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Guofan Zhang - One of the best experts on this subject based on the ideXlab platform.
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de novo transcriptome sequencing reveals candidate genes involved in orange shell coloration of bay scallop Argopecten irradians
Journal of Oceanology and Limnology, 2018Co-Authors: Wen Teng, Rihao Cong, Huayong Que, Guofan ZhangAbstract:Molluscan shell color has received persistent attention for its distinctive diversity and complexity. In the present study, six transcriptome libraries obtained from two developmental stages, pre-pigmentation and post-pigmentation, were used for paired-end sequencing in the bay scallop Argopecten irradians. In total, 289 839 646 paired-end reads were assembled into 70 929 transcripts. Using BLASTX and BLASTN, 30 896 unigenes were successfully annotated against the SWISS-PROT, NR, and KOG database. Gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes classification identified numbers of unigenes involved in biomineralization and pigmentation. Digital gene expression analysis revealed that melanin, trace metal elements and porphyrins are potentially involved in shell coloration of A. irradians.
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Draft genome and SNPs associated with carotenoid accumulation in adductor muscles of bay scallop (Argopecten irradians).
Journal of genomics, 2017Co-Authors: Xuedi Du, Rihao Cong, Kai Song, Jinpeng Wang, Li Li, Guofan ZhangAbstract:Carotenoids are commonly deposited in the gonads of marine bivalves but rarely in their adductor muscles. An orange-adductor variant was identified in our breeding program for the bay scallop Argopecten irradians. In the present study, bay scallop genome survey sequencing was conducted, followed by genotyping by sequencing (GBS)-based case-control association analysis in a selfing family that exhibited segregation in adductor color. K-mer analysis (K=17) revealed that the bay scallop genome is about 990 Mb in length. De novo assembly produced 217,310 scaffold sequences, which provided 72.1% coverage of the whole genome and covered 72,187 transcripts, thereby yielding the most informative sequence resource for bay scallop to date. The average carotenoid content of the orange-adductor progenies was significantly higher than that of the white-adductor progenies. Thus, 20 individuals of each subgroup were sampled for case-control analysis. As many as 15,224 heterozygous loci were identified in the parent, among which 9280 were genotyped in at least 10 individuals of each of the two sub-groups. Association analysis indicated that 126 SNPs were associated with carotenoid accumulation in the adductor muscle and that 88 of these were significantly enriched on 28 scaffolds (FDR controlled P < 0.05). The SNPs and genes located on these scaffolds can serve as valuable candidates for further research into the mechanisms by which marine bivalves accumulate carotenoids in their adductor muscles.
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SNP Identification by Transcriptome Sequencing and Candidate Gene-Based Association Analysis for Heat Tolerance in the Bay Scallop Argopecten irradians
2016Co-Authors: Shoudu Zhang, Fei Meng, Guofan ZhangAbstract:The northern bay scallop Argopecten irradians irradians (Lamarck) and the southern bay scallop Argopecten irradians concentricus (Say) were introduced into China in the 1980s and 1990s, and are now major aquaculture molluscs in China. Here, we report the transcriptome sequencing of the two subspecies and the subsequent association analysis on candidate gene on the trait of heat tolerance. In total, RNA from six tissues of 67 and 42 individuals of northern and southern bay scallops, respectively, were used and 55.5 and 34.9 million raw reads were generated, respectively. There were 82,267 unigenes produced in total, of which 32,595 were annotated. Altogether, 32,206 and 23,312 high-quality SNPs were identified for northern and southern bay scallops, respectively. For case-control analysis, two intercrossed populations were heat stress treated, and both heat-susceptible and heat-resistant individuals were collected. According to annotation and SNP allele frequency analysis, 476 unigenes were selected, and 399 pairs of primers were designed. Genotyping was conducted using the high-resolution melting method, and Fisher’s exact test was performed for allele frequency comparison between the heat-susceptible and heat-resistant groups. SNP all-53308-760 T/C showed a significant difference in allele frequency between the heat-susceptible and heat-resistant groups. Notably, considerable difference in allele frequency at this locus was also observed between the sequenced natural populations. These results suggest that SNP all-53308-760 T/C may be related to the heat tolerance of the bay scallop. Moreover, quantitative expression analysis reveale
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snp identification by transcriptome sequencing and candidate gene based association analysis for heat tolerance in the bay scallop Argopecten irradians
