基于长片段PCR扩增的牡蛎疱疹病毒基因组高通量测序

为获取2001年低温冻存栉孔扇贝感染牡蛎疱疹病毒(Os HV-1)变异株(ZK2001)基因组序列,并分析ZK2001与其他Os HV-1变异株的序列差异和系统发育关系,利用基于长片段PCR的基因组DNA的扩增和富集技术,获取2001年栉孔扇贝感染Os HV-1变异株的基因组DNA;再使用Illumina Hiseq 2500 PE250高通量测序平台对其测序。最后分析ZK2001与Os HV-1其他变异株基因组的序列差异和系统发育关系。测序数据组装后获得8个Scaffold。基因组变异分析结果显示,ZK2001与参考基因组相比存在328个SNP位点,SNP和序列插入/缺失变异是导致Os HV-1基因组序列变异的主要变异类型。系统发育分析结果显示,ZK2001变异株与分离自我国的Os HV-1变异株亲缘关系最近,与分离自欧洲的Os HV-1μvar及其相关变异株的亲缘关系最远,说明中国和欧洲分布Os HV-1间存在因地理隔离导致的遗传分化。研究表明,基于长片段PCR的DNA富集技术,可以有效地扩增和富集冷冻样本中Os HV-1基因组DNA,并应用于高通量测序。Os HV-1不同变异株基因组序列数据的获取和积累,将为其基因组尺度的基因变异、株系演化和系统发育关系等研究提供重要基础。     

宏基因组技术在开发未培养微生物资源中的应用

不可培养微生物占微生物种类99%以上,使得微生物的多样性资源难以得到全面的开发和利用。宏基因组是指生境中全部微小生物遗传物质的总和。宏基因组学的基本方法是分析微生物环境中的基因组组合,直接分离未培养土壤微生物基因组DNA克隆到可培养微生物中,最后筛选所需要克隆。综述了宏基因组技术在开发和利用未培养微生物资源中的应用概况。     

长牡蛎食物组成的高通量测序分析

为了更加细致地甄别滤食性贝类的食物组成,于2019年8月,以北方规模化典型养殖海湾——桑沟湾养殖的长牡蛎(Crassostrea gigas)为研究对象,运用Illumina高通量测序技术对长牡蛎的胃含物及所处养殖水体中的真核生物进行分析研究.结果显示,扩增18S rDNA V4区平均得到111,359个有效序列短片段...     

牡蛎疱疹病毒(OsHV-1)研究进展

牡蛎疱疹病毒(ostreid herpesvirus-1,OsHV-1)是引起多种双壳贝类特别是牡蛎大规模死亡的致死性病毒,在世界范围内广泛流行,主要危害牡蛎、扇贝、菲律宾蛤仔及魁蚶等种类,对贝类养殖业造成重大的损害。在我国,也存在2个对贝类危害较大的OsHV-1变异株。文章综述了OsHV-1的分类与命名、病毒形态学、理化性质、基因组、遗传多样性及病毒的检测方法。     

牡蛎中诺如病毒的感染及其防控研究进展

诺如病毒(Norovirus,NoV)是非细菌性急性胃肠炎的主要病原体.牡蛎可通过滤食作用富集海水和环境中污染的NoV,是NoV传播的重要载体.人们倾向于食用生的或轻微烹煮的牡蛎,导致NoV感染事件时有发生.与牡蛎相关的食源性疾病中,约50％由NoV引起.荧光定量PCR是检测NoV的主要方法,但其不能有效区分感染性与非...     

太平洋牡蛎不同组织DNA甲基化的F-MSAP分析

采用荧光标记的甲基化敏感性扩增多态性(F-MSAP)技术对太平洋牡蛎(Crassostrea gigas)的6个组织进行全基因组CCGG位点甲基化水平的检测。结果表明: 鳃、闭壳肌、外套膜、唇瓣、性腺、消化盲囊6个组织的甲基化水平分别为: 31.77%、36.41%、32.00%、36.47%、32.77%和37.92%。甲基化模式分为全甲基化和半甲基化, 在太平洋牡蛎中, 全甲基化模式与总体甲基化水平一致, 消化盲囊、唇瓣、闭壳肌组织的甲基化水平较高, 而鳃、外套膜、性腺组织的甲基化程度较低; 半甲基化位点显著少于全甲基化位点, 并且不同组织间的半甲基化位点不存在显著性差异, 而从全甲基化位点及总甲基化水平分析, 不同组织之间甲基化水平差异显著。太平洋牡蛎中存在组织特异性甲基化片段和非组织特异性甲基化片段, 但却只在一个或部分个体中出现, 没有发现在所有研究个体中都存在的甲基化差异片段, 这可能与牡蛎较高的杂合度相关。对实验样品进行的荧光标记的扩增片段长度多态性(F-AFLP)分析发现, 样品间的确存在较大的遗传差异, 基于以上结果可以推测基因组甲基化水平可能与个体遗传背景相关联。

