Genomic cloning and expression of vitellogenin gene from the self-fertilizing fish Rivulus marmoratus (Cyprinodontiformes, Rivulidae)

We cloned the vitellogenin gene from the self-fertilizing fish Rivulus marmoratus, and sequenced 12,326 bp. The number of exons of R. marmoratus and rainbow trout vitellogenin genes were different, and also the splicing junctions are different throughout most of the exons and introns but the amino acid similarity of R. marmoratus vitellogenin gene to other species was rather high. In promoter region of R. marmoratus vitellogenin gene, there were several E2 binding sites and the estrogen response element (ERE). We discuss here the gene structure and expression of R. marmoratus vitellogenin gene.     

Cloning of cytochrome P450 1A (CYP1A) genes from the hermaphrodite fish Rivulus marmoratus and the Japanese medaka Oryzias latipes

To use two small fish Rivulus marmoratus (Cyprinodontiformes, Rivulidae) and the Japanese medaka Oryzias latipes (Belloniformes) as testing models in molecular ecotoxicology, we have cloned the cytochrome P450 1A (CYP1A) gene after screening of both genomic DNA libraries, and sequenced 11,863 and 7,243 bp including all the exons and introns with promoter regions, respectively. The Rivulus and the medaka CYP1A gene consisted of seven exons (including non-coding exons) with high homology to mammals. In the promoter region, Rivulus CYP1A gene has seven xenobiotic response elements (XREs) and two metal response elements (MREs), while the Japanese medaka CYP1A gene has six XREs and four MREs. Interestingly, medaka CYP1A gene has a number of MREs at the promoter, which may affect its response on metal exposure. We describe here the gene structure of both fish CYP1A genes.     

Cloning and sequence analysis of the self-fertilizing fish Rivulus marmoratus immediate early gene c-fos

We have cloned the proto-oncogene c-fos from a self-fertilizing fish Rivulus marmoratus (Cyprinodontiformes, Rivulidae) after screening of R. marmoratus lambdaGEM-11 genomic DNA library, and sequenced over 12 kb including all exons, introns and the promoter region. The R. marmoratus c-fos gene consisted of one noncoding exon and four exons with high similarity to those of fugu and mammals. We sequenced approximately 7 kb of the R. marmoratus c-fos gene promoter region to gain a better understanding of the molecular anatomy of the immediate response of this gene upon cellular damage. In the promoter region, R. marmoratus c-fos gene has seven xenobiotic response elements (XREs) and eight metal response elements (MREs) as well as two estradiol (E2), 4 NFkappaB, 2 CarG, 2 prolactin (PRL) motifs and one pit1 site, while the 3'-UTR of this gene contains the estrogen response element (ERE). The seven XRE and eight MRE motifs raise the possibility of its regulation by exposure to environmental pollutants. In this paper, we discuss the gene structure of R. marmoratus c-fos gene and compare its promoter region with those of other organisms' c-fos genes. We propose its potential use in ecotoxicology.     

10个菲律宾蛤仔野生群体的遗传多样性研究

对我国沿海地区10个菲律宾蛤仔野生群体线粒体16S r RNA和COI基因部分序列进行测序,分别得到了长度为473bp和632bp的片段。结果表明,16S r RNA 193条序列A+T平均含量为66.6%,共检测到21个变异位点,193个个体具有22种单倍型;COI基因183条序列A+T平均含量为64.8%,共检测到126个变异位点,183个个体具有67种单倍型。基于群体间遗传距离利用Mega5.1软件构建10个群体的NJ树,聚类结果表明,大连群体和荣成群体聚为一支,其余8个群体聚为一支。AMOVA分析表明,大连群体和荣成群体间分化不显著,而荣成、大连群体与其余8个群体间的分化达到极显著水平(P0.01),说明我国沿海的菲律宾蛤仔野生群体存在一定的遗传分化。     

烃降解菌假交替单胞菌N289的全基因组序列及其进化关系

假交替单胞菌属归属于交替假单胞菌科。交替假单胞菌N289菌株分离自南极海冰,我们通过二代测序技术获得了其全基因组序列,组装后获得2条染色体和1条质粒,大小分别是3.2M、636kb和1.8kb。全基因组共包含3,589个ORF,GC含量为40.83%。基因功能分析表明,该菌酶活性高,具有很强的环境适应性。这项研究有助于了解生物多样性、该菌株的进化地位和微生物相互作用关系。     

