Pacific white shrimp has become a major aquaculture and fishery species worldwide.Although a large scale EST resource has been publicly available since 2008,the data have not yet been widely used for SNP discovery or ...Pacific white shrimp has become a major aquaculture and fishery species worldwide.Although a large scale EST resource has been publicly available since 2008,the data have not yet been widely used for SNP discovery or transcriptome-wide assessment of selective pressure.In this study,a set of 155 411 expressed sequence tags(ESTs) from the NCBI database were computationally analyzed and 17 225 single nucleotide polymorphisms(SNPs) were predicted,including 9 546 transitions,5 124 transversions and 2 481 indels.Among the 7 298 SNP substitutions located in functionally annotated contigs,58.4%(4 262) are non-synonymous SNPs capable of introducing amino acid mutations.Two hundred and fifty nonsynonymous SNPs in genes associated with economic traits have been identified as candidates for markers in selective breeding.Diversity estimates among the synonymous nucleotides were on average 3.49 times greater than those in non-synonymous,suggesting negative selection.Distribution of non-synonymous to synonymous substitutions(Ka/Ks) ratio ranges from 0 to 4.01,(average 0.42,median 0.26),suggesting that the majority of the affected genes are under purifying selection.Enrichment analysis identified multiple gene ontology categories under positive or negative selection.Categories involved in innate immune response and male gamete generation are rich in positively selected genes,which is similar to reports in Drosophila and primates.This work is the first transcriptome-wide assessment of selective pressure in a Penaeid shrimp species.The functionally annotated SNPs provide a valuable resource of potential molecular markers for selective breeding.展开更多
Distribution of extracellular β-glucosidase activity (β-GlcA), bacteria abundance andTOC were investigated during tbe SCSMEX98 cruise in May and June 1998 in the South China Sea. Re-sults showed that β-GlcA varied ...Distribution of extracellular β-glucosidase activity (β-GlcA), bacteria abundance andTOC were investigated during tbe SCSMEX98 cruise in May and June 1998 in the South China Sea. Re-sults showed that β-GlcA varied significantly in both vertical and horizontal distribution. Hydrolysis rateranged from under detectable limit to 29% /h. In most cases, β-GlcA was highest in surface water; some-times there was a second-highest value at the bottom of the euphotic zone. Temperature controlled experi-ments showed that low temperature could significantly decrease β-GlcA; but that the low β-GlcA in展开更多
Concentrations of dimethylsulfide (DMS) and dimethylsulfoniopropionate (DMSP) were measured from Nov. 1995 to Sep. 1997 in seawater of Jiaozhou Bay, other ecological factors such as water temperature, salinity, Chl a ...Concentrations of dimethylsulfide (DMS) and dimethylsulfoniopropionate (DMSP) were measured from Nov. 1995 to Sep. 1997 in seawater of Jiaozhou Bay, other ecological factors such as water temperature, salinity, Chl a and zooplankton were also investigated. Distribution of DMS showed remarkable variation spatially and temporally, ranging from 0.3 to 52.3 nmol/L. Seasonally, DMS concentration was high in late spring and low in autumn and winter. There was similar but weaker seasonal variation of DMSP. Generally, DMS concentration inside the bay was higher than that outside the bay; highest concentration often occurred nearshore. In some summer and autumn cruises DMS surface water was significantly higher than that in bottom water. Analysis indicated that salinity and zooplankton had significant influence on total DMS level in seawater. The estimation of sea-air flux of DMS showed significant seasonal variation, was the highest in spring [2441 μgS/(m2·d)] and lowest in winter [272 (m2 · d) ], with an annual average of 924 μgS/(m2 ·d) .展开更多
