实验红鲫线粒体DNA条形码特征分析及应用

为探索建立具有实验红鲫品系特异性的线粒体DNA条形码,对鲫属品种进行鉴定.本研究以实验红鲫和鲫属其他鱼类(洞庭湖鲫、日本白鲫、大眼鲫、兰氏鲫、金鱼、湘军金鱼和湘军花鲫)为测试群体,利用Sanger测序对所有个体的线粒体COⅠ、COⅢ、Cytb这3个基因和D-loop进行测序,同时构建3个基因的拼接序列,并分析它们的序列...     

一株鲈鲤源鲤春病毒血症病毒的分离鉴定及其病理观察

2016年4月,四川某鲈鲤(Percocypris pingi)养殖场流行一种以鳃、鱼鳔和内脏器官出血为临床特征的传染病。组织病理学观察发现,患病鲈鲤全身多组织器官均发生明显的病理损伤,尤其是肝、脾、肾、鳃和肠表现为明显的出血、变性、坏死以及炎症细胞浸润。取病鱼组织匀浆滤液接种鲤上皮瘤细胞(epithelioma papulosum cyprini, EPC),盲传3代出现典型的细胞病变(cytopathic effects, CPE)。将自然发病鱼组织匀浆滤液和细胞培养病毒液分别接种健康鲈鲤,实验鱼出现与自然发病鱼相同的症状,死亡率分别为60%和50%,而对照组未见异常。对经分离毒株ZLP160415感染出现CPE的EPC细胞制备超薄切片进行电镜观察,发现病毒呈弹状,长90～150 nm,宽40～60 nm;对自然发病鱼、人工感染发病鱼内脏组织和细胞培养病毒液进行鲤春病毒血症病毒(springviremiaofcarpvirus,SVCV)的RT-PCR检测,均扩增出目的条带。基于SVCV糖蛋白基因进行系统发育分析,结果显示分离毒株(ZLP160415)属于Ia型。结合本次疾病的流行病学与病理损伤特点、病毒分离鉴定、人工感染试验结果和透射电镜检查,确定此次流行病的病原为SVCV。     

奥利亚罗非鱼线粒体基因组全序列测定与系统进化分析

采用LA-PCR(long amplification polymerase chain reaction)扩增方法获得奥利亚罗非鱼(Oreochromis aureus)线粒体基因组全序列.分析表明,序列全长16 632 bp,包括13个蛋白质编码基因、22个tRNA基因、2个rRNA基因和1个长度为931 bp的主非编码区.A、T、G、C碱基的组成分别为27.89％、25.50％、15.62％、30.99％.基因排列与罗非鱼属的其他物种一致.13个蛋白质基因除COX1用TGT做起始密码子外,其他均以ATG为起始,终止密码子除COX2、Cyt b、ND4为不完整的T,其余基因均以典型的TAA做终止密码子.22个tRNA的二级结构都具有典型三叶草结构.系统发育分析显示,罗非鱼属与丽鱼科(Cichlidae)其他物种分开,聚为单系群,其中奥利亚罗非鱼与尼罗罗非鱼亲缘关系较近,莫桑比克非鱼和罗非鱼KM-2006亲缘关系较近.本研究旨在为进一步利用线粒体基因组分析罗非鱼群体遗传多样性、亲缘关系以及丽鱼科系统进化提供基础依据.     

东太平洋公海茎柔鱼种群遗传结构初步研究

根据2009年7月到10月我国大型鱿钓渔船在东太平洋(81.9°～94.9°W,8.9°N～11.3°S)秘鲁和哥斯达黎加外海作业期间采集的样本,利用线粒体DNA细胞色素b基因的724 bp部分序列,分析了采自秘鲁7个采样点和哥斯达黎加3个采样点的155个个体的序列多样性与种群遗传结构.结果显示,724 bp片段中发现了16个变异位点,155个个体出现43个单倍型.序列多样性分析结果揭示,155个个体的平均单倍型多样性指数为0.873,核苷酸多样性指数为0.003 69.群体间共享6个单倍型,秘鲁外海茎柔鱼群体享有最多特有单倍型(20个).分子方差分析揭示,82.70％的遗传变异性出现在种群内;群体间的FST分析揭示部分秘鲁群体与哥斯达黎加群体,部分秘鲁群体间存在着显著的遗传分化;而哥斯达黎加群体内部不存在显著的遗传分化.     