海蜇dmrta2基因的克隆及其在横裂生殖中的表达分析

Dmrt基因家族在后生动物性别决定与分化以及组织和器官的形成等发育过程中发挥着重要作用。为探究dmrt家族基因在海蜇(Rhopilema esculentum)横裂生殖中的功能,本研究以海蜇转录组测序获得的dmrta2基因片段为基础,通过RACE技术获得了海蜇dmrta2基因的cDNA全长,并分析了其在横裂生殖不同时期的表达模式。结果显示海蜇dmrta2基因cDNA全长为1 804 bp,开放阅读框为1 011 bp,所编码蛋白质含336个氨基酸,分子质量为37.25 kDa,理论等电点为9.11。预测海蜇dmrta2编码蛋白为亲水性蛋白质,无跨膜区域,不含信号肽。在33至79位氨基酸之间具有dmrt基因家族保守的DM结构域,与珊瑚、果蝇等物种的同源基因相应区域高度一致。系统进化分析显示,海蜇DMRTA2与鹿角珊瑚DMRTA2和DMRT3以及海葵DMRTA2的亲缘关系最近。原位杂交显示dmrta2基因在海蜇横裂生殖后期主要表达于感觉缘叶原基位置,在初生碟状体中表达于感觉棍位置。研究结果表明,dmrta2基因参与海蜇横裂生殖过程,可能主要与感觉棍神经系统的分化发育相关,研究为进一步解析海蜇等钵水母横裂生殖的分子调控机制提供了基础数据。     

大黄鱼cGAS-like基因isofrom X1的克隆鉴定及在感染刺激隐核虫后的表达变化

cGAS(cyclic GMP-AMP synthase)基因是近几年来新发现的先天免疫中一个新型的信号分子。作者基于大黄鱼(Larimichthys crocea)基因组信息,用cDNA末端快速扩增(RACE)技术在鳃组织中克隆鉴定了cGAS基因cDNA全长序列:包含1个231 bp的5′端-非翻译区(5′-UTR)、207 bp的3′-UTR和1 488 bp的开放阅读框(ORF),命名为Lc-cGAS-like X1。该基因编码1个由495个氨基酸残基组成的多肽,预测的分子量(Mw)大小为56.57kDa,理论等电点(pI)为9.45;序列分析表明其预测的蛋白无信号肽,第115～431位氨基酸序列为Mab-21功能域,第470～492位氨基酸序列为跨膜结构域。基因组全长3 153 bp,包含8个外显子和7个内含子,所有内含子的剪切特点都符合GT-AG规则。同源比对结果显示:Lc-cGAS-likeX1与鱼类cGAS的相似性大于66%,与高等脊椎动物的相似性较低。系统进化分析表明Lc-cGAS-like X1与鱼类cGAS聚成一支。荧光定量PCR(qPCR)检测显示Lc-cGAS基因(X1/X2两种剪切体)在大黄鱼9种组织中均有表达,其中在鳃中的表达量最高;刺激隐核虫感染后,大黄鱼免疫器官头肾中Lc-cGASmRNA分别在刺激隐核虫幼虫感染阶段和滋养体脱落阶段出现了极显著上调(P0.01);解毒器官肝脏中分别在滋养体脱落阶段和细菌感染阶段出现极显著上调变化(P0.01)。本研究结果暗示大黄鱼cGAS基因参与了大黄鱼感染刺激隐核虫的免疫防御过程,为进一步了解鱼类cGAS基因的多样化功能提供参考。     

杜氏盐藻叶绿体ATP合酶α亚单位基因启动子的克隆及初步功能分析

采用DraⅠ,EcoRⅤ,PvuⅡ,ScaⅠ,SmaⅠ和StuⅠ六种内切酶消化杜氏盐藻（Dunaliella salina）叶绿体基因组DNA,与相应DNA接头连接,构建成无载体连接的盐藻叶绿体Genome Walker DNA文库。利用长距离PCR（long distance-polymerase chain rea...     

Differential distribution of the two cryptic species, Pomatoschistus microps and P. marmoratus, in the lagoons of southern France, with an emphasis on the genetic organisation of P. microps

The presence and the distribution of two cryptic sedentary gobies, Pomatoschistus microps and Pomatoschistus marmoratus, were investigated in several lagoons stretching along the Golfe du Lion, southern France Mediterranean coast, and Corsica. Pomatoschistus microps is the only sedentary Pomatoschistus species in two shallow lagoons with large variations of salinity and temperature. In contrast, P. marmoratus, another sedentary species, can be found preferentially in a deep salty lagoon with small salinity variations. Both species occur sympatrically in the Rhone Delta and hybridise, producing fertile offspring. Using allozymes, competition, linked to fitness, is invoked to explain the distribution pattern of these sibling species.     