Acting as one of the pattern recognition receptors (PRRs), C-type lectin is believed to mediate pathogen recognition and plays an important role in the clearance of pathogens as part of the innate immune system. In ...Acting as one of the pattern recognition receptors (PRRs), C-type lectin is believed to mediate pathogen recognition and plays an important role in the clearance of pathogens as part of the innate immune system. In this work, a novel C-type lectin gene (named LvLecl) was cloned from the shrimp Litopenaeus vannamei, The ORF of LvLecl is 510 bp, encoding 169 amino acids. The deduced amino acid sequence contains a putative signal peptide of 19 amino acids at the N-terminal and a carbohydrate recognition domain (CRD) at the C-terminal. LvLecl was mainly expressed in the hepatopancreas. Real-time PCR analysis indicated that the level of LvLecl transcripts significantly changed in the hepatopancreas after the shrimp were artificially challenged with LPS, Micrococcus lysodeikticus and white spot syndrome virus (WSSV). RNAi-based silencing of LvLecl resulted in increases in mortality when the shrimp were challenged with WSSV, and the median lethal time was reduced compared with controls. Although there was no characteristic "EPN" (Glu-Pro-Ser) or "QPD" (Gin-Pro-Asp) motif, the recombinant LvLecl, expressed in Escherichia coli BL21 (DE3), could also agglutinate M. lysodeikticus and Vibrio anguillarum. The agglutinating activities were calcium-dependent and could be inhibited by D-mannose, D-glucose, D-galactose and N-Acetyl-D-mannose. These results suggest that LvLecl might be involved in the immune response against WSSV and bacterial infections and contribute to non-self recognition as a pattern recognition receptor in the innate immune system of the shrimp L. vannamei.展开更多
Little is known about the genome of Pacific white shrimp (Litopenaeus vannamei). To address this, we conducted BAC (bacterial artificial chromosome) end sequencing of L. vannamei. We selected and sequenced 7 812 BAC c...Little is known about the genome of Pacific white shrimp (Litopenaeus vannamei). To address this, we conducted BAC (bacterial artificial chromosome) end sequencing of L. vannamei. We selected and sequenced 7 812 BAC clones from the BAC library LvHE from the two ends of the inserts by Sanger sequencing. After trimming and quality filtering, 11 279 BAC end sequences (BESs) including 4 609 paired- ends BESs were obtained. The total length of the BESs was 4 340 753 bp, representing 0.18% of the L. vannamei haploid genome. The lengths of the BESs ranged from 100 bp to 660 bp with an average length of 385 bp. Analysis of the BESs indicated that the L. vannamei genome is AT-rich and that the primary repeats patterns were simple sequence repeats (SSRs) and low complexity sequences. Dinucleotide and hexanucleotide repeats were the most common SSR types in the BESs. The most abundant transposable element was gypsy, which may contribute to the generation of the large genome size of L. vannamei. We successfully annotated 4 519 BESs by BLAST searching, including genes involved in immunity and sex determination. Our results provide an important resource for functional gene studies, map construction and integration, and complete genome assembly for this species.展开更多
基金Supported by the Key Program of National Natural Science Foundation of China (No.30730071)the National High Technology R&D Program of China(863 Program)(No.2012AA10A404)the Agricultural Science and Technology Achievements Transformation Funds Project(No.2010GB24910700)
文摘Pacific white shrimp has become a major aquaculture and fishery species worldwide.Although a large scale EST resource has been publicly available since 2008,the data have not yet been widely used for SNP discovery or transcriptome-wide assessment of selective pressure.In this study,a set of 155 411 expressed sequence tags(ESTs) from the NCBI database were computationally analyzed and 17 225 single nucleotide polymorphisms(SNPs) were predicted,including 9 546 transitions,5 124 transversions and 2 481 indels.Among the 7 298 SNP substitutions located in functionally annotated contigs,58.4%(4 262) are non-synonymous SNPs capable of introducing amino acid mutations.Two hundred and fifty nonsynonymous SNPs in genes associated with economic traits have been identified as candidates for markers in selective breeding.Diversity estimates among the synonymous nucleotides were on average 3.49 times greater than those in non-synonymous,suggesting negative selection.Distribution of non-synonymous to synonymous substitutions(Ka/Ks) ratio ranges from 0 to 4.01,(average 0.42,median 0.26),suggesting that the majority of the affected genes are under purifying selection.Enrichment analysis identified multiple gene ontology categories under positive or negative selection.Categories involved in innate immune response and male gamete generation are rich in positively selected genes,which is similar to reports in Drosophila and primates.This work is the first transcriptome-wide assessment of selective pressure in a Penaeid shrimp species.The functionally annotated SNPs provide a valuable resource of potential molecular markers for selective breeding.