PLOS ONE, 2014Co-Authors: Shoudu Zhang, Fei Meng, Guofan ZhangAbstract:The northern bay scallop Argopecten irradians irradians (Lamarck) and the southern bay scallop Argopecten irradians concentricus (Say) were introduced into China in the 1980s and 1990s, and are now major aquaculture molluscs in China. Here, we report the transcriptome sequencing of the two subspecies and the subsequent association analysis on candidate gene on the trait of heat tolerance. In total, RNA from six tissues of 67 and 42 individuals of northern and southern bay scallops, respectively, were used and 55.5 and 34.9 million raw reads were generated, respectively. There were 82,267 unigenes produced in total, of which 32,595 were annotated. Altogether, 32,206 and 23,312 high-quality SNPs were identified for northern and southern bay scallops, respectively. For case-control analysis, two intercrossed populations were heat stress treated, and both heat-susceptible and heat-resistant individuals were collected. According to annotation and SNP allele frequency analysis, 476 unigenes were selected, and 399 pairs of primers were designed. Genotyping was conducted using the high-resolution melting method, and Fisher’s exact test was performed for allele frequency comparison between the heat-susceptible and heat-resistant groups. SNP all-53308-760 T/C showed a significant difference in allele frequency between the heat-susceptible and heat-resistant groups. Notably, considerable difference in allele frequency at this locus was also observed between the sequenced natural populations. These results suggest that SNP all-53308-760 T/C may be related to the heat tolerance of the bay scallop. Moreover, quantitative expression analysis revealed that the expression level of all-53308 was negatively correlated with heat tolerance of the bay scallop.
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BROADENING OF THE GENETIC BASIS OF THE ATLANTIC BAY SCALLOP Argopecten irradians AFTER INTERSPECIFIC HYBRIDIZATION AND BACKCROSSING
Journal of Shellfish Research, 2014Co-Authors: Shoudu Zhang, Guofan ZhangAbstract:The growth characteristics and morphological features of the Atlantic bay scallop (Argopecten irradians irradians Lamarck), Chilean scallop (Argopecten purpuratus Lamarck), F1 hybrids of these species, and the offspring produced via 2 cycles of backcrossing between hybrid populations and the Atlantic bay scallop were examined to determine the feasibility of broadening the genetic basis of the bay scallop. Bidirectional fertilization and successful hatching were observed in F1 hybrids. Notable heterosis (i.e., >1% of the midparent values) was detected in growth and survival throughout the whole life span of the scallops. The F1 hybrids showed universal feminization, but with low fertilization and hatching rates observed in backcrosses with bay scallops (partial sterility). Hematoxylin-eosin staining of paraffin sections of the feminine gonads of the hybrids was performed in this study. The male gonad was found to be vestigial, without any active sperm, whereas the female gonad was well developed and presented abundant eggs with a normal appearance. Increasing fertilization and hatching rates were observed in the second generation of backcrosses between hybrid populations and bay scallops compared with the first backcrosses. At the same time, a growth advantage and low temperature resistance were regained in the offspring produced from backcrossed breeding. This study describes a promising way to broaden the genetic basis of bay scallops with the aim of improving the growth characteristics of cultured scallop stocks.
Linsheng Song - One of the best experts on this subject based on the ideXlab platform.
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X (2007) Loss of allele diversity in introduced populations of the hermaphroditic bay scallop Argopecten irradians. Aquaculture 271
2020Co-Authors: Lingling Wang, Linsheng Song, Huan Zhang, Ximing GuoAbstract:Abstract The bay scallop Argopecten irradians is a hermaphroditic bivalve native to the Atlantic coast of the United States that was introduced to China for aquaculture production in 1982. It now supports a major aquaculture industry in China. Introduced species often start with limited genetic variability, which is problematic for the further selective breeding. Bay scallop aquaculture is exclusively hatchery based and as the initial introduction consisted of only 26 scallops, there have been concerns about inbreeding and inbreeding depression in cultured populations in China. In this study, eleven simple sequence repeat (SSR) markers were used to compare genetic variation in cultured populations from China with that in a natural population from the east coast of America. Although the difference in heterozygosity was small, the Chinese populations lost 9 of the 45 alleles (20%) found in the wild population. The reduced allele diversity suggests that the Chinese bay scallop populations experienced a bottleneck in genetic diversity that remains significant despite several recent introductions of new stocks aimed at expanding the gene pool. The loss of allele diversity may affect future efforts in selective breeding and domestication, and results of this study highlight the need for additional introductions, advanced breeding programs that minimize inbreeding and continued genetic monitoring
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a new fibrinogen related protein from Argopecten irradians aifrep 2 with broad recognition spectrum and bacteria agglutination activity