     

牡蛎养殖技术

太平洋牡蛎具有体型大、生长快、味美、产量高、适应性强等优点,是浅海养殖的优良品种之一。本文概述了太平洋牡蛎的人工养殖技术,同时介绍了一种牡蛎的室内控温育苗技术;旨在为牡蛎养殖单位的生产实践提供参考。     

基于宏基因组比较分析石斑鱼育苗两种模式水体中的菌群多样性和分布特点

为比较分析石斑鱼育苗新旧模式水体中菌群的分布差异性,研究应用高通量测序技术测定六批次(A1、A2、B1、B2、C1和C2)水样的菌群16S r DNA V4变异区序列,并使用Qiime和Mothur等软件整理和统计样品序列数目和操作分类单元(OTUs)数量,分析物种的丰度、分布和Alpha多样性以及物种丰度的差异性。结果显示,获得用于分析的序列和OTU数为667 27/3 724(A1)、66 418/3 391(A2)、87 403/3 980(B1)、57 519/3 438(B2)、62 349/3 530(C1)和66 673/3 004(C2);稀疏曲线表明测序深度充分,OTU的数量接近实际情况。A1、A2、B1、B2、C1和C2六个样品的丰富度指数分别为6 535.21/8 872.16、6 583.85/8 855.40、8 062.60/10 640.49、6 878.85/9 352.25、6 859.85/9 295.45和5 291.87/6 868.28,多样性指数分别为0.05/4.72、0.04/4.77、0.04/4.69、0.04/4.74、0.05/4.45和0.08/4.06。传统模式育苗场暴发石斑鱼病毒性神经坏死病的同一时期,对两种模式育苗水体中的菌群在门、属水平分别进行单样品物种丰度、多样品物种分布和物种丰度差异性分析。在门水平,两种育苗模式育苗水体的优势菌群分布相似,但在属水平,传统模式育苗水体的优势菌群中易致病菌假单胞菌属含量显著高于新模式育苗水体。获得了暴发病毒性神经坏死病前后,石斑鱼育苗新旧两种模式共6批次育苗水样的细菌均匀度、丰富度和菌群结构,推测石斑鱼"生态优化及病害防控人工育苗创新模式"可能有利于抑制致病菌,富集益生菌。     

太平洋牡蛎中诺瓦克样病毒的RT-PCR法检测和病毒聚合酶区部分序列的分析

利用pH9.5的甘氨酸缓冲液性处理太平洋牡蛎(Crassostrea gigas)匀浆液,PEG沉淀病毒粒子的方法对未知的是否污染有诺瓦克样病毒(Norwalk-like Virus,NLVs)的牡蛎样品进行处理,并提取病毒RNA,进行RT-PCR,凝胶电泳检测扩增结果。初步建立了牡蛎中NVLs的检测方法。纯化所得的特异PCR产物,克隆到T-载体中,筛选转化子,提取质粒,并进行PCR电泳鉴定。重组质粒序列测定结果在NCBI上进行BLASTn显示所得产物与已发表的诺瓦克样病毒的相应序列具有极高的同源性(>95％);根据Genebee在线分析系统AliBee-Multiple Alignment进行对中国的诺瓦克样病毒粪便分离株和牡蛎分离株的扩增序列进行相似性分析,结果从我国养殖的牡蛎样品中和胃肠炎病人粪便中分离出2个的诺瓦克样病毒之间无显著的差异。     

牡蛎三倍体育种技术研究进展

牡蛎味道鲜美,富含锌、牛磺酸、糖原等营养物质,其生长快速、产量高、食物链短、经济效益良好,成为中国乃至世界重要的水产养殖贝类.我国牡蛎主要的养殖品种为长牡蛎(又称太平洋牡蛎,Crassostrea gigas)、福建牡蛎(又称葡萄牙牡蛎,C.angulata)、香港牡蛎(C.hongkongensis)、近江牡蛎(C....     