基金This study was supported by NSFC project No.40232021,30170189 and 40176037
文摘Distribution of extracellular β-glucosidase activity (β-GlcA), bacteria abundance andTOC were investigated during tbe SCSMEX98 cruise in May and June 1998 in the South China Sea. Re-sults showed that β-GlcA varied significantly in both vertical and horizontal distribution. Hydrolysis rateranged from under detectable limit to 29% /h. In most cases, β-GlcA was highest in surface water; some-times there was a second-highest value at the bottom of the euphotic zone. Temperature controlled experi-ments showed that low temperature could significantly decrease β-GlcA; but that the low β-GlcA in
基金This study was supported by the NSFC project No.40232021,30170189 and 40176037
文摘Concentrations of dimethylsulfide (DMS) and dimethylsulfoniopropionate (DMSP) were measured from Nov. 1995 to Sep. 1997 in seawater of Jiaozhou Bay, other ecological factors such as water temperature, salinity, Chl a and zooplankton were also investigated. Distribution of DMS showed remarkable variation spatially and temporally, ranging from 0.3 to 52.3 nmol/L. Seasonally, DMS concentration was high in late spring and low in autumn and winter. There was similar but weaker seasonal variation of DMSP. Generally, DMS concentration inside the bay was higher than that outside the bay; highest concentration often occurred nearshore. In some summer and autumn cruises DMS surface water was significantly higher than that in bottom water. Analysis indicated that salinity and zooplankton had significant influence on total DMS level in seawater. The estimation of sea-air flux of DMS showed significant seasonal variation, was the highest in spring [2441 μgS/(m2·d)] and lowest in winter [272 (m2 · d) ], with an annual average of 924 μgS/(m2 ·d) .
基金Supported by the National Basic Research Program of China (973 Program) (No. 2006CB101804)the National Natural Science Foundation of China (No. 30972245)Public Industry (Agriculture) Specific Research Program (No. 200803012)
文摘Acting as one of the pattern recognition receptors (PRRs), C-type lectin is believed to mediate pathogen recognition and plays an important role in the clearance of pathogens as part of the innate immune system. In this work, a novel C-type lectin gene (named LvLecl) was cloned from the shrimp Litopenaeus vannamei, The ORF of LvLecl is 510 bp, encoding 169 amino acids. The deduced amino acid sequence contains a putative signal peptide of 19 amino acids at the N-terminal and a carbohydrate recognition domain (CRD) at the C-terminal. LvLecl was mainly expressed in the hepatopancreas. Real-time PCR analysis indicated that the level of LvLecl transcripts significantly changed in the hepatopancreas after the shrimp were artificially challenged with LPS, Micrococcus lysodeikticus and white spot syndrome virus (WSSV). RNAi-based silencing of LvLecl resulted in increases in mortality when the shrimp were challenged with WSSV, and the median lethal time was reduced compared with controls. Although there was no characteristic "EPN" (Glu-Pro-Ser) or "QPD" (Gin-Pro-Asp) motif, the recombinant LvLecl, expressed in Escherichia coli BL21 (DE3), could also agglutinate M. lysodeikticus and Vibrio anguillarum. The agglutinating activities were calcium-dependent and could be inhibited by D-mannose, D-glucose, D-galactose and N-Acetyl-D-mannose. These results suggest that LvLecl might be involved in the immune response against WSSV and bacterial infections and contribute to non-self recognition as a pattern recognition receptor in the innate immune system of the shrimp L. vannamei.
基金Supported by the National Natural Science Foundation of China (Nos.30972245, 30730071)the National Basic Research Program of China (973 Program) (No. 2012CB114403)
文摘Little is known about the genome of Pacific white shrimp (Litopenaeus vannamei). To address this, we conducted BAC (bacterial artificial chromosome) end sequencing of L. vannamei. We selected and sequenced 7 812 BAC clones from the BAC library LvHE from the two ends of the inserts by Sanger sequencing. After trimming and quality filtering, 11 279 BAC end sequences (BESs) including 4 609 paired- ends BESs were obtained. The total length of the BESs was 4 340 753 bp, representing 0.18% of the L. vannamei haploid genome. The lengths of the BESs ranged from 100 bp to 660 bp with an average length of 385 bp. Analysis of the BESs indicated that the L. vannamei genome is AT-rich and that the primary repeats patterns were simple sequence repeats (SSRs) and low complexity sequences. Dinucleotide and hexanucleotide repeats were the most common SSR types in the BESs. The most abundant transposable element was gypsy, which may contribute to the generation of the large genome size of L. vannamei. We successfully annotated 4 519 BESs by BLAST searching, including genes involved in immunity and sex determination. Our results provide an important resource for functional gene studies, map construction and integration, and complete genome assembly for this species.