Fish & Shellfish Immunology, 2014Co-Authors: Chuanyan Yang, Huan Zhang, Lingling Wang, Leilei Wang, Mengmeng Huang, Zhibin Sun, Ying Sun, Linsheng SongAbstract:Fibrinogen-related proteins (FREPs) are a kind of pattern recognition receptors (PRRs) containing fibrinogen-like (FBG) domains, and they play curial roles in the innate immune response. In the present study, a new FREP protein was identified from bay scallop Argopecten irradians (designated as AiFREP-2). The full-length cDNA of AiFREP-2 was of 1299 bp with an open reading frame of 762 bp encoding a polypeptide of 253 amino acids, including a signal sequence and an FBG domain. The FBG domain in AiFREP-2 was highly similar to those of ficolins, tenascins and other FREPs. The mRNA expression of AiFREP-2 could be detected in all the examined tissues with the highest level in gill. The mRNA expression of AiFREP-2 in hemocytes was significantly up-regulated post the stimulation of lipopolysaccharide (LPS), peptidoglycan (PGN) and β-glucan (GLU) (P < 0.01). The recombinant AiFREP-2 (rAiFREP-2) could bind not only different PAMP ligands including LPS, PGN and GLU, but also various microbes including Gram-negative bacteria (Vibrio anguillarum), Gram-positive bacteria (Staphylococcus aureus) and fungus (Pichia pastoris and Yarrowia lipolytica). Additionally, rAiFREP-2 exhibited obvious agglutination activity towards Gram-negative bacteria V. anguillarum and Gram positive bacteria S. aureus. The results indicated that AiFREP-2 was involved in the immune response against Gram-negative bacteria, Gram-positive bacteria and fungus as a PRR in bay scallop, and the information was helpful to understand the innate immune defense mechanisms of mollusks.
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The Polymorphism in the Promoter of HSP70 Gene Is Associated with Heat Tolerance of Two Congener Endemic Bay Scallops (Argopecten irradians irradians and A. i. concentricus)
2014Co-Authors: Chuanyan Yang, Huan Zhang, Lingling Wang, Limei Qiu, Jingjing Wang, Qiufen Jiang, Linsheng SongAbstract:BackgroundThe heat shock protein 70 (HSP70) is one kind of molecular chaperones, which plays a key role in protein metabolism under normal and stress conditions.MethodologyIn the present study, the mRNA expressions of HSP70 under normal physiological condition and after acute heat stress were investigated in gills of two bay scallop populations (Argopecten irradians irradians and A. i. concentricus). The heat resistant scallops A. i. concentricus showed significantly lower basal level and higher induction of HSP70 compared with that of the heat sensitive scallops A. i. irradians. The promoter sequence of HSP70 gene from bay scallop (AiHSP70) was cloned and the polymorphisms within this region were investigated to analyze their association with heat tolerance. Totally 11 single nucleotide polymorphisms (SNPs) were identified, and four of them (−967, −480, −408 and −83) were associated with heat tolerance after HWE analysis and association analysis. Based on the result of linkage disequilibrium analysis, the in vitro transcriptional activities of AiHSP70 promoters with different genotype were further determined, and the results showed that promoter from A. i. concentricus exhibited higher transcriptional activity than that from A. i. irradians (P
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a c type lectin aictl 3 from bay scallop Argopecten irradians with mannose galactose binding ability to bind various bacteria
Gene, 2013Co-Authors: Mengmeng Huang, Huan Zhang, Jianmin Zhao, Lingling Wang, Zhi Zhou, Xiaoyan Song, Xiaolin Liu, Linsheng SongAbstract:C-type lectins are a family of Ca(2+)-dependent carbohydrate-binding proteins playing crucial roles in innate immunity of vertebrates and invertebrates. In the present study, the cDNA of a C-type lectin with one carbohydrate-recognition domain (CRD) of 127 amino acids was cloned from bay scallop Argopecten irradians (designated AiCTL-3) by rapid amplification of cDNA end (RACE) techniques based on expressed sequence tag (EST) analysis. The mRNA transcripts of AiCTL-3 could be detected in all the tested tissues including hepatopancreas, gonad, adductor muscle, heart, hemocytes, mantle and gill, with the highest expression level in hepatopancreas. After the challenges with Vibrio anguillarum and Micrococcus luteus, the mRNA expression level of AiCTL-3 was obviously up-regulated and reached the maximum level at 9h (11.87fold, P<0.01, and 20.02-fold, P<0.05, respectively). The recombinant AiCTL-3 (designated as rAiCTL-3) could bind LPS, PGN, and glucan in vitro, but could not bind mannan. And it also bound Gram-positive bacteria Staphylococcus aureus as well as Gram-negative bacteria Escherichia coli and V. anguillarum. With a Ca(2+) binding site 2 EPN (Glu-Pro-Asn) motif, rAiCTL-3 could bind both mannose and galactose which was quite different from those in vertebrate. Meanwhile, it could significantly enhance the phagocytosis of scallop hemocytes in vitro. The results clearly suggested that AiCTL-3 could serve not only as a PRR participated in the immune response against various PAMPs and bacteria in non-self recognition via mannose/galactose binding specificity but an opsonin playing an important part in clearance of invaders.