利用牡蛎制作海鲜调味汁的试验

研究了混合酶水解牡蛎蛋白质的技术条件，并和单酶水解结果进行了比较。结果表明，混合酶水解可提高水解率和水解液中氨基态氮(AAN)的含量，同时改善了水解液风味。     

Identification and counting of Pacific oyster Crassostrea gigas larvae by object detection using deep learning

Natural seedling collection is widely used in the culture of various bivalve species. For successful natural seedling collection, collectors must be installed when larvae appear in the water column at a stage immediately before attachment. Aquaculture farmers generally identify target larvae by morphological features through microscopic examination in a time- and labor-expensive exercise, which also requires a level of expertise to ensure accurate larval identification. We develop a deep-learning-based object-detection technique that ultimately might reduce the time and effort required to accurately identify and count Pacific oyster larvae, render their identification more consistent, and negate the need for expertise. Images of plankton net samples collected in Matsushima and Sendai bays, Japan, were taken using a new photographic device with a CMOS image sensor. Images of oyster larvae identified by an expert were used to create a library of labeled images to train a deep-learning model, which proved to be 82.4% accurate in precision, 90.8% in recall, and 86.4% in F-measure. A further method for estimating larval shell height from the rectangular shape of oyster larval images is also developed. The standardized mean difference in shell height between measurements and estimates is 3.3%. This deep-learning model has the potential to significantly reduce the time and effort required to identify oyster larvae in plankton samples, and thereby costs of this exercise.     

牡蛎壳作为生物絮凝养殖系统缓释碱度源的效果

为优化生物絮凝系统碱度调控策略,实验研究了在生物絮凝—罗非鱼养殖系统中牡蛎壳补充碱度的可行性。在系统启动阶段评估了不同牡蛎壳添加量0 g/L(对照组,A组)、0.36 g/L(B组)和0.72 g/L(C组)补充碱度的可行性。结果显示,C组碱度、pH和钙离子水平显著高于A组,但B与C组组间的水质差异不显著,牡蛎壳补充碱度效果明显。在生物絮凝系统启动阶段的基础上,对比研究了两种形态的牡蛎壳[(壳粉,E组)、(壳,F组)]为生物絮凝在罗非鱼养殖系统中补充碱度的效果。各组的水质指标、鱼体酶活免疫性能以及细菌群落组成均无显著差异,牡蛎壳及壳粉对罗非鱼生长没有明显的负面影响,可以被应用到生物絮凝养殖系统中,但补充碱度效果不明显。牡蛎壳补充碱度与形态无关。研究表明,在目前实验条件下,牡蛎壳在生物絮凝养殖系统中不能完全替代碳酸氢钠,还需进一步优化相关工艺。     

Hatchery cultivation of Pacific oyster juveniles using algae produced in outdoor bloom-tanks

Algae were bloomed as batch cultures by adding fertilizers to natural seawater in 500 l outdoor tanks, from mid-June to mid-August, over a period of 2 y. In the first year of experiments the bloomed algae were fed to Pacific oyster (Crassostrea gigas Thunberg) juveniles at a range of rations from 0.06 to 1.63 g (organic weight of algae) g–1 (live weight of spat) week–1. At rations of 0.5 g g–1 week–1 or higher, growth rates of juveniles were similar (mean, 97%) to those fed a control diet of intensively cultured algae (Tetraselmis suecica Kylin) Butch and Chaetoceros calcitrans (Paulsen) Takano at a ration of 0.3 g g–1 week–1). In the second year, the bloomed algae were fed at a ration of 0.5 g g–1 week–1 throughout all the experiments, and gave growth rates of 70–98% (mean, 85.6%), compared with the control diet. The proportion (by weight) of the diet consumed by the juveniles was about 70% for the control diet and 78% for the bloomed algae. Total lipid and essential fatty acid content of the bloomed algae were similar and total carbohydrate content was lower, when compared with typical published values for intensively cultured algae food species. © Rapid Science Ltd. 1998     

Varying the timing of oyster transplant: implications for management from simulation studies

