaeus japonicus)的种质资源、选择育种、多倍体诱导育种、分子标记辅助育种等方面的研究进展,总结虾类杂交育种、转基因育种研究现状,对日本囊对虾相关研究进行展望;针对当前日本囊对虾遗传育种研究落后、数量遗传学应用不够、育种工艺不足的现状,认为在日本囊对虾遗传改良时,应用高新分子标记辅助育种技术与传统选择育种相结合的综合育种技术是良种培育的有效途径。     

Identification and characterization of 43 microsatellite markers derived from expressed sequence tags of the sea cucumber (Apostichopus japonicus)

The sea cucumber Apostichopus japonicus is a commercially and ecologically important species in China. A total of 3056 potential unigenes were generated after assembling 7597 A. japonicus expressed sequence tags (ESTs) downloaded from Gen-Bank. Two hundred and fifty microsatellite-containing ESTs (8.18%) and 299 simple sequence repeats (SSRs) were detected. The average density of SSRs was 1 per 7.403 kb of EST after redundancy elimination. Di-nucleotide repeat motifs appeared to be the most abundant type with a percentage of 69.90%. Of the 126 primer pairs designed, 90 amplified the expected products and 43 showed polymorphism in 30 individuals tested. The number of alleles per locus ranged from 2 to 26 with an average of 7.0 alleles, and the observed and expected heterozygosities varied from 0.067 to 1.000 and from 0.066 to 0.959, respectively. These new EST-derived microsatellite markers would provide sufficient polymorphism for population genetic studies and genome mapping of this sea cucumber species.     

Development and characterization of novel polymorphic microsatellite markers for the Korean freshwater snail Semisulcospira coreana and cross-species amplification using next-generation sequencing

Korean freshwater snails of the genus Semisulcospira are widely distributed across East Asia.It has been a very popular nutritional food in Korea,and is an ecologically important water quality indicator because it lives only in clean water.However,no microsatellite markers have been generated to study the population genetic diversity of this genus.In the present study,we developed and characterized 18 novel microsatellite loci from Semisulcospira coreana genomic DNA.The microsatellites were isolated using 454 GS-FLX titanium sequencing and 18 markers were used for genotyping in S.coreana.In addition,we also tested the cross-species transferability of the microsatellite markers in four additional Semisulcospira spp.We identified 18 polymorphic loci and the number of alleles per loci,and their polymorphism information content values ranged from 2 to 17 and 0.203 to 0.902,respectively.The observed and expected heterozygosities of the loci ranged from 0.063 to 0.924 and 0.226 to 0.924,respectively.According to the analysis of the cross-species transferability of these markers,four species,S.forticosta,S.gottschei,S.tegulata,and S.libertina,showed a very high transferability(80%–85%).These results show that this set of nuclear markers could be useful for population genetics studies of this species and closely related species.     

Transcriptome of hepatopancreas in kuruma shrimp Marsupenaeus japonicus under low-salinity stress

Journal of Oceanology and Limnology - The kuruma shrimp Marsupenaeus japonicus is one of the most commercially important shrimp species in the world. Low salinity would affect the penetration and...     

Profile and development of microsatellite primers for Acanthogobius ommaturus based on high-throughput sequencing technology

Journal of Oceanology and Limnology - Acanthogobius ommaturus, a fish species of the Family Gobiidae, is a marine commercial fish perched on the bottom of seawater. In this study, Illumina...     

Effects of the Dietary Probiotic Clostridium butyricum on Intestine Digestive and Metabolic Capacities,SCFA Content and Body Composition in Marsupenaeus japonicus

A 56-day feeding trial was performed to evaluate the effects of dietary probiotic Clostridium butyricum(CB) on intestine digestive and metabolic capacities, intestine short-chain fatty acids(SCFA) content and body composition of kuruma shrimp Marsupenaeus japonicus. Shrimp s were randomly allocated into 9 tanks, 30 each, and f ed with diets containing different levels of C. butyricum(1×10~9 cfug~(-1)): 0 mgg~(-1) feed(Control), 100 mgg~(-1) feed(CB-100), 200 mgg~(-1) feed(CB-200), while each level was triplicated. The results indicated that compared with the control group, the intestine pepsin(Pep) activity and 5-hydroxytryptamine(5-HT) concentration of two C. butyricum group s were both increased. Amylase(AM Y) and lipase(LPS) activities wer e only induced in CB-200 group. Alanine aminotransferase(ALT) and aspartate aminotransferase(A ST) activities of two C. butyricum group s showed no significant change. The α-amylase(AM Y) gene expression was induced in CB-200 group, and tryp sin gene expression of two C. butyricum treated group s were both induced. Intestine SCFA content and body composition analysis showed that the contents of propionic acid, butyric acid and the crude protein of two C. butyricum group s were all higher than those of control. These results revealed that C. butyricum can modulate intestine digestive and metabolic capacities, improve intestine SCFA content and body crude protein content in M. japonicus.     