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a novel c1qdc protein acting as pattern recognition receptor in scallop Argopecten irradians
Fish & Shellfish Immunology, 2012Co-Authors: Leilei Wang, Huan Zhang, Lingling Wang, Pengfei Kong, Jialong Yang, Mengqiang Wang, Zhi Zhou, Limei Qiu, Linsheng SongAbstract:The C1q domain containing (C1qDC) proteins refer to a family of proteins containing the versatile charge pattern recognition globular C1q domain in the C-terminus, which could bind various ligands including PAMPs and trigger a serial of immune response. In this study, a novel C1qDC protein was identified from Argopecten irradians (designated as AiC1qDC-2). Its full-length cDNA was of 1062 bp with an open reading frame of 720 bp encoding a polypeptide of 240 amino acids containing a typical gC1 q domain. This gC1q domain possessed the typical 10-stranded beta-sandwich fold with a jelly-roll topology common to all C1q family members, and shared high homology with most of the other identified gC1q domains. The mRNA transcripts of AiC1qDC-2 were mainly detected in hepatopancreas, and also marginally detectable in mantle, gonad, adductor, gill and hemocytes. Its relative expression level in hemocytes was significantly up-regulated after challenges of fungi Pichia pastoris GS115 (P < 0.05), Gram-positive bacteria Micrococcus luteus (P < 0.05) and Gram-negative bacteria Vibrio anguillarum (P < 0.05). The recombinant protein of AiC1qDC-2 (rAiC1qDC-2) could bind various PAMPs, including LPS, PGN, polyI:C, mannan, beta-1,3-glucan as well as Yeast-glucan, and displayed agglutinating activity to fungi P. pastoris GS115, Gram-positive bacteria Bacillus subtilis and Gram-negative bacteria Escherichia coli TOP10F as well as V. anguillarum. All these results indicated that AiC1qDC-2 could function as a pattern recognition receptor to recognize various PAMPs on different pathogens in the innate immune responses of scallop, and provided new clues to understand the role of invertebrate C1qDC proteins in the ancient complement system. (c) 2012 Elsevier Ltd. All rights reserved.
Huan Zhang - One of the best experts on this subject based on the ideXlab platform.
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X (2007) Loss of allele diversity in introduced populations of the hermaphroditic bay scallop Argopecten irradians. Aquaculture 271
2020Co-Authors: Lingling Wang, Linsheng Song, Huan Zhang, Ximing GuoAbstract:Abstract The bay scallop Argopecten irradians is a hermaphroditic bivalve native to the Atlantic coast of the United States that was introduced to China for aquaculture production in 1982. It now supports a major aquaculture industry in China. Introduced species often start with limited genetic variability, which is problematic for the further selective breeding. Bay scallop aquaculture is exclusively hatchery based and as the initial introduction consisted of only 26 scallops, there have been concerns about inbreeding and inbreeding depression in cultured populations in China. In this study, eleven simple sequence repeat (SSR) markers were used to compare genetic variation in cultured populations from China with that in a natural population from the east coast of America. Although the difference in heterozygosity was small, the Chinese populations lost 9 of the 45 alleles (20%) found in the wild population. The reduced allele diversity suggests that the Chinese bay scallop populations experienced a bottleneck in genetic diversity that remains significant despite several recent introductions of new stocks aimed at expanding the gene pool. The loss of allele diversity may affect future efforts in selective breeding and domestication, and results of this study highlight the need for additional introductions, advanced breeding programs that minimize inbreeding and continued genetic monitoring
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a new fibrinogen related protein from Argopecten irradians aifrep 2 with broad recognition spectrum and bacteria agglutination activity