翘嘴红鲌(Erythroculter ilishaeformis)果糖-1,6-二磷酸醛缩酶(ALDO-C)基因定位、克隆及表达分析

翘嘴红鲌(Erythroculterilishaeformis)是大型淡水鱼类鳊鲌亚科(Abramidinae)中最大的一种鱼,具有较高的经济价值。但其饲料转化率及抗病性研究相对较少,相关基因信息缺乏。本研究以翘嘴红鲌为对象,利用RACE技术克隆翘嘴红鲌果糖-1.6-二磷酸醛缩酶(ALDO-C)基因,该基因cDNA全长1945bp,其中ORF区975bp,编码325个氨基酸.5′非编码区933bp.3′非编码区37bp。通过实时荧光定量PCR检测了ALDO-C在不同组织中相对表达水平。发现ALDO-C基因在翘嘴红鲌的肾、肝、肌肉、性腺中均有表达,且在肾中表达量最高,显著高于其他组织。同时采用石蜡切片、H.E染色和原位杂交染色,观察分析翘嘴红鲌的肾组织显微结构和ALDO-C基因的表达定位,结果表明,ALDO-C在鱼类肾单位和集合管结构、调节肾组织水平衡及抗病性方面有重要作用。可以考虑将翘嘴红鲌醛缩酶C基因作为生长发育及抗病性相关的候选基因,用于翘嘴红鲌鱼的分子辅助育种,以期为今后的研究提供理论基础。     

凡纳滨对虾4种血蓝蛋白亚型的特征分析

血蓝蛋白是对虾体内的氧运输蛋白,占血浆中蛋白含量的95%以上.研究表明,它参与了许多生理功能,包括蛋白储运,渗透压调节,蜕皮过程以及骨架形成等等.近年来的研究表明,血蓝蛋白还参与了对虾的先天性免疫反应,具有酚氧化酶,抗菌肽、抗病毒等相关生物活性.本研究从凡纳滨对虾中克隆获得了血蓝蛋白L亚基LvHcL,并对其基因组织结构进行了分析.该基因具有丰富的多态性,含有多个SNP位点.研究中发现该基因亚基至少存在4种亚型,其中一种亚型缺失第二个外显子,仅含有2个外显子.对各个亚型的转录水平分析表明,抗病对虾在病毒感染刺激下,各个亚型的转录水平均会被诱导提高.而普通对虾在病毒感染刺激下,各个亚型的转录水平则被抑制.研究结果表明,血蓝蛋白参与了对虾的抗病毒免疫反应.这些结果不仅有助于深入了解对虾血蓝蛋白的免疫学特点,也有助于促进对无脊椎动物抗病毒免疫机制的认识.     

脊尾白虾(Exopalaemon carinicauda)vasa基因cDNA克隆及其在卵巢发育中的表达分析

VASA蛋白属于DEAD-box家族蛋白,是一种RNA解旋酶,在生殖细胞的分化中具有重要作用。本研究从脊尾白虾(Exopalaemon carinicauda)卵巢中克隆得到vasa基因cDNA全长(将其命名为Ec-vasa),Ec-vasa序列长度为2516bp,开放阅读框(ORF)长度为1800bp,编码600个氨基酸,具有DEAD-box家族蛋白的8个高度保守的结构域,与日本沼虾(Macrobrachium nipponense)的同源性最高(80%)。半定量RT-PCR结果显示,Ec-vasa在卵巢组织中特异表达,在肌肉、肝胰腺、心脏和鳃等组织中均未检测到表达。荧光定量结果显示,Ec-vasa在卵巢发育Ⅰ期具有较高表达量,随着卵巢的发育,表达量逐渐降低,在第Ⅳ期达到最低水平。结果表明,Ec-vasa基因可能在脊尾白虾卵巢的早期分化和卵子发生过程中起重要作用。     