基于线粒体D-loop基因序列研究我国5种虾虎鱼类的系统进化关系

利用PCR技术扩增河川沙塘鳢(Odontobutis potamophila)、鸭绿沙塘鳢(Odontobutis yaluensis)、中华沙塘鳢(Odontobutis sinensis)、葛氏鲈塘鳢(Perccottus glenii)及尖头塘鳢(Eleotris oxycephala)的线粒体D-loop区并测序,获得河川沙塘鳢、鸭绿沙塘鳢、中华沙塘鳢、葛氏鲈塘鳢及尖头塘鳢线粒体D-loop区全序列分别为853bp、853bp、1028bp、852bp、848bp,结合GenBank中平头沙塘鳢(Odontobutis platycephala)、刺盖塘鳢(Eleotris acanthopoma)、黑体塘鳢(Eleotris melanosoma)、褐塘鳢(Eleotris fusca)、中华乌塘鳢(Bostrychussinensis)、云斑尖塘鳢(Oxyeleotris marmorata)、溪鳢(Rhyacichthys aspro))等7种虾虎鱼类同源的D-loop区序列,分析了这12种虾虎鱼类的系统发育关系。所使用的同源序列长度为832～846bp,其中保守位点452个,变异位点405个,简约信息位点258个,单态位点145个,转换/颠换平均值为0.8。基于Kimura2-parameter模型的12种虾虎鱼类遗传距离范围为0.043～0.312,在Kimura2-parameter模型构建的邻接树和非加权配对法系统树中,河川沙塘鳢、鸭绿沙塘鳢、中华沙塘鳢、平头沙塘鳢聚为一大支,刺盖塘鳢、黑体塘鳢、褐塘鳢、尖头塘鳢、溪鳢、葛氏鲈塘鳢聚为另一支。     

北部湾3种金线鱼属鱼类CO I基因序列的比较分析

运用直接测序法对产自北部湾的日本金线鱼(Nemipterus,japonicus)、红棘金线鱼(N.nemurus)和苏门答腊金线鱼(N.mesoprion)3种金线鱼属鱼类的线粒体DNA细胞色素氧化酶Ⅰ(C0Ⅰ)基因序列进行了测序分析,并探讨了3种金线鱼之间的亲缘关系.在所分析的48条COⅠ同源序列片段(696 bp)中共检测到29个单倍型和104个核苷酸多态位点.单倍型分析结果显示,日本金线鱼和红棘金线鱼之间有明显的基因交流.序列差异分析和遗传距离比较结果显示,日本金线鱼与红棘金线鱼之间亲缘关系较近,无明显遗传分化.利用最大简约法(MP)和邻接法(NJ)构建的系统发育树显示,日本金线鱼和红棘金线鱼混杂聚为一支,而苏门答腊金线鱼单独聚为一支.研究结果表明,日本金线鱼与红棘金线鱼的亲缘关系较近,二者可能为同种,而苏门答腊金线鱼则与日本金线鱼、红棘金线鱼亲缘关系较远.本研究为证实红棘金线鱼和苏门答腊金线鱼是2个不同的种提供了分子生物学的证据.     

中国鲎血蓝蛋白提纯及其纯化物的液相色谱串联质谱分析

为了获得高纯度的中国鲎血蓝蛋白并探究其潜在的应用价值,实验从中国鲎血淋巴中提取了血蓝蛋白,并用AKTA蛋白纯化系统进行纯化,使用液相色谱串联质谱(LC-MS/MS)技术对纯化后的血蓝蛋白进行定性分析,最后从uniprot蛋白数据库下载了22条分属5个物种的血蓝蛋白的氨基酸序列,并构建了N-J系统进化树。结果显示,制备的血蓝蛋白纯度较高,从纯化后的中国鲎血蓝蛋白中鉴定到了12种血蓝蛋白的亚基,包括Hemocyanin subunitⅠ、Hemocyanin subunitⅡ、Hemocyanin subunitⅢa、Hemocyanin subunitⅢb、Hemocyanin subunitⅣ、Hemocyanin subunitⅤ、Hemocyanin subunitⅥ等。uniprot数据库显示,这些亚基最早在圆尾鲎和美洲鲎体内被发现。N-J系统进化树显示,中国鲎血蓝蛋白与圆尾鲎和美洲鲎血蓝蛋白具有高度的同源性,并且鲎科动物血蓝蛋白与凡纳滨对虾、锯缘青蟹的血蓝蛋白有较近的进化关系,这意味着可根据虾蟹血蓝蛋白的功能推测中国鲎血蓝蛋白的功能。本研究结果有助于中国鲎血蓝蛋白的功能预测和应...     