Development and Characterization of Microsatellite Markers for the Pacific Abalone （Haliotis discus） via EST Database Mining

The EST database of the Pacific abalone (Haliotis discus) was mined for developing mierosatellite markers. A total of 1476 EST sequences were registered in GenBank when data mining was performed. Fifty sequences (approximately 3.4%) were found to contain one or more mierosatellites. Based on the length and GC content of the flanking regions, duster analysis and BLASTN, 13 microsatellite-containing ESTs were selected for PCR primer design. The results showed that 10 out of 13 primer pairs could amplify seorable PCR products and showed polymorphism. The number of alleles ranged from 2 to 13 and the values of Hoand He varied from 0.1222 to 0.8611 and 0.2449 to 0.9311, respectively. No significant linkage disequilibrium (LD) between any pairs of these loci was found, and 6 of 10 loci conformed to the Hardy-Weinberg equilibrium (HWE). These EST-SSRs are therefore potential tools for studies of intraspecies variation and hybrid identification.     

PCR-DGGE analysis of intestinal bacteria and effect of Bacillus spp.on intestinal microbial diversity in kuruma shrimp(Marsupenaeus japonicus)

In this study,the intestinal microbiota of kuruma shrimp(Marsupenaeus japonicus) was examined by molecular analysis of the 16S rDNA to identify the dominant intestinal bacteria and to investigate the effects of Bacillus spp.on intestinal microbial diversity.Samples of the intestines of kuruma shrimp fed normal feed and Bacillus spp.amended feed.PCR and denaturing gradient gel electrophoresis(DGGE) analyses were then performed on DNA extracted directly from the guts.Population fingerprints of the predominant organisms were generated by DGGE analysis of the universal V3 16S rDNA amplicons,and distinct bands in the gels were sequenced.The results suggested that the gut of kuruma shrimp was dominated by Vibrio sp.and uncultured gamma proteobacterium.Overall,the results of this study suggest that PCR-DGGE is a possible method of studying the intestinal microbial diversity of shrimp.     

Isolation, cloning and sequencing of AFLP markers related to disease-resistance traits in Fenneropenaeus chinensis

Amplified fragment length polymorphisms （AFLP） technique was used to analyze the fingerprinting of four successive generations of Fenneropenaeus chinensis to reveal their disease-resistance traits. Some loci showed quite different genetic frequencies due to artificial selection, which implied that these fragments were putative markers related to the disease-resistance trait. We developed a simple and effective method to further characterize these AFLP fragments. Specific AFLP bands were cut directly from polyacrylamide gels, re-amplified, cloned and sequenced. Eight putative genetic markers were sequenced and their sizes ranged from 63 to 209 bp. The sequences were submitted to dbGSS （database of Genome Sequence Survey）; and the BLAST analysis showed low similarity to the function genes, indicating these markers were tightly linked to a disease-resistance trait but were not functional genes.     

PCR-DGGE analysis of intestinal bacteria and effect of Bacillus spp. on intestinal microbial diversity in kuruma shrimp (Marsupenaeus japonicus)

In this study, the intestinal microbiota of kuruma shrimp (Marsupenaeus japonicus) was examined by molecular analysis of the 16S rDNA to identify the dominant intestinal bacteria and to investigate the effects of Bacillus spp. on intestinal microbial diversity. Samples of the intestines of kuruma shrimp fed normal feed and Bacillus spp. amended feed. PCR and denaturing gradient gel electrophoresis (DGGE) analyses were then performed on DNA extracted directly from the guts. Population fingerprints of the predominant organisms were generated by DGGE analysis of the universal V3 16S rDNA amplicons, and distinct bands in the gels were sequenced. The results suggested that the gut of kuruma shrimp was dominated by Vibrio sp. and uncultured gamma proteobacterium. Overall, the results of this study suggest that PCR-DGGE is a possible method of studying the intestinal microbial diversity of shrimp.     