合浦珠母贝基因组微卫星富集文库的构建与分析

采用生物素标记的(AC)_(15)探针和磁珠富集法构建合浦珠母贝(Pinctada fucata)基因组DNA微卫星富集文库。随机挑选2097个克隆进行筛选,得到483个候选克隆(23.03%),对其中135个阳性克隆测序分析发现122个克隆含有微卫星重复单元(90.37%)。进一步通过序列比对,最终得到65个具有特异微卫星序列的阳性克隆(53.28%),其中包含85个微卫星DNA结构域,其中完美型(perfect)70个,占82.36%;非完美型(imperfect)7个,占8.24%;混合型(compound)8个,占9.41%,重复次数主要分布在5~20(95.74%),平均重复次数为7.83,(AC/GT)n重复所占比例最高(75.53%)。基于微卫星两端的侧翼序列,利用Primer Premier 5.0设计引物,获得11对具有多态性的微卫星引物。本研究为开展合浦珠母贝分子育种及资源评价分析提供了基础资料。     

基于Ecopath模型的舟山海域褐菖鲉(Sebastiscus marmoratus)生态容量评估

根据2021年渔业资源调查数据构建了含有23个功能组的舟山海域生态系统Ecopath模型,分析了当前舟山海域生态系统总体特征并估算了褐菖鲉在舟山海域的生态容量。结果表明:舟山海域生态系统营养级范围为1.000 (浮游植物和有机碎屑)～4.277 ( 鳐类),石首鱼科、虾类和 鳐类为舟山海域生态系统中的关键种。碎屑食物链和牧食食物链是舟山海域生态系统主要的食物链。碎屑和浮游植物对食物网的贡献率分别为61.32%和38.69%。始于浮游植物和碎屑的营养传递效率分别是9.34%和10.50%,系统总营养传递效率是9.82%。总初级生产量/总呼吸量为2.26,系统连接指数为0.372,系统杂食性指数为0.222。生态系统总体特征反映了舟山海域生态系统的成熟状态较低,生态系统处于不稳定阶段,容易受到外界环境变化的影响。根据模型估算,当褐菖鲉生物量增加至8.6倍时,褐菖鲉达到生态容量0.007 95 t/km²,此时生态系统仍保持平衡,且生态系统总体特征基本稳定。因此,褐菖鲉在舟山海域尚有较大增殖潜力。     

Uptake and metabolism of arsenate by anexic cultures of the microalgae Dunaliella tertiolecta and Phaeodactylum tricornutum

Axenic cultures of the microalgae species, Dunaliella tertiolecta and Phaeodactylum tricornutum were grown at arsenic (As) concentrations typically found in uncontaminated marine environments ( 2 µg L^− 1) under different phosphorus concentrations. D. tertiolecta accumulated higher arsenic concentrations (mean: 13.7 ± 0.7 µg g^− 1 dry mass) than P. tricornutum (mean: 1.9 ± 0.2 µg g−1 dry mass). Media phosphorus concentrations (0.6–3 mg/L) had little influence on microalgae growth rates or arsenic accumulation. Arsenic was present as lipid bound (29–38%; 4.2–9.5%), water-soluble (20–29%; 26–34%) and residue bound (41–45%; 57–69%) arsenic species in D. tertiolecta and P. tricornutum respectively. Hydrolysed lipids contained mostly glycerol arsenoribose (OH- ribose), dimethylarsinate (DMA) and inorganic arsenic (As(V)) moieties. Water-soluble species of microalgae were very different. D. tertiolecta contained inorganic arsenic (54–86%) with variable amounts of DMA (7.4–20%), arsenoriboses (5–25%) and traces of methylarsonate (MA) ( 1%). P. tricornutum contained mostly DMA (32–56%) and phosphate arsenoribose (PO₄-ribose, 23–49%) and small amounts of OH-ribose (3.8–6.5%) and As(V) (9–16%). Both microalgae contained an unknown cationic arsenic species. The residue fractions of both microalgae contained predominately inorganic arsenic (99–100%). These results show that at natural seawater arsenic concentrations, both algae take up substantial amounts of inorganic arsenic that is complexed with structural elements or sequestered in vacuoles as stable complexes. A significant portion is also incorporated into lipids. Arsenic is metabolised to simple methylated species and arsenoriboses.     

Lipid biomarkers of deep-sea hydrothermal vent polychaetes—Alvinella pompejana, A. caudata, Paralvinella grasslei and Hesiolyra bergii