Body size evolution and habitat colonization across 100 million years (Late Jurassic–Paleocene) of the actinopterygian evolutionary history

Fishes are characterized by their capacity to occupy all aquatic environments and by their amazing range of size and morphology. While it is known that habitat influenced the diversity dynamics of fish clades, studies on environmental colonization events through the evolutionary history of ray‐finned fishes have yielded conflicting results as to the origin of modern clades and preferential directions of shifts. The effects of habitat over morphological evolution such as body size remain poorly known in vertebrates. However, body size evolution is more frequently addressed in terms of variation through time and numerous studies have demonstrated that successive taxa within a clade tend to increase in size through time (Cope's or Depéret's rule). We use phylogenetic comparative methods on a genus‐level actinopterygian super‐tree based on extant and fossil data covering the Late Jurassic‐Paleogene interval. Results indicate marine ancestry for freshwater lineages and a dominance of colonizations from marine clades towards other habitats. Similar trends in environment occupancy among different ray‐finned clades are explored. Three main trends affecting non‐closely‐related clades are recognized: (i) the freshwater invaders, (ii) the predominantly marine dwellers and (iii) the environmentally labile fishes. Habitat effects on body size evolution are not statistically supported, but most actinopterygian subclades originate from small‐sized ancestors and tend to increase in size in the course of their evolutionary history. This trend is clear for lineages restricted for long periods of time in the same environments, either marine or freshwater, but it is not observed in environmentally labile fish lineages.     

Evaluation of genetic relationship among six Labeo species using randomly amplified polymorphic DNA (RAPD)

Labeo species constitute an important group of fish with intense diversity and potential for commercial aquaculture in many Southeast Asian nations including the Indian subcontinent. The present investigation involves the comparative analysis of randomly amplified polymorphic DNA (RAPD) profiles of six Labeo species viz., L. bata (bata), L. calbasu (calbasu), L. dyocheilus (dyocheilus), L. fimbriatus (fimbriatus), L. gonius (gonius) and L. rohita (rohu) at the nuclear DNA variation level. Fifteen decamer random primers were chosen from 40, which amplified a total of 449 DNA fragments ranging in size from 400 to 3000 bp. Both monomorphic and polymorphic DNA bands were identified based on their presence or absence that could be used for specieswise differentiation. Similarity coefficients were calculated to quantify the genetic variation within and between species. On an average, the highest intra‐species genetic similarity value was found in calbasu (0.93) followed by rohu and fimbriatus (0.91), bata (0.87), gonius (0.86) and dyocheilus (0.77). The interspecies genetic similarity estimates among the species of Labeo were used to deduce their phylogenetic relationships. The cluster analysis showed two main clusters, one with calbasu, rohu, fimbriatus and gonius and another with bata and dyocheilus. The study provides evidence that RAPD could be used for genetic differentiation of closely related species.     

Characterization of nodavirus and viral encephalopathy and retinopathy in farmed turbot, Scophthalmus maximus (L.)

An outbreak of nodavirus infection in turbot larvae is described with respect to histopathology, immunohistochemistry, cell culture cultivation, RT-PCR amplification and sequence analysis of the capsid protein gene RNA2. Affected turbot developed classical signs of viral encephalopathy and retinopathy (VER) with abnormal swimming behaviour and high mortality levels. In the acute stage of infection, light microscopy revealed vacuolation of the central nervous system (CNS), with positive immunohistochemical staining for nodavirus. Later in the infection, CNS lesions appeared more chronic and contained clusters of cells immunopositive for nodavirus. Bacterial overgrowth in the intestines of the fish may have provoked or influenced the course of the nodavirus infection. We were unable to propagate the virus in cell culture. While RT-PCR using primers designed to detect Atlantic halibut nodavirus gave negative results, further testing with primers complementary to a more conserved region of RNA2 resulted in amplification of a product of the expected size. The entire RNA2 segment was cloned and sequenced. Sequence alignment showed that the turbot nodavirus (TNV) was different from previously described fish nodaviruses. In addition, phylogenetic analysis based on an 823 nt region of the sequence indicated that TNV clustered outside the four established fish nodavirus genotypes, suggesting a fifth genotype within the betanodaviruses.