Identification and characterization of a new IgE-binding protein in mackerel (Scomber japonicus) by MALDI-TOF-MS

As fish is one source of the ‘big eight’ food allergens,the prevalence of fish allergy has increased over the past few years.In order to better understand fish allergy,it is necessary to identify fish allergens.Based on the sera from fish-allergenic patients,a 28 kDa protein from local mackerel (Scomber japonicus),which has not been reported as a fish allergen,was found to be reactive with most of the patients’ sera.The 28 kDa protein was analyzed by MALDI-TOF-MS (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry).Mascot search in NCBI database (Date: 08/07/2010) showed that the top protein matched,i.e.triosephosphate isomerase (TPI) from Xiphophorus maculatus and Poecilia reticulata,had a mowse (molecular weight search) score of 98.In addition,TPI from Epinephelus coioides also matched this mackerel protein with a mowse score of 96.Because TPI is con-sidered as an allergen in other non-fish organisms,such as lychee,wheat,latex,archaeopotamobius (Archaeopotamobius sibiriensis) and crangon (Crangon crangon),we consider that it may also be an allergen in mackerel.     

Profile of candidate microsatellite markers in Sebastiscus marmoratus using 454 pyrosequencing

Sebastiscus marmoratus is an important sedentary ovoviparous fish distributed in near-shore coastal waters from the coast of China to Japan. Candidate S. marmoratus microsatellite markers were developed in the present study using 454 pyrosequencing, and the marker profile was analyzed. A total of 2 000 000 raw sequence reads were assembled to reduce redundancy. Among them, 1 043 dinucleotide, 925 trinucleotide, 692 tetranucleotide, and 315 pentanucleotide repeats were detected. AC repeats were the most frequent motifs among the dinucleotide repeats, and AAT was the most abundant among the trinucleotide repeats. AAAT, ATAG, and ATCC were the three most common tetranucleotide motifs, and AAGAT and AATAT were the most dominant pentanucleotide motifs. The greatest numbers of loci and potentially amplifiable loci were found in dinucleotide repeats, whereas trinucleotide repeats had the fewest. In summary, a wide range of candidate microsatellite markers were identified in the present study using a rapid and efficient 454 pyrosequencing approach.     

Isolation, cloning and sequencing of AFLP markers related to disease-resistance traits in Fenneropenaeus chinensis

Amplified fragment length polymorphism (AFLP) technique was used to analyze the fingerprinting of four successive generations ofFenneropenaeus chinensis to reveal their disease-resistance traits. Some loci showed quite different genetic frequencies due to artificial selection, which implied that these fragments were putative markers related to the disease-resistance trait. We developed a simple and effective method to further characterize these AFLP fragments. Specific AFLP bands were cut directly from polyacrylamide gels, re-amplified, cloned and sequenced. Eight putative genetic markers were sequenced and their sizes ranged from 63 to 209 bp. The sequences were submitted to dbGSS (database of Genome Sequence Survey); and the BLAST analysis showed low similarity to the function genes, indicating these markers were tightly linked to a disease-resistance trait but were not functional genes. This research was supported by special funds from the National Key Basic Research Program (G1999012007) and the National High-Tech Research and Development Program of China (863 Program. 2001AA620105).     

Isolation,Identification, and Quantitative Determination of Saponin in Apostichopus japonicus by HPLC-DAD

Apostichopus japonicus is an important invertebrate that is widely used as a tonic food in Asian countries.The purpose of this study is to purify and identify a class of compound,the saponins,from the body wall of A.japonicus,and to establish a new me-thod to determine the quantity of saponins in the sea cucumber.In this study,the saponins of A.japonicus,cladoloside A(CA),were ob-tained from 80%ethanol extract by column chromatography for the first time and were characterized using the spectral method.The resulting purified saponins were then profiled using ¹HNMR,¹³CNMR,and ESI-MS,which revealed the CA molecular formula of C₅₃H₈₂O₂ and contained a triterpenoid backbone,a methylglucopyranosyl moiety,a quinovopyranosyl,and two xylopyranosyls.A me-thod for the quantitative determination of CA,comprising microwave-assisted extraction,high-performance liquid chromatography,and diode array detector method,was established.Extraction efficiency was optimized by changing microwave power,extraction sol-vent,volume,time,and temperature.Results showed that under the optimum conditions(extraction time of 10 min,temperature of 45℃,and solvent of 25 mL 70%ethanol under 400 W),the detection limit of CA was 0.0015 mg mL^?1,and the recoveries of CA from samples at spiking levels of 10,20,and 50μg g^?1 ranged from 90.1%-104%.The proposed method was successfully applied to ana-lyze the saponins in different tissues of A.japonicus collected in different seasons.The method developed in this study can provide quantitative technical support for the quality control of A.japonicus.