The lipid composition was determined for 5 species of polychaete annelids collected by the Deep Submergence Vehicle ALVIN from high temperature chimneys at the 2500 m depth hydrothermal vent field of the East Pacific Rise. These are the first lipid biomarker analyses reported for these hydrothermal vent polychaetes. Lipid content was low in all samples (1.6–35.9 mg g^–1 wet mass) and was dominated by polar lipid (78–90% of total lipid) with 8–19% sterol (ST), and very low storage lipid (triacylglycerol and wax ester). Total polyunsaturated fatty acids (PUFA) were moderately high (22–31% of total fatty acids (FA)) with extremely low or no docosahexaenoic acid (DHA, 22:6(n-3)). Eicosapentaenoic acid (EPA, 20:5(n-3)) levels were 5–6% in Alvinella pompejana and A. caudata and 10.3–13.7% in an errantiate polychaete (likely Hesionidae) and Hesiolyra bergii. There were greater PUFA and a greater EPA/AA (AA is arachidonic acid, 20:4(n-6)) ratio in the anterior versus the posterior half of A. pompejana, which may correlate to the strong temperature gradient reported in its tube. Total nonmethylene interrupted diunsaturated fatty acids (NMID) were 4–9% of total FA for most polychaete species and included several 20:2 and 22:2 components. The principal monounsaturated fatty acids (MUFA) included 18:1(n-7)c (14–19%), 16:1(n-7)c (2.6–10%) and 20:1(n-11)c (3–7% of total FA). These polychaete species may desaturate and elongate the bacterial-derived 18:1(n-7)c to obtain the essential FA EPA and AA. The major ST in the polychaetes is cholesterol (89–98% of total ST) with less cholesterol in the gut contents of A. pompejana. Other ST included 24-ethylcholesterol (1.5–5% of total ST) with lesser amounts of 24-methylenecholesterol, desmosterol, lathosterol, 24-methylcholesterol, 24-ethylcholesterol, and the stanols dehydrocholestanol and cholestanol. The high ST levels could play a role in thermal adaptation of membranes at the hydrothermal vent environment. Differences in the FA profiles separated the closely related species A. pompejana and A. caudata from Paralvinella grasslei, H. bergii, and the errantiate polychaete (likely Hesionidae).     

斑节对虾TSG101基因的克隆及表达分析

为探究肿瘤易感基因101(简称TSG101)对斑节对虾(Penaeusmonodon)的免疫应答作用,了解在细菌刺激下斑节对虾的机体发生的变化机制,本研究以哈维弧菌(Vibrioharveyi)和金黄色葡萄球菌(Staphylococcusaureus)为实验组,以磷酸缓冲液(PBS)为对照组,通过荧光定量分析展开对斑节对虾对菌刺激的免疫应答作用。结果显示,斑节对虾的TSG101在各组织中均有表达,在肝胰腺中的表达量最高。在金黄色葡萄球菌刺激下,斑节对虾的TSG101在肝胰腺中的表达量与对照组相比呈极显著上调(P0.01),第12小时的TSG101 mRNA的表达量达到最大(为对照组的21.60倍);在鳃中的表达量与对照组相比呈极显著上调(P0.01),第6小时斑节对虾TSG101的表达量达到最大值(为对照组的3.64倍)。在注射哈维弧菌第9小时,肝胰腺中的PmTSG101 mRNA表达量极显著上调(P0.01)且达到最大(为对照组的2.50倍)。实验结果初步表明,斑节TSG101参与斑节对虾的先天免疫反应,在金黄色葡萄球菌和哈维弧菌的刺激的情况下,该基因RNA水平的表达情况发生明显变化。     

缢蛏HAT基因家族的全基因组鉴定及在环境因子、细菌胁迫下的表达分析

组蛋白乙酰化酶(histone acetyltransferases, HATs)在机体发育和环境胁迫响应的调控中发挥着重要作用,但在海洋贝类中研究极少。缢蛏(Sinonovacula constricta)作为典型的滩涂双壳贝类,经常面临多种极端环境和细菌胁迫的挑战,基于全基因组和转录组数据系统分析了缢蛏HAT基因家族(ScHATs)的系统发育关系,以及它们在不同发育时期、不同环境因子和细菌胁迫下的表达模式。结果共鉴定出11个ScHATs基因,根据序列同源性分为GNAT、MYST和p300/CBP三类,每个亚家族中几乎所有的HAT都具有特定的保守结构域和保守基序。基因表达谱和qRT-PCR分析显示,ScHATs在幼虫发育前期表达量普遍高于发育后期;在氨氮胁迫下,ScKAT2B、ScKAT8、ScKAT9-2、Scp300在鳃中的表达量显著变化(P<0.05);在高温胁迫下,ScHATs在鳃和肝胰腺中表现出相似的表达模式,而Scp300在肝胰腺中的表达量显著降低(P<0.05);在副溶血弧菌胁迫下,ScHATs的表达均出现显著上调(P<0.05)。综上结果提示, Sc...