The transplanting of oysters from one ground to another is a common practice in the oyster industry. In Delaware Bay, for instance, oysters are typically transplanted from upper-bay low-salinity seed beds onto lower-bay leased grounds for growth and conditioning before market. The higher salinity on the leased grounds, however, also favours higher losses to predation and disease. A coupled oyster–Perkinsus marinus–predator model was used to investigate how varying the timing of transplant affects the ultimate yield of Eastern oysters, Crassostrea virginica, in Delaware Bay. Simulations were run in which oysters were moved from seed beds to leased grounds in November, January, March, April and May. The number of market-size (≥ 76 mm) adults available for harvest in the following July to November was compared for populations undergoing mortality from predation (crabs, oyster drills) and/or disease (Perkinsus marinus). In all simulations, the abundance of market-size oysters declined between July and November. However, transplanting oysters in November resulted in the largest yield of market-size oysters for all harvest times; transplanting in May resulted in the smallest yield. The autumn transplant allows oysters to benefit from the larger spring phytoplankton bloom over the leased grounds in the lower estuary. The effect of varying the season of transplant was most noticeable if oysters were harvested early (July or August). In all simulations, transplanting resulted in a higher abundance of market-size oysters than direct harvest from the seed beds. Direct harvest would rarely be advantageous if the cost of transplant were insignificant and the relative rates of mortality were as stipulated. However, a May transplant is only moderately better than a direct harvest and the economic benefits of either option are likely to be determined by the cost of transplanting and the mortality associated with the process. In the same vein, the decision as to when to harvest relies on balancing the increased price obtained for oysters in the autumn with the increased loss owing to predation and disease. Awaiting an autumn harvest is clearly much riskier if the principal source of mortality is disease rather than predation, because disease mortality is concentrated on the market-size oysters and is greatest in the autumn.     

福建漳浦太平洋牡蛎微卫星等位基因比较

本文采用Ucdcg153、157、202微卫星分子标记对福建漳浦从广东饶平引人的太平洋牡蛎育苗亲贝进行等位基因比较.两组样品(Cg♀和cg♂)携带的等位基因在微卫星重复区间及其附近存在高度相似的变异特征.这些特征区间分别是:Ucdcg153 23～40位碱基区间,Ucdcg157 73～100位碱基区间,Ucd-cg2...     

中国沿海主要牡蛎养殖品种的营养品质和风味特征比较分析

为了给牡蛎肉深加工及综合利用提供具有应用价值的基础数据,系统地探讨了中国主要养殖区新鲜牡蛎食品化学特性的差异性。结果显示,不同养殖海域及不同品种牡蛎的粗蛋白、脂肪、灰分、糖原和牛磺酸含量均具有显著差异(P<0.05)。牡蛎中锌(Zn)含量最高,各金属元素含量具有显著的地域差异性(P<0.05),其中汕头牡蛎的锌、铜(Cu)、镉(Cd)和铅(Pb)含量均显著高于其他样品(P<0.05)。呈味物质特征表现为,呈味氨基酸含量丰富,核苷酸及其关联化合物和甜菜碱含量均具有较强的地域和品种间差异性(P<0.05),其中甜菜碱含量呈"南低北高"的特征,品种间差异表现为香港牡蛎含量最低,福建牡蛎最高。醛类是新鲜牡蛎特征气味的重要组分,各地区牡蛎中检出的气味物质数量和种类有所不同;关键风味物质(ROAV≥1)中,1-辛烯-3-酮是汕头牡蛎最关键风味物质,而其他牡蛎中(E,Z)-2,6-壬二烯醛对风味贡献最大。综上,不同地理群体牡蛎的一般营养成分、牛磺酸、呈味物质和气味成分差异性显著。     

Characterization,fluctuation and tissue differences in nutrient content in the Pacific oyster (Crassostrea gigas) in Qingdao,northern China

The Pacific oyster (Crassostrea gigas) is one of the most important aquaculture species worldwide. Its meat quality is vital for consumer satisfaction, and nutrient content, especially glycogen, is closely associated with oyster fatness and meat colour. Fluctuations in nutrient content of short‐term starvation have not been previously reported, and seasonal variation in glycogen content in different tissues has rarely been reported. In the present study, we investigated these important aspects of oyster production and found that short‐term starvation (50 hr) did not significantly alter glycogen, protein or lipid content. The seasonal variation assay showed that glycogen and lipid accumulation was high in autumn and winter and that seawater temperature and protein content were inversely related to glycogen content. Glycogen content of the whole flesh was higher from January to April and was positively related to the condition index before the onset of gametogenesis. Glycogen content was higher in the gonad, labial palp and mantle compared to the gill or adductor muscle. Relative expression of genes encoding proteins involved in glycogen metabolism (glycogen synthase, glycogen phosphorylase, glycogen debranching enzyme and glycogen branching enzyme) was closely associated with the glycogen content in the corresponding tissues. Glycogen content in the gonad was regulated by glycogen metabolic and glycolysis pathway genes (6‐phosphofructo kinase, phosphoglycerate kinase, pyruvate kinase, hexokinase and glucose transporters), and stored glycogen was the main energy source for gametogenesis. These findings contribute to oyster aquaculture management and glycogen improvement and expand our understanding of glycogen metabolism in oysters.