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Marc Suquet - One of the best experts on this subject based on the ideXlab platform.
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ATP content and viability of spermatozoa drive variability of fertilization success in the Pacific Oyster (Crassostrea gigas)
Aquaculture, 2017Co-Authors: Myrina Boulais, Claudie Quéré, Pierre Boudry, Philippe Soudant, Nelly Le Goïc, Marc SuquetAbstract:Fertilization of the oocyte is a critical process of sexual reproduction depending among other factors on spermatozoa functionality. Mitochondria participate in many crucial processes for spermatozoa motility and fertilizing ability. The Pacific Oyster, Crassostrea gigas, is characterized by a high inter-individual variability of its reproductive success which has been shown to be partially due to the variability of gamete quality. The present study explored spermatozoa characteristics such as: i) relationships among mitochondrial functionality (ATP content, mitochondrial membrane potential (MMP), reactive oxygen species production); sperm viability (percentages of live, dying, and dead); and motility; and ii) their involvement in inter-Oyster variability of fertilizing ability demonstrated using simple and multiple regressions. Our results showed that ATP content depends on both MMP and viability of spermatozoa. Using multiple regressions, 61% of the variability of the trochophore-larval yield was explained by a model combining the ATP content and the percentage of dying spermatozoa (P\textless0.001). Our results reveal that capacity of spermatozoa to maintain a high level of ATP via OXPHOS partly explains the inter-individual variability of fertilization success in the Pacific Oyster. Sperm ATP content and viability assays will provide valuable tools for assessing sperm quality of this species in aquaculture production, cryopreservation, and bioassays.
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Seasonal variation of sperm quality in Pacific Oyster (Crassostrea gigas)
Aquaculture, 2016Co-Authors: Marc Suquet, Isabelle Queau, Florent Malo, Dominique Ratiskol, Claudie Quéré, Jacqueline Le Grand, Christian FauvelAbstract:Seasonal changes of sperm quality which can affect sperm biological parameters throughout the breeding period, have been little studied in mollusc species. Controlling gamete quality would aid the management of gametes in hatcheries and the development of selection programs. The aim of the present study was to describe the changes in sperm quality of wild Pacific Oysters through the spawning season by comparing sperm parameters at the beginning (May), middle (July) and end (October) of this period using a panel of bio-descriptors. These parameters were studied over the 2014 breeding season based on shed sperm collected after serotonin injection of wild breeders. A significantly higher percentage of motile sperm was observed at the end of the spawning season (+ 78% relative to the value observed at the beginning) althought a lower total number of spermatozoa was collected (− 59%). The mean condition index of Oysters, however, was no different between the three sampling dates. For intratesticular sperm, the increase of the percentage of motile sperm and Velocity of the Average Path (VAP) in relation to time post activation was not significantly different among sperm sampling periods, suggesting that the kinetic of the sperm maturation process was similar. Furthermore, the mean VAP observed on shed sperm did not change through the spawning season. The sub-continuous gametogenesis of Pacific Oyster can help to explain why only limited consequences of sperm ageing are observed in this species. Furthermore, the effects of sperm ageing may depend on the annual reproductive pattern of Pacific Oyster. Statement of relevance This study showed the effect of sperm ageing on sperm quality parameters. This knowledge is useful for aquaculture and would support the recent trends of mollusc farming, allowing a better management of the gametes in hatchery.
