Structure Analysis of the Complete Mitochondrial Genome in Cultivation Variety 'Rongfu'     

ZHANG Jing  LI Ning  ZHANG Zhifeng  LIU Tao 《中国海洋大学学报(英文版)》2011,10(4)

In this report,complete mitochondrial genome sequences of Laminaria cultivation variety 'Rongfu' were obtained.The results showed the length of circular molecule of mtDNA was 37 638 bp(64.7% A+T),encoding three rRNAs(23S,16S and 5S),25 tRNAs,35 known mitochondrial proteins and 3 ORFs.Sequence alignment indicated its mtDNA genome was very similar to that of Laminaria japonica.Phylogenetic trees inferred from concatenated 30 mitochondrial genes showed that 'Rongfu',Laminaria japon-ica,Laminaria longipedalis,L...  相似文献   

Phylogenetic analysis of cultivable bacteria isolated from Arctic sea-ice     

林学政  沈继红  黄晓航  高爱国 《极地研究(英文版)》2007,18(1):84-89

Phylogenetic analysis based on 16S rDNA of 8 strains of cultivable bacteria isolated from Arctic sea-ice was studied.The results showed that strain BJ1 belonged to genus Planococcus,which was a genus of low mole percent G C gram-positive bacteria;strain BJ6 belonged to genus Burkholderia of β-proteobacteria and the rest 6 strain all belonged to γ-proteobacteria,of which strain BJ8 was a species of Pseudoalteromonas,strain BJ2-BJ5 and BJ7 were members of genus Psychrobacter.Phylogenetic analysis also indicated that bacteria of genus Psychrobacter of the isolates formed a relatively independent phylogenetic cluster in comparison with other bacteria belonged to genus Psychrobacter.  相似文献   

Structure of mitochondrial DNA control region of Pholis fangi and its phylogenetic implication     

Lin Li  Hui Zhang  Dianrong Sun  Tianxiang Gao 《中国海洋大学学报(英文版)》2014,13(3):491-496

In this study, the entire mitochondrial DNA （mtDNA） control region （CR） of Pholis fangi was amplified via polymerase chain reaction followed by direct sequencing. The length of the mtDNA CR consensus sequence of P. fangi was 853 bp in length. In accordance with the recognition sites as were previously reported in fish species, the mtDNA CR sequence of P. fangi can be divided into 3 domains, i.e., the extended terminal associated sequence （ETAS）, the central conserved sequence block （CSB）, and the CSB domain. In addition, the following structures were identified in the mtDNA CR sequence of P. fangi：2 ETASs in the ETAS domain （TAS and cTAS）, 6 CSBs in the central CSB domain （CSB-F to CSB-A）, and 3 CSBs in the CSB domain （CSB-1 to CSB-3）. These demonstrated that the structure of the mtDNA CR of P. fangi was substantially different from those of most other fish species. The mtDNA CR sequence of P. fangi contained one conserved region from 656 bp to 815 bp. Similar to most other fish species, P. fangi has no tandem repeat sequences in its mtDNA CR sequence. Phylogenetic analysis based on the complete mtDNA CR sequences showed that there were no genetic differences within P. fangi populations of the same geographical origin and between P. fangi populations of different geographical origins.  相似文献   