Fish & Shellfish Immunology, 2014Co-Authors: Chuanyan Yang, Huan Zhang, Lingling Wang, Leilei Wang, Mengmeng Huang, Zhibin Sun, Ying Sun, Linsheng SongAbstract:Fibrinogen-related proteins (FREPs) are a kind of pattern recognition receptors (PRRs) containing fibrinogen-like (FBG) domains, and they play curial roles in the innate immune response. In the present study, a new FREP protein was identified from bay scallop Argopecten irradians (designated as AiFREP-2). The full-length cDNA of AiFREP-2 was of 1299 bp with an open reading frame of 762 bp encoding a polypeptide of 253 amino acids, including a signal sequence and an FBG domain. The FBG domain in AiFREP-2 was highly similar to those of ficolins, tenascins and other FREPs. The mRNA expression of AiFREP-2 could be detected in all the examined tissues with the highest level in gill. The mRNA expression of AiFREP-2 in hemocytes was significantly up-regulated post the stimulation of lipopolysaccharide (LPS), peptidoglycan (PGN) and β-glucan (GLU) (P < 0.01). The recombinant AiFREP-2 (rAiFREP-2) could bind not only different PAMP ligands including LPS, PGN and GLU, but also various microbes including Gram-negative bacteria (Vibrio anguillarum), Gram-positive bacteria (Staphylococcus aureus) and fungus (Pichia pastoris and Yarrowia lipolytica). Additionally, rAiFREP-2 exhibited obvious agglutination activity towards Gram-negative bacteria V. anguillarum and Gram positive bacteria S. aureus. The results indicated that AiFREP-2 was involved in the immune response against Gram-negative bacteria, Gram-positive bacteria and fungus as a PRR in bay scallop, and the information was helpful to understand the innate immune defense mechanisms of mollusks.
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The Polymorphism in the Promoter of HSP70 Gene Is Associated with Heat Tolerance of Two Congener Endemic Bay Scallops (Argopecten irradians irradians and A. i. concentricus)
2014Co-Authors: Chuanyan Yang, Huan Zhang, Lingling Wang, Limei Qiu, Jingjing Wang, Qiufen Jiang, Linsheng SongAbstract:BackgroundThe heat shock protein 70 (HSP70) is one kind of molecular chaperones, which plays a key role in protein metabolism under normal and stress conditions.MethodologyIn the present study, the mRNA expressions of HSP70 under normal physiological condition and after acute heat stress were investigated in gills of two bay scallop populations (Argopecten irradians irradians and A. i. concentricus). The heat resistant scallops A. i. concentricus showed significantly lower basal level and higher induction of HSP70 compared with that of the heat sensitive scallops A. i. irradians. The promoter sequence of HSP70 gene from bay scallop (AiHSP70) was cloned and the polymorphisms within this region were investigated to analyze their association with heat tolerance. Totally 11 single nucleotide polymorphisms (SNPs) were identified, and four of them (−967, −480, −408 and −83) were associated with heat tolerance after HWE analysis and association analysis. Based on the result of linkage disequilibrium analysis, the in vitro transcriptional activities of AiHSP70 promoters with different genotype were further determined, and the results showed that promoter from A. i. concentricus exhibited higher transcriptional activity than that from A. i. irradians (P
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a c type lectin aictl 3 from bay scallop Argopecten irradians with mannose galactose binding ability to bind various bacteria
Gene, 2013Co-Authors: Mengmeng Huang, Huan Zhang, Jianmin Zhao, Lingling Wang, Zhi Zhou, Xiaoyan Song, Xiaolin Liu, Linsheng SongAbstract:C-type lectins are a family of Ca(2+)-dependent carbohydrate-binding proteins playing crucial roles in innate immunity of vertebrates and invertebrates. In the present study, the cDNA of a C-type lectin with one carbohydrate-recognition domain (CRD) of 127 amino acids was cloned from bay scallop Argopecten irradians (designated AiCTL-3) by rapid amplification of cDNA end (RACE) techniques based on expressed sequence tag (EST) analysis. The mRNA transcripts of AiCTL-3 could be detected in all the tested tissues including hepatopancreas, gonad, adductor muscle, heart, hemocytes, mantle and gill, with the highest expression level in hepatopancreas. After the challenges with Vibrio anguillarum and Micrococcus luteus, the mRNA expression level of AiCTL-3 was obviously up-regulated and reached the maximum level at 9h (11.87fold, P<0.01, and 20.02-fold, P<0.05, respectively). The recombinant AiCTL-3 (designated as rAiCTL-3) could bind LPS, PGN, and glucan in vitro, but could not bind mannan. And it also bound Gram-positive bacteria Staphylococcus aureus as well as Gram-negative bacteria Escherichia coli and V. anguillarum. With a Ca(2+) binding site 2 EPN (Glu-Pro-Asn) motif, rAiCTL-3 could bind both mannose and galactose which was quite different from those in vertebrate. Meanwhile, it could significantly enhance the phagocytosis of scallop hemocytes in vitro. The results clearly suggested that AiCTL-3 could serve not only as a PRR participated in the immune response against various PAMPs and bacteria in non-self recognition via mannose/galactose binding specificity but an opsonin playing an important part in clearance of invaders.