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Assessment of oocyte and trochophore quality in Pacific Oyster, Crassostrea gigas
Aquaculture, 2015Co-Authors: Myrina Boulais, Claudie Quéré, Charlotte Corporeau, Arnaud Huvet, Ismaël Bernard, Virgile Quillien, Caroline Fabioux, Marc SuquetAbstract:Pacific Oyster hatchery production remains highly variable, partially due to inconsistent gamete quality. However, little attention has been paid to oocyte quality in Pacific Oyster compared to important vertebrate aqua-culture species such as fishes. The aims of the present study were to identify criteria of oocyte and trochophore quality used as predictive tools for embryo developmental success at the D-larval stage. Twenty-six potential proxies of oocyte and trochophore quality were studied on 25 mature females, as determined using histology. Some morphological and biochemical characteristics of mature oocytes were described. Protein appeared to be the main constituent of fully mature Pacific Oyster oocytes. Neutral lipids accounted for 61% of the total lipids and triglycerides for 85% of the neutral lipids. Oocyte fertilization capacity was assessed by determining the D-larval yield. High inter-individual variation of D-larval yield was observed (ranging from 1% to 58%). D-larval yield was positively correlated with the percentage of motile trochophores (R-2 = 0.237) and with trochophore velocity of the average path (VAP; R-2 = 0.255) and negatively correlated with oocyte total steryl esters (R-2 = 0.244). The use of a multivariate model, including D-larval yield, trochophore VAP and total steryl esters, led to a higher coefficient of determination (R-2 = 0.352), highlighting that the prediction of embryo development in mollusks is a complex process requiring sophisticated multi-factor models.
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Involvement of Mitochondrial Activity and OXPHOS in ATP Synthesis During the Motility Phase of Spermatozoa in the Pacific Oyster, Crassostrea gigas
Biology of Reproduction, 2015Co-Authors: Myrina Boulais, Claudie Quéré, Pierre Boudry, Philippe Soudant, Nelly Le Goïc, Marc SuquetAbstract:In the Pacific Oyster, spermatozoa are characterized by a remarkably long movement phase (i.e., over 24 h) sustained by a capacity to maintain intracellular ATP level. To gain information on oxidative phosphorylation (OXPHOS) functionality during the motility phase of Pacific Oyster spermatozoa, we studied: i) changes in spermatozoa mitochondrial activity (i.e., mitochondrial membrane potential, MMP) and intracellular ATP content in relation to motion parameters and ii) the involvement of OXPHOS for spermatozoa movement using CCCP. The percentage of motile spermatozoa decreased over a 24 h movement period. MMP increased steadily during the first 9 h of the movement phase and was subsequently maintained at a constant level. Conversely, spermatozoa ATP content decreased steadily during the first 9 h post activation and was maintained at this level during the following hours of the movement phase. When OXPHOS was decoupled by CCCP, the movement of spermatozoa was maintained 2 h and totally stopped after 4 h of incubation, whereas spermatozoa were still motile in the control after 4 h. Our results suggest that ATP sustaining flagellar movement of spermatozoa may partially originate from glycolysis or from mobilization of stored ATP or potential phosphagens during the first 2 h of movement as OXPHOS was decoupled by CCCP. However, OXPHOS is required to sustain the long motility phase of Pacific Oyster spermatozoa. In addition, spermatozoa may hydrolyse intracellular ATP content during the early part of the movement phase, stimulating mitochondrial activity. This stimulation seems to be involved in sustaining a high ATP level until the end of the motility phase.
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Marathon vs sprint racers: an adaptation of sperm characteristics to the reproductive strategy of Pacific Oyster, turbot and seabass
Journal of Applied Ichthyology, 2012Co-Authors: Marc Suquet, J. Cosson, A. Donval, Catherine Labbé, M. Boulais, P. Haffray, I. Bernard, Christian FauvelAbstract:This work assesses the present knowledge on Pacific Oyster sperm biology in comparison to two marine fish species (turbot and seabass) whose sperm characteristics are well described. Sperm morphology mainly differs by the presence of an acrosome in Pacific Oyster which is absent in both fish species. In turbot as in Pacific Oyster, a sperm 'maturation process' along the genital tract is observed. Sperm motility is triggered by changes in osmolality for seabass and turbot and in pH for Pacific Oyster. However, complementary factors are involved to maintain sperm immotile in the genital tract. Sperm movement duration is very long in Pacific Oyster (20-24 h), compared to turbot (3-5 min) and seabass (40-50 s). A high capacity of ATP regeneration is observed in Pacific Oyster sperm, sustained by the limited changes in its morphology observed at the end of the swimming phase. Then, the total distance covered by spermatozoa is very different among the studied species (seabass: 2 mm, turbot: 12 mm, Pacific Oyster: 1 m). Considering the main characteristics of sperm movement, the three studied species can be separated in two groups: the sprint racer group (seabass: high velocity and short distance covered) and the marathonian racer one (Pacific Oyster: low velocity but covering long distances). To an intermediate extent, turbot sperm belongs to the sprint racer group. Then, the two different sperm movement strategies observed in the three species, are compensated by the behaviour of the breeders.
