The oyster genome reveals stress adaptation and complexity of shell formation
Guofan ZhangXiaodong FangXiming GuoLi LiRuibang LuoFei XuPengcheng YangLinlin ZhangXiaotong WangHaigang QiZhiqiang XiongHuayong QueYinlong XiePeter W. H. HollandJordi PapsYabing ZhuFucun WuChen Yuan-xinJiafeng WangChunfang PengJie MengYang LanJun LiuBo WenNa ZhangZhiyong HuangQihui ZhuYue FengAndrew S. MountDennis HedgecockZhe XuYunjie LiuTomislav Domazet‐LošoYishuai DuXiaoqing SunShoudu ZhangBinghang LiuPeizhou ChengXuanting JiangJuan LiDingding FanWei WangWenjing FuTong WangBo WangJibiao ZhangZhiyu PengYingxiang LiNa LiJinpeng WangMaoshan ChenYan HeFengji TanXiaorui SongQiumei ZhengRonglian HuangHailong YangXuedi DuLi ChenMei YangPatrick M. GaffneyShan WangLonghai LuoZhicai SheYao MingWen HuangShu ZhangBaoyu HuangYong ZhangTao QuPeixiang NiGuoying MiaoJunyi WangQiang WangChristian E. W. SteinbergHaiyan WangNing LiLumin QianGuojie ZhangYingrui LiHuanming YangXiao LiuJian WangYe YinJun Wang
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Abstract:
The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa. The sequencing and assembly of the highly polymorphic oyster genome through a combination of short reads and fosmid pooling, complemented with extensive transcriptome analysis of development and stress response and proteome analysis of the shell, provides new insight into oyster biology and adaptation to a highly changeable environment. Oysters are keystone species in estuarine ecology and among the most important aquaculture species worldwide. The sequencing and assembly of the genome of the Pacific oyster, Crassostrea gigas, are now reported. Comparisons with other genomes reveal an expansion of defence genes as an adaptation to life as a sessile species in the intertidal zone, a surprisingly complex pathway for shell formation and dramatic evolution of genes related to larval development, highlighting their adaptive significance for marine invertebrates.Keywords:
Pacific oyster
Pacific oyster
Ostreidae
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The colour of oyster shells is a very diverse characteristic morphotype, forming intriguing vivid patterns both on the inside and outside of the shell. In the present study, we have identified for the first time, the presence of several porphyrins as constituents of the shell pigmentation of the Crassostrea gigas oyster consumed worldwide. The precise molecular structures of halochromic, fluorescent and acid-soluble porphyrins, such as uroporphyrin and turacin, are unambiguously determined by reverse phase liquid chromatography combined with high resolution mass spectrometry. Their presence account for the purple colouration of shells but also for the dark colouration of adductor muscle scars. We have also defined the endogenous origin of these porphyrins, specifically secreted or accumulated by the shell forming tissue. These findings are pioneering analytical proofs of the existence of the haem pathway in the edible oyster Crassostrea gigas, evidenced by the chemical identification of haem side-products and supported by the recent publication of the corresponding oyster genome.
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Pacific oyster
genomic DNA
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The Pacific oyster, Crassostrea gigas, an oyster species indigenous to Japan, has been introduced globally becoming the primary species of oyster cultured in many areas of the world. In Tomales Bay, California, seed mortalities have occurred in Pacific oysters nearly annually since 1993, and the oyster herpesvirus (OsHV), a virulent pathogen of larval and juvenile bivalves (particularly known in Pacific oysters) was first detected in 2002. Sentinel field studies (2000-2003) were conducted in Tomales Bay in order to better understand the role of environmental factors (temperature, phytoplankton, and salinity) and oyster health (measured using histology and/or OsHV-specific Polymerase Chain Reaction (PCR)) on Pacific oyster survival. Elevated temperatures were the only environmental factor consistently related to mortalities (2000-2003), and in 2003, elevated temperature means predicted OsHV presence (p < 0.005); OsHV presence predicted mortality (p=0.01). A separate survey conducted in 2003 detected OsHV in multiple species of bivalves grown in Tomales Bay (C. gigas, Ostrea edulis, C. virginica, C. sikamea, Mytilus galloprovincialis, and Venerupis phillipinarum) and C. gigas grown in nearby Drakes Bay using OsHV-specific PCR and/or quantitative PCR (qPCR); qPCR copy numbers were low in each species tested but were significantly greater in C. gigas (p < 0.0001) the only species that appear to be impacted by mortalities. To confirm the infectious etiology of OsHV detected in Tomales Bay, Pacific oyster larvae were exposed to either filtered homogenates from OsHV-infected Pacific oysters in Tomales Bay or uninfected oyster tissue. OsHV was detected and quantified only in oyster larvae exposed to OsHV using qPCR and reverse transcriptase qPCR, and confirmed using transmission electron microscopy. Taken together, data from field and lab-based experiments indicates an infectious disease (OsHV) acts in synergy with temperature to kill Pacific oysters in Tomales Bay, California. Preliminary gene identification of both upregulated host and OsHV genes in larvae exposed to OsHV was conducted using SOLiD sequencing and GeneFishing PCR. Genes identified may provide a foundation to better understand both host response and virus infection, ultimately better defining the hostpathogen relationship between OsHV and Pacific oysters.
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Ostrea edulis
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Pacific oysters were introduced into the Eastern Scheldt in 1964 for breeding purposes. The first spatfall of wild Pacific oysters was recorded in 1976, and a second larval outburst in 1982 definitely settled wild Pacific oysters in the Eastern Scheldt waters. Oyster beds on intertidal and subtidal areas have been growing since. The objective of this study is to research the potential of aerial photography for estimating surface areas of intertidal Pacific oyster beds. Black & white and false-color aerial photographs were used to locate Pacific oyster beds. For verification purposes, oyster bed contours were measured in the field. The accuracy of the method used was comparable with accuracies found in other studies, with a chance of underestimating the surface areas in the field. With aerial photographs of 1980 and 1990 the surface areas of Pacific oysters in both years were reconstructed, showing an increase in surface area of Pacific oyster beds. The study shows aerial photography has the potential to be an aid in surveying intertidal Pacific oyster beds
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Pacific oyster Crassostrea gigas summer mortality frequently occurs in Sanggou Bay recent years,but the oyster appears low mortality rate in its neighboring region-Ailian bay. In this study,two typical Pacific oyster culture areas of these bays have been selected as experimental sites. The environmental factors including water temperature,salinity,pH and DO,superoxide dismutase (SOD) activity and growth situation of oysters have been monitored,and the oyster summer mortalities of two sites have been researched. The reason of Pacific oyster summer mortality in Sanggou bay has been analyzed. The results show that: in experiment period (from May to October),the total mortality rate was 37% in Yatou marine culture region of Sanggou bay (E122.498,N37.151),the highest mortality rate that appeared on August 17 was 51%. The total mortality rate was 2.5% in Ailian bay (E122.582,N37.179),the highest mortality rate that appeared on September 28 was 4.5%. One-way ANOVA results show that: the mortality rate has significant positive correlation with water temperature (R=0.804,P0.01),negative correlation with the dissolved oxygen (R=-0.377,P0.01),negative correlation with body weight,soft weight and gonad weight and so on (R=-0.690,-0.498,-0.358,respectively),positive correlation with superoxide dismutase activity (R=0.21,P0.05).
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Ostreidae
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Pacific oyster
Vibrio Infections
Ostreidae
Hemolymph
Strain (injury)
Pathogenic bacteria
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