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a novel c1qdc protein acting as pattern recognition receptor in scallop Argopecten irradians
Fish & Shellfish Immunology, 2012Co-Authors: Leilei Wang, Huan Zhang, Lingling Wang, Pengfei Kong, Jialong Yang, Mengqiang Wang, Zhi Zhou, Limei Qiu, Linsheng SongAbstract:The C1q domain containing (C1qDC) proteins refer to a family of proteins containing the versatile charge pattern recognition globular C1q domain in the C-terminus, which could bind various ligands including PAMPs and trigger a serial of immune response. In this study, a novel C1qDC protein was identified from Argopecten irradians (designated as AiC1qDC-2). Its full-length cDNA was of 1062 bp with an open reading frame of 720 bp encoding a polypeptide of 240 amino acids containing a typical gC1 q domain. This gC1q domain possessed the typical 10-stranded beta-sandwich fold with a jelly-roll topology common to all C1q family members, and shared high homology with most of the other identified gC1q domains. The mRNA transcripts of AiC1qDC-2 were mainly detected in hepatopancreas, and also marginally detectable in mantle, gonad, adductor, gill and hemocytes. Its relative expression level in hemocytes was significantly up-regulated after challenges of fungi Pichia pastoris GS115 (P < 0.05), Gram-positive bacteria Micrococcus luteus (P < 0.05) and Gram-negative bacteria Vibrio anguillarum (P < 0.05). The recombinant protein of AiC1qDC-2 (rAiC1qDC-2) could bind various PAMPs, including LPS, PGN, polyI:C, mannan, beta-1,3-glucan as well as Yeast-glucan, and displayed agglutinating activity to fungi P. pastoris GS115, Gram-positive bacteria Bacillus subtilis and Gram-negative bacteria Escherichia coli TOP10F as well as V. anguillarum. All these results indicated that AiC1qDC-2 could function as a pattern recognition receptor to recognize various PAMPs on different pathogens in the innate immune responses of scallop, and provided new clues to understand the role of invertebrate C1qDC proteins in the ancient complement system. (c) 2012 Elsevier Ltd. All rights reserved.
Anne L. Cohen - One of the best experts on this subject based on the ideXlab platform.
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elevated pco2 exposure during fertilization of the bay scallop Argopecten irradians reduces larval survival but not subsequent shell size
Marine Ecology Progress Series, 2014Co-Authors: Meredith M. White, Daniel C. Mccorkle, Lauren S. Mullineaux, Anne L. CohenAbstract:Ocean acidification, characterized by elevated partial pressure of CO2 (pCO2), gen- erally has negative effects on early life stages of invertebrates. We tested the idea that fertilization is a critical CO2 exposure stage for the bay scallop Argopecten irradians by determining the effects on bay scallops of exposure to high CO2 (pCO2 ~2600 ppm, pH ~7.30) from fertilization to 7 d old. To assess the possibility of persistent effects of exposure during fertilization, further treat- ments included switches from high CO2 to ambient CO2 (pCO2 ~480 ppm, pH ~7.96) and from ambient CO2 to high CO2 at 2 h post-fertilization. Survival of larvae decreased significantly when they were fertilized in high CO2. A switch in CO2 conditions 2 h post-fertilization did not change this effect, suggesting that the critical exposure window for this survival effect is within the first 2 h. In contrast, CO2 conditions during fertilization did not affect larval shell size, but the switch treatments showed that exposure to high CO2 after 2 h post-fertilization decreased shell size, indi- cating that the exposure window for a size effect was later in development, possibly during shell calcification. Finally, a shell deformity was seen in scallops with continuous exposure to high CO2 and those switched from ambient CO2 to high CO2 at 2 h post-fertilization. Decreased survival during fertilization and smaller larval shell size due to ocean acidification could ultimately reduce the population size of this commercially important bivalve, which has already seen dramatic population decline due to loss of juvenile habitat.