Guofan Zhang - One of the best experts on this subject based on the ideXlab platform.
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identification of hsf1 target genes involved in thermal stress in the Pacific Oyster crassostrea gigas by chip seq
Marine Biotechnology, 2020Co-Authors: Youli Liu, Wei Wang, Qihui Zhu, Guofan ZhangAbstract:The Pacific Oyster Crassostrea gigas, a commercially important species inhabiting the intertidal zone, facing enormous temperature fluctuations. Therefore, it is important to identify candidate genes and key regulatory relationships associated with thermal tolerance, which can aid the molecular breeding of Oysters. Heat shock transcription factor 1 (HSF1) plays an important role in the thermal stress resistance. However, the regulatory relationship between the expansion of heat shock protein (HSP) HSP 70 and HSF1 is not yet clear in C. gigas. In this study, we analyzed genes regulated by HSF1 in response to heat shock by chromatin immunoprecipitation followed by sequencing (ChIP-seq), determined the expression patterns of target genes by qRT-PCR, and validated the regulatory relationship between one HSP70 and HSF1. We found 916 peaks corresponding to HSF1 binding sites, and these peaks were annotated to the nearest genes. In Gene Ontology analysis, HSF1 target genes were related to signal transduction, energy production, and response to biotic stimulus. Four HSP70 genes, two HSP40 genes, and one small HSP gene exhibited binding to HSF1. One HSP70 with a binding site in the promoter region was validated to be regulated by HSF1 under heat shock. These results provide a basis for future studies aimed at determining the mechanisms underlying thermal tolerance and provide insights into gene regulation in the Pacific Oyster.
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rnai based transcriptome suggests genes potentially regulated by hsf1 in the Pacific Oyster crassostrea gigas under thermal stress
BMC Genomics, 2019Co-Authors: Youli Liu, Baoyu Huang, Wei Wang, Guofan ZhangAbstract:The Pacific Oyster Crassostrea gigas is an important fishery resource that is sensitive to temperature fluctuations. Thus, it has evolved a protection mechanism against heat stress by increasing the expression of the gene coding for heat shock protein (HSP) 70 under elevated temperatures. In other animals, heat shock response is a transcriptional response driven by the heat shock transcription factor 1 (HSF1) and thermal stress can trigger HSP70 expression to protect the organism via HSF1. However, the regulatory relationship between HSF1 and HSP remains unclear in Pacific Oyster. Therefore, in the present study, we examined the transcriptomic response of several to thermal stress following HSF1 interference. We identified 150 genes responsive to heat shock including seven HSP genes, six of which belonging to the group of 17 HSP genes enriched in response to heat shock, according to weighted gene co-expression network analysis (WGCNA). The other gene was enriched in the module correlated with HSF1 interference. In addition, we found 48 and 47 genes that were upregulated and downregulated by HSF1 in response to heat shock, respectively. In the upregulated genes, we identified one HSP70 potentially regulated by HSF1 in response to heat shock. Furthermore, based on differentially expressed genes and WGCNA analyses, we found that the hypoxia signaling pathway was enriched under heat shock conditions. Five genes were then selected to detect dynamic changes through time. The results suggested that gene expression was correlated with HSF1 expression. The regulation of HSP70 by HSF1 was preliminarily confirmed by binding site predictions and by a dual luciferase assay. Our results revealed that the expression of HSP70 and HSP20 was initially triggered after 2 h of heat shock, and one of the HSP70 genes was potentially regulated by HSF1. From these results, it is evident that not all heat-inducible genes were triggered simultaneously in response to heat shock stress. Overall, the results revealed a possible HSF1–HSP regulatory relationship in Pacific Oyster, providing valuable information on the mechanisms of thermal tolerance in this commercially important Oyster.
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construction and evaluation of a high density snp array for the Pacific Oyster crassostrea gigas
PLOS ONE, 2017Co-Authors: Kai Song, Wei Wang, Guofan ZhangAbstract:Single nucleotide polymorphisms (SNPs) are widely used in genetics and genomics research. The Pacific Oyster (Crassostrea gigas) is an economically and ecologically important marine bivalve, and it possesses one of the highest levels of genomic DNA variation among animal species. Pacific Oyster SNPs have been extensively investigated; however, the mechanisms by which these SNPs may be used in a high-throughput, transferable, and economical manner remain to be elucidated. Here, we constructed an Oyster 190K SNP array using Affymetrix Axiom genotyping technology. We designed 190,420 SNPs on the chip; these SNPs were selected from 54 million SNPs identified through re-sequencing of 472 Pacific Oysters collected in China, Japan, Korea, and Canada. Our genotyping results indicated that 133,984 (70.4%) SNPs were polymorphic and successfully converted on the chip. The SNPs were distributed evenly throughout the Oyster genome, located in 3,595 scaffolds with a length of ~509.4 million; the average interval spacing was 4,210 bp. In addition, 111,158 SNPs were distributed in 21,050 coding genes, with an average of 5.3 SNPs per gene. In comparison with genotypes obtained through re-sequencing, ~69% of the converted SNPs had a concordance rate of >0.971; the mean concordance rate was 0.966. Evaluation based on genotypes of full-sib family individuals revealed that the average genotyping accuracy rate was 0.975. Carrying 133 K polymorphic SNPs, our Oyster 190K SNP array is the first commercially available high-density SNP chip for mollusks, with the highest throughput. It represents a valuable tool for Oyster genome-wide association studies, fine linkage mapping, and population genetics.
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Molecular characterization and functional analysis of tumor necrosis factor receptor-associated factor 2 in the Pacific Oyster
Fish & Shellfish Immunology, 2015Co-Authors: Baoyu Huang, Xueying Tang, Yishuai Du, Linlin Zhang, Li Li, Guofan ZhangAbstract:Tumor necrosis factor receptor (TNFR)-associated factors (TRAFs) are a family of crucial adaptors, playing vital roles in mediating signal transduction in immune signaling pathways, including RIG-I-like receptor (RLR) signaling pathway. In the present study, a new TRAF family member (CgTRAF2) was identified in the Pacific Oyster, Crassostrea gigas. Comparison and phylogenetic analysis revealed that CgTRAF2 could be a new member of the invertebrate TRAF2 family. Quantitative real-time PCR revealed that CgTRAF2 mRNA was highly expressed in the digestive gland, gills, and hemocytes, and it was significantly up regulated after Vibrio alginolyticus and ostreid herpesvirus 1 (OsHV-1) challenge. The CgTRAF2 mRNA expression profile in different developmental stages of Oyster larvae suggested that CgTRAF2 could function in early larval development. CgTRAF2 mRNA expression pattern, after the silence of CgMAVS (Mitochondrial Antiviral Signaling) -like, indicated that CgTRAF2 might function downstream of CgMAVS-like. Moreover, the subcellular localization analysis revealed that CgTRAF2 was localized in cytoplasm, and it may play predominately important roles in signal transduction. Collectively, these results demonstrated that CgTRAF2 might play important roles in the innate immunity and larval development of the Pacific Oyster. (C) 2015 Elsevier Ltd. All rights reserved.
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Fosmid library construction and end sequences analysis of the Pacific Oyster, Crassostrea gigas
Molluscan Research, 2013Co-Authors: Linlin Zhang, Xiaotong Wang, Huayong Que, Guofan ZhangAbstract:The Pacific Oyster (Crassostrea gigas) is globally distributed and is one of the most commercially and ecologically important marine organisms. However, little is known about the genome of this species. In this study, a C. gigas fosmid library was constructed that contains 459,936 clones with an average insert size of approximately 40 kb, representing 22.34-fold haploid genome equivalents. End sequencing generated 90,240 fosmid end sequences (FESs) with an average length of 384.27 base pairs (bp), covering approximately 2.58% of the Pacific Oyster genome. The FESs were subsequently assembled and annotated, resulting in 6332 sequences with predicted open reading frames >= 300 and 1,189,100 bp repeats. Furthermore, a total of 3200 microsatellite repeats were identified, and dinucleotide repeats were found to occur most abundantly, with AG and AAT being the most abundant repeat class of dinucleotides and trinucleotides. We also found that the repeat number was generally negatively proportional to the repeat element length. Microsatellites composition between the transcribed sequences and genomic sequences was shown to be different. Point mutations of microsatellite were non-random and underwent strong selection stress. Overall, a comprehensive sequence resource for the Pacific Oyster was created, including annotated transposable elements, tandem repeats, protein coding sequences and microsatellites. These initial findings will serve as resources for further in-depth studies of physical mapping, gene discovery, microsatellite marker developing and evolution studies.