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early exposure of bay scallops Argopecten irradians to high co2 causes a decrease in larval shell growth
PLOS ONE, 2013Co-Authors: Meredith M. White, Daniel C. Mccorkle, Lauren S. Mullineaux, Anne L. CohenAbstract:Ocean acidification, characterized by elevated pCO2 and the associated decreases in seawater pH and calcium carbonate saturation state (Ω), has a variable impact on the growth and survival of marine invertebrates. Larval stages are thought to be particularly vulnerable to environmental stressors, and negative impacts of ocean acidification have been seen on fertilization as well as on embryonic, larval, and juvenile development and growth of bivalve molluscs. We investigated the effects of high CO2 exposure (resulting in pH = 7.39, Ωar = 0.74) on the larvae of the bay scallop Argopecten irradians from 12 h to 7 d old, including a switch from high CO2 to ambient CO2 conditions (pH = 7.93, Ωar = 2.26) after 3 d, to assess the possibility of persistent effects of early exposure. The survival of larvae in the high CO2 treatment was consistently lower than the survival of larvae in ambient conditions, and was already significantly lower at 1 d. Likewise, the shell length of larvae in the high CO2 treatment was significantly smaller than larvae in the ambient conditions throughout the experiment and by 7 d, was reduced by 11.5%. This study also demonstrates that the size effects of short-term exposure to high CO2 are still detectable after 7 d of larval development; the shells of larvae exposed to high CO2 for the first 3 d of development and subsequently exposed to ambient CO2 were not significantly different in size at 3 and 7 d than the shells of larvae exposed to high CO2 throughout the experiment.
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One-way ANOVAs of mean shell length (µm) of Argopecten irradians larvae raised in three CO2 treatment regimes (Ambient CO2, High CO2/Ambient, and High CO2) at 1, 3, and 7 d; n = 6 replicate culture containers per treatment.
2013Co-Authors: Meredith M. White, Daniel C. Mccorkle, Lauren S. Mullineaux, Anne L. CohenAbstract:One-way ANOVAs of mean shell length (µm) of Argopecten irradians larvae raised in three CO2 treatment regimes (Ambient CO2, High CO2/Ambient, and High CO2) at 1, 3, and 7 d; n = 6 replicate culture containers per treatment.
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One-way ANOVAs of mean percent survival (arcsine-square root-transformed) of Argopecten irradians larvae raised in three CO2 treatment regimes (Ambient CO2, High CO2/Ambient, and High CO2) at 1, 3, and 7 d; n = 5 replicate culture containers for Ambient CO2 treatment, n = 6 replicate culture containers each for High CO2/Ambient and High CO2 treatments.
2013Co-Authors: Meredith M. White, Daniel C. Mccorkle, Lauren S. Mullineaux, Anne L. CohenAbstract:One-way ANOVAs of mean percent survival (arcsine-square root-transformed) of Argopecten irradians larvae raised in three CO2 treatment regimes (Ambient CO2, High CO2/Ambient, and High CO2) at 1, 3, and 7 d; n = 5 replicate culture containers for Ambient CO2 treatment, n = 6 replicate culture containers each for High CO2/Ambient and High CO2 treatments.
Xiao Liu - One of the best experts on this subject based on the ideXlab platform.