Shikai Liu - One of the best experts on this subject based on the ideXlab platform.
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Comparative Transcriptome Analysis Reveals Molecular Basis Underlying Fast Growth of the Selectively Bred Pacific Oyster, Crassostrea gigas.
Frontiers in genetics, 2019Co-Authors: Fuqiang Zhang, Zexin Jiao, Shikai LiuAbstract:Fast growth is one of the most desired traits for all food animals, which affects the profitability of animal production. The Pacific Oyster, Crassostrea gigas, is an important aquaculture shellfish around the world with the largest annual production. Growth of the Pacific Oyster has been greatly improved by artificial selection breeding, but molecular mechanisms underlying growth remains poorly understood, which limited the molecular integrative breeding of fast growth with other superior traits. In this study, comparative transcriptome analyses between the fast-growing selectively bred Pacific Oyster and unselected wild Pacific Oysters were conducted by RNA-Seq. A total of 1,303 protein-coding genes differentially expressed between fast-growing Oysters and wild controls were identified, of which 888 genes were expressed at higher levels in the fast-growing Oysters. Functional analysis of the differentially expressed genes (DEGs) indicated that genes involved in microtubule motor activity and biosynthesis of nucleotides and proteins are potentially important for growth in the Oyster. Positive selection analysis of genes at the transcriptome level showed that a significant number of ribosomal protein genes had undergone positive selection during the artificial selection breeding process. These results also indicated the importance of protein biosynthesis and metabolism for the growth of Oysters. The alternative splicing (AS) of genes was also compared between the two groups of Oysters. A total of 3,230 differential alternative splicing events (DAS) were identified, involved in 1,818 genes. These DAS genes were associated with specific functional pathways related to growth, such as "long-term potentiation," "salivary secretion," and "phosphatidylinositol signaling system." The findings of this study will be valuable resources for future investigation to unravel molecular mechanisms underlying growth regulation in the Oyster and other marine invertebrates and to provide solid support for breeding application to integrate fast growth with other superior traits in the Pacific Oyster.
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Inheritance of shell pigmentation in Pacific Oyster Crassostrea gigas
Aquaculture, 2019Co-Authors: Shikai Liu, Lingfeng Kong, Jindou ChongAbstract:Abstract The Pacific Oyster ( Crassostrea gigas ) is one of the most important species which has the largest production among all cultured shellfish. Recently, several shell color strains of C. gigas have been developed to improve the commercial values, however the inheritance of shell pigmentation is still unclear. A total of 29 families cross-mated between different pigmented Oysters were produced to investigate the inheritance of the shell pigmentation and purple pigmentation. Random samples from each family were obtained and their shell pigmentation were recorded. Results revealed that shell pigmentation was controlled by two genetic locus, among which one is responsible for secretion of pigmentation and the other is responsible for distribution mode of pigmentation. The locus controlling the secretion of pigmentation has two alleles with the allele for the presence of pigmentation being dominant to the allele for the absence of pigmentation. Similarly, another locus controlling the distribution mode of pigmentation has two alleles with the allele for striped distribution being dominant to the allele for solid distribution. In addition, one independent locus with two alleles was suggested to control the purple-striped pigmentation, which one allele for shell devoid of purple pigmentation is dominant to another allele for shell with purple pigmentation. The findings will provide valuable information for the efficient selective breeding of shell color strains in the Pacific Oyster.
Xiaotong Wang - One of the best experts on this subject based on the ideXlab platform.
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Nanopore Sequencing and De Novo Assembly of a Black-Shelled Pacific Oyster (Crassostrea gigas) Genome.
Frontiers in genetics, 2019Co-Authors: Xiaotong Wang, Lei Wei, Chenglong Zhu, Hongce Song, Zhongqiang Cai, Qiuyun JiangAbstract:The Pacific Oyster, Crassostrea gigas, belongs to one of the most species-rich phyla and provides important ecological and economical services. Here we present a genome assembly for a variety of this species, black-shelled Pacific Oyster, using a combination of 61.8 Gb Nanopore long reads and 105.6 Gb raw BGI-seq short reads. The genome assembly comprised 3,676 contigs, with a total length of 587 Mb and a contig N50 of 581 kb. Annotation of the genome assembly identified 283 Mb (48.32 %) of repetitive sequences and a total of 26,811 protein-coding genes. A long-term transposable element active, accompanied by recent expansion (1 million years ago), was detected in this genome. The divergence time between black-shelled and the previous published Pacific Oyster genome was estimated at about 2.2 million years ago, which implied that species C. gigas had great intraspecific genetic variations. Moreover, we identified 148/188 specifically expanded/contracted gene families in this genome. We believe this genome assembly will be a valuable resource for understanding the genetic breeding, conservation, and evolution of Oysters and bivalve.
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A Rhodopsin-Like Gene May Be Associated With the Light-Sensitivity of Adult Pacific Oyster Crassostrea gigas.
Frontiers in physiology, 2018Co-Authors: Wu Changlu, Lei Wei, Zhongqiang Cai, Qiuyun Jiang, Jun Chen, Wang Jiao, Wen Guo, Xiaotong WangAbstract:Light-sensitivity is important for mollusc survival, as it plays a vital role in reproduction and predator avoidance. Light-sensitivity has been demonstrated in the adult Pacific Oyster Crassostrea gigas, but the genes associated with light perception remain unclear. In the present study, we designed experiments to identify the genes associated with light-sensitivity in adult Oysters. First, we assessed the Pacific Oyster genome and identified 368 genes annotated with the terms associated with light-sensitivity. Second, the function of the above four rhodopsin-like superfamily member genes was tested by using RNAi. The results showed that the highest level of mRNA expression of the vision-related genes was in the mantle; however, this finding is not true for all Oyster genes. Interestingly, we also found four rhodopsin-like superfamily member genes expressed at an exceptionally high level in the mantle tissue. In the RNAi experiment, when one of rhodopsin-like superfamily member genes (CGI_1001253) was inhibited, the light-sensitivity capacity of the injected Oysters was significantly reduced, suggesting that CGI_10012534 may be associated with light-sensitivity in the adult Pacific Oyster.
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extraction and identification of the pigment in the adductor muscle scar of Pacific Oyster crassostrea gigas
PLOS ONE, 2015Co-Authors: Jian Li, Zhonghu Li, Xiaotong WangAbstract:In this study, UV (ultraviolet) and IR (infrared radiation) spectral analysis were integrated to identify the pigment in the adductor muscle scar of the Pacific Oyster Crassostrea gigas. The pigment was extracted from the adductor muscle scars of cleaned Oyster shells that were pulverized, hydrolyzed in hot hydrochloric acid, purified with diethyl ether, and dissolved in 0.01 mL/L NaOH. The maximum absorption of the pigment in the UV absorption spectrum within the range of 190–500 nm was observed between 210–220 nm. The UV absorbance decreased with increasing wavelength which was consistent with the UV spectral absorption characteristics of melanin. In addition, Fourier transform infrared spectroscopy scanning revealed characteristic absorption peaks that emerged near 3440 cm-1 and 1630 cm-1, which was consistent with infrared scanning features of eumelanin (a type of melanin). This study has demonstrated for the first time that the pigment in the adductor muscle scar of the Pacific Oyster is melanin, hinting that the adductor muscle could be another organ pigmenting the mollusc shell with melanin other than mantle.