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draft genomes of two atlantic bay scallop subspecies Argopecten irradians irradians and a i concentricus
Scientific Data, 2020Co-Authors: Xiao Liu, Min Chen, Bo Liu, Guilong Liu, Zhaoshan Zhong, Qiong Shi, Xiaojun Yan, Junhao Ning, Yanglei Jia, Chunde WangAbstract:The two subspecies of Atlantic bay scallop (Argopecten irradians), A. i. irradians and A. i. concentricus, are economically important aquacultural species in northern and southern China. Here, we performed the whole-genome sequencing, assembly, and gene annotation and produced draft genomes for both subspecies. In total, 253.17 and 272.97 gigabases (Gb) of raw reads were generated from Illumina Hiseq and PacBio platforms for A. i. irradians and A. i. concentricus, respectively. Draft genomes of 835.7 Mb and 874.82 Mb were assembled for the two subspecies, accounting for 83.9% and 89.79% of the estimated sizes of their corresponding genomes, respectively. The contig N50 and scaffold N50 were 78.54 kb and 1.53 Mb for the A. i. irradians genome, and those for the A. i. concentricus genome were 63.73 kb and 1.25 Mb. Moreover, 26,777 and 25,979 protein-coding genes were predicted for A. i. irradians and A. i. concentricus, respectively. These valuable genome assemblies lay a solid foundation for future theoretical studies and provide guidance for practical scallop breeding. Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.11961984
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Genome annotation for Argopecten irradians irradians and Argopecten irradians concentricus
2019Co-Authors: Chunde Wang, Xiao Liu, Min Chen, Bo Liu, Guilong Liu, Zhaoshan Zhong, Qiong ShiAbstract:Genome annotation for Argopecten irradians irradians and Argopecten irradians concentricu
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development and linkage analysis of 104 new microsatellite markers for bay scallop Argopecten irradians
Marine Biotechnology, 2012Co-Authors: Xiao Liu, Guofan ZhangAbstract:For genetic analysis and linkage mapping of bay scallop (Argopecten irradians), a set of 120 novel simple sequence repeat markers were developed from microsatellite-enriched libraries and expressed sequence tags. An inter-subspecies hybrid bay scallop family (CC5) of 46 progeny was analyzed as the reference population to confirm polymorphism and test the segregation patterns of these loci. A total of 104 microsatellite markers were polymorphic in the reference family, among which 36 in female, 28 in male, and 40 in both parents, respectively. Linkage analysis allowed mapping these markers to 15 linkage groups, which is close to the haploid chromosome number of bay scallop (n = 16). Analysis of the 40 markers segregating in both parents showed a higher recombination rate in the female parent, with the average of female-to-male recombination ratio of 1.09:1 between linked pairs of markers. When null alleles were considered, there were 17 loci showing segregation distortion at the 5% significance level using the chi-square test. The microsatellite markers developed in this study provide a useful resource for future linkage mapping and quantitative loci analysis in A. irradians.
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production of a base population and its responses to f1 selection in the bay scallop Argopecten irradians irradians lamarck 1819
Aquaculture Research, 2008Co-Authors: Haibin Zhang, Guofan Zhang, Xiao Liu, Chunde WangAbstract:A base population of the bay scallop, Argopecten irradians irradians Lamarck, was produced by crossing two cultured bay scallop populations. After 1 year of rearing, the top 10% truncation selection of the top 10% (i=1.755) was carried out in the base population of about 1300 adults. A control parental group with a an identical number to the select parental group was randomly selected from the entire population before isolation of the select parental group. The result showed that, at the larval stage, the growth rate of larvae in the selected line was significantly higher than that of the control (P < 0.05), and that the genetic gain was 6.78%. Owing to the lower density of control at the spat stage, the mean shell length of the control line was larger than that of the select line at day 100. When the same density was adjusted between two lines in the grow-out stage (from day 100 to 160), the daily growth rate of the selected line was significantly higher than that of the control line (P < 0.05). Survival of the select line was significantly larger than that of the control line in the grow-out stage. In conclusion, the results obtained from this experiment indicate that selective breeding from a base population with a high genetic diversity established by mass spawning between different populations appears to be a promising method of genetic improvement in bay scallop, A. irradians irradians Lamarck.
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genetic mapping of size related quantitative trait loci qtl in the bay scallop Argopecten irradians using aflp and microsatellite markers
Aquaculture, 2007Co-Authors: Yanjie Qin, Xiao Liu, Guofan Zhang, Haibin Zhang, Ximing GuoAbstract:We constructed genetic linkage maps for the bay scallop Argopecten irradians using AFLP and microsatellite markers and conducted composite interval mapping (CIM) of body-size-related traits. Three hundred seventeen AFLP and 10 microsatellite markers were used for map construction. The female parent map contained 120 markers in 15 linkage groups, spanning 479.6 cM with an average interval of 7.0 cM. The male parent map had 190 markers in 17 linkage groups, covering 883.8 cM at 7.2 cM per marker. The observed coverage was 70.4% for the female and 81.1% for the male map. Markers that were distorted toward the same direction were closely linked to each other on the genetic maps, suggesting the presence of genes important for survival. Six size-related traits, shell length, shell height, shell width, total weight, soft tissue weight, and shell weight, were measured for QTL mapping. The size data were significantly correlated with each other. We subjected the data, log transformed firstly, to a principle component analysis and use the first principle component for QTL mapping. CIM analysis revealed one significant QTL (LOD=2.69, 1000 permutation, P<0.05) in linkage group 3 on the female parent map. The mapping of size-related QTL in this study raises the possibility of improving the growth of bay scallops through marker-assisted selection. (c) 2007 Published by Elsevier B.V.