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Adult Pacific Oyster (Crassostrea gigas) may have light sensitivity
PLoS ONE, 2015Co-Authors: Changlu Wu, Yanjian Yang, Yongchuan Li, Jiao Wang, Zhuang Li, Ting Guo, Xiaotong WangAbstract:Light-sensitivity is an important aspect of mollusk survival as it plays a vital role in reproduction and predator avoidance. In the Pacific Oyster Crassostrea gigas light sensitivity has been demonstrated in the larval stage but has not yet been conclusively demonstrated in adult Oysters. In this paper we describe an experiment which was undertaken to determine if adult Pacific Oysters were sensitive to light. One LED flashlight was used to shine light onto adult Oysters while they were filtering seawater through their shell openings. We found that the degree of opening increased gradually during the light period but rapidly decreased when the flashlight was turned off in the treated group but not in the control group. These results suggest that adult Pacific Oyster may be sensitive to light.
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Fosmid library construction and end sequences analysis of the Pacific Oyster, Crassostrea gigas
Molluscan Research, 2013Co-Authors: Linlin Zhang, Xiaotong Wang, Huayong Que, Guofan ZhangAbstract:The Pacific Oyster (Crassostrea gigas) is globally distributed and is one of the most commercially and ecologically important marine organisms. However, little is known about the genome of this species. In this study, a C. gigas fosmid library was constructed that contains 459,936 clones with an average insert size of approximately 40 kb, representing 22.34-fold haploid genome equivalents. End sequencing generated 90,240 fosmid end sequences (FESs) with an average length of 384.27 base pairs (bp), covering approximately 2.58% of the Pacific Oyster genome. The FESs were subsequently assembled and annotated, resulting in 6332 sequences with predicted open reading frames >= 300 and 1,189,100 bp repeats. Furthermore, a total of 3200 microsatellite repeats were identified, and dinucleotide repeats were found to occur most abundantly, with AG and AAT being the most abundant repeat class of dinucleotides and trinucleotides. We also found that the repeat number was generally negatively proportional to the repeat element length. Microsatellites composition between the transcribed sequences and genomic sequences was shown to be different. Point mutations of microsatellite were non-random and underwent strong selection stress. Overall, a comprehensive sequence resource for the Pacific Oyster was created, including annotated transposable elements, tandem repeats, protein coding sequences and microsatellites. These initial findings will serve as resources for further in-depth studies of physical mapping, gene discovery, microsatellite marker developing and evolution studies.
Lingfeng Kong - One of the best experts on this subject based on the ideXlab platform.
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Inheritance of shell pigmentation in Pacific Oyster Crassostrea gigas
Aquaculture, 2019Co-Authors: Shikai Liu, Lingfeng Kong, Jindou ChongAbstract:Abstract The Pacific Oyster ( Crassostrea gigas ) is one of the most important species which has the largest production among all cultured shellfish. Recently, several shell color strains of C. gigas have been developed to improve the commercial values, however the inheritance of shell pigmentation is still unclear. A total of 29 families cross-mated between different pigmented Oysters were produced to investigate the inheritance of the shell pigmentation and purple pigmentation. Random samples from each family were obtained and their shell pigmentation were recorded. Results revealed that shell pigmentation was controlled by two genetic locus, among which one is responsible for secretion of pigmentation and the other is responsible for distribution mode of pigmentation. The locus controlling the secretion of pigmentation has two alleles with the allele for the presence of pigmentation being dominant to the allele for the absence of pigmentation. Similarly, another locus controlling the distribution mode of pigmentation has two alleles with the allele for striped distribution being dominant to the allele for solid distribution. In addition, one independent locus with two alleles was suggested to control the purple-striped pigmentation, which one allele for shell devoid of purple pigmentation is dominant to another allele for shell with purple pigmentation. The findings will provide valuable information for the efficient selective breeding of shell color strains in the Pacific Oyster.
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heritability estimates for growth related traits in the Pacific Oyster crassostrea gigas using a molecular pedigree
Aquaculture Research, 2015Co-Authors: Ning Kong, Lingfeng KongAbstract:Pacific Oyster is one of the leading species in world aquaculture, but heritability estimation applying mixed-family approach has not been actively pursued. In this study, heritability for growth-related traits in the Pacific Oyster was first estimated by creating a single cohort of 45 families in a full-factorial mating design consisting of nine sires and five dams. A total of 270 offspring were analysed and parentage assignment inferred by six microsatellite markers achieved 100% success. All parents contributed to the spawn and a total of 42 full-sib families were represented. Using an animal model, heritability estimates at 12 months of age were 0.49 ± 0.25 for shell height, 0.36 ± 0.19 for shell length, 0.45 ± 0.23 for shell width and 0.35 ± 0.17 for wet weight. Genetic correlation between shell height and wet weight was quite high (0.79 ± 0.25), suggesting that direct selection of shell height, which is an easily measurable trait, also improves wet weight. The results obtained in this study indicate that growth-related traits could be improved by exploiting additive genetic effects through selective breeding.
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Phylogenetic analysis of tyrosinase gene family in the Pacific Oyster (Crassostrea gigas Thunberg)
Yi chuan = Hereditas, 2014Co-Authors: Lingfeng KongAbstract:The deduced amino acid sequence characteristics, classification and phylogeny of tyrosinase gene family in the Pacific Oyster (Crassostrea gigas Thunberg) were analyzed using bioinformatics methods. The results showed that gene duplication was the major cause of tyrosinase gene expansion in the Pacific Oyster. The tyrosinase gene family in the Pacific Oyster can be further classified into three types: secreted form (Type A), cytosolic form (Type B) and membrane-bound form (Type C). Based on the topology of the phylogenetic tree of the Pacific Oyster tyrosinases, among Type A isoforms, tyr18 seemed divergent from other Type A tyrosinases early, while tyr2 and tyr9 appeared divergent early in Type B. In Type C tyrosinses, tyr8 was divergent early. The cluster of the Pacific Oyster tyrosinasesis determined by their classifications and positions in the scaffolds. Further analysis suggested that Type A tyrosinases of C. gigas clustered with those from cephalopods and then with nematodes and cnidarians. Type B tyrosinases were generally clustered with the same type of tyrosinases from molluscas and nematodes, and then with those from platyhelminths, cnidarians and chordates. Type A tyrosinases in the Pacific Oyster and the Pearl Oyster expanded independently and were divergent from membrane-bound form of tyrosinases in chordata, platyhelminthes and annelida. These observations suggested that Type C tyrosinases in the bivalve had a distinct evolution direction.
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transcriptomic responses to salinity stress in the Pacific Oyster crassostrea gigas
PLOS ONE, 2012Co-Authors: Xuelin Zhao, Lingfeng KongAbstract:Background Low salinity is one of the main factors limiting the distribution and survival of marine species. As a euryhaline species, the Pacific Oyster Crassostrea gigas is considered to be tolerant to relative low salinity. The genes that regulate C. gigas responses to osmotic stress were monitored using the next-generation sequencing of whole transcriptome with samples taken from gills. By RNAseq technology, transcript catalogs of up- and down-regulated genes were generated from the Oysters exposed to low and optimal salinity seawater.
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Response to selection for fast growth in the second generation of Pacific Oyster ( Crassostrea gigas )
Journal of Ocean University of China, 2012Co-Authors: Qingzhi Wang, Lingfeng KongAbstract:Mass selection for fast growth was conducted in three Pacific Oyster (Crassostrea gigas) stocks from China, Japan and Korea using previously established lines (CS1, JS1, and KS1). To determine whether continuous progress can be achieved by selection for growth, the progeny of three second-generation Pacific Oyster lines was selected for shell height and evaluated via a 400-day farming experiment. When harvested at the end of the experiment, the selected crosses of CS2, JS2, and KS2 lines grew by 9.2%, 10.2% and 9.6% larger than the control crosses, respectively. During grow-out stage, the genetic gain of three selected lines was (10.2 ± 1.4)%, (10.4 ± 0.3)%, and (8.4 ± 1.6)%, respectively; and the corresponding realized heritability was 0.457 ± 0.143, 0.312 ± 0.071 and 0.332 ± 0.009, respectively. These results indicated that the selection for fast growth achieved steady progress in the second generation of Oyster. Our work provides supportive evidence for the continuity of the Pacific Oyster selective breeding program.