高体(鱼狮)(Seriola dumerili)线粒体全基因组测定及结构特征分析     

王开杰  徐永江  崔爱君  柳学周  姜燕  王滨 《海洋与湖沼》2022,53(1):120-132

为快速有效鉴别(鱼师)属鱼类物种、加强(鱼师)鱼遗传多样性管理与种质资源保护,通过Illumina测序技术,获得了东海海域养殖高体(鱼师)(Seriola dumerili)线粒体基因组全序列(16 530bp),碱基组成为A (26.83%)、G (17.6%)、C (30.04%)和T (25.53%), A+T含量为52.36%,且非编码控制区(D-loop)A+T富含61.64%,表现明显的AT偏好性。与其他硬骨鱼一样,高体(鱼师)线粒体基因组包含13条蛋白编码基因, 22个tRNA基因, 2个rRNA基因,除ND6、tRNA^Gln、tRNA^Ala、tRNA^Asn、tRNA^Cys、tRNA^Tyr、tRNA^Ser、tRNA^Glu、tRNA^Pro基因外,其余均位于H链编码;蛋白编码基因中,除COⅠ、COⅡ和ND5的起始密码子分别为ATC、ATA和ATA外,其余10个蛋白编码基因的起始密码子均为ATG,以典型的TAA和TAG为终止密码子,在ND4和Cytb中存在不完全密码子T;除tRNA^Ser-GCT外,其余21个tRNA均为典型三叶草二级结构。比较中国和日本海域高体(鱼师)线粒体基因组发现, CO Ⅰ、CO Ⅱ和ND5蛋白编码基因在起止位置、片段长度及起止密码子上存在显著差异。此外,与同属的黄条(Seriola aureovittata)和五条(鱼师)(Seriola quinqueradiata)的线粒体基因组13个蛋白编码基因进行两两对比分析,结果表明3种(鱼师)属鱼类的蛋白编码基因的相似性在85%~100%之间。基于线粒体基因组全序列构建的系统发育树,成功将高体(鱼师)与其他(鱼师)属鱼类有效区分,高体(鱼师)与长鳍(鱼师)同属一支,亲缘关系最近;黄条(鱼师)和五条(鱼师)聚为一支,亲缘关系最近。  相似文献   

Comparative mitochondrial genome analysis of Sesarmidae and its phylogenetic implications     

Ying Zhang  Lei Meng  Liming Wei  Bingjian Liu  Liqin Liu  Zhenming Lü  Yang Gao  Li Gong 《海洋学报(英文版)》2022,41(8):62-73

Here, we sequenced the complete mitogenome of Parasesarma eumolpe (Brachyura: Grapsoidea: Sesarmidae) for the first time. The characteristics of this newly sequenced mitogenome were described and compared with other Sesarmidae species. The 15 646-bp mitogenome contains 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A-T rich region. All of the PCGs are initiated by the start codon ATN and terminated by the standard TAN codon or an incomplete T. The pairwise Ka/Ks ratio analysis shows that all 13 PCGs are under purifying selection, whereas the ATP8 gene is an outlier, with pairwise comparison values ranging from neutral selection (0.000) to positive selection (1.039). The gene arrangement of P. eumolpe compared with ancestral Decapoda shows the translocation of two tRNAs (tRNA-His and tRNA-Gln), which is identical to other Sesarmidae species. Phylogenetic analyses show that all Sesarmidae species are placed into one group, and the polyphyly of Eriphioidea, Ocypodoidea, and Grapsoidea is well supported. The relationship between gaps in the QIM region and the phylogeny of Sesarmidae is analyzed. It is obvious that both the G5 (the gap between Q and I) and G6 (the gap between I and M) decrease progressively with the evolution process. These results will help to better understand the genomic evolution within Sesarmidae and provide insights into the phylogeny of Brachyura.  相似文献   

北部湾棕囊藻藻华原因种分析     

徐轶肖  何喜林  张腾  蓝文陆 《热带海洋学报》2020,39(6):122-130

近年来, 棕囊藻已成为我国北部湾海域藻华发生的主要原因种, 严重影响北部湾海洋生态环境、水产增养殖业和防城港核电安全, 急切需要对棕囊藻藻华原因种作进一步分析确认。2017年2月和3月在钦州湾和涠洲岛藻华发生海域分离得到9株棕囊藻, 采用光学显微镜进行形态学初步鉴定, 并通过核糖体小亚基序列(SSU rDNA)进行系统进化分析。研究结果表明, 北部湾9株棕囊藻与球形棕囊藻形态特征基本符合, 系统发育树与不同海域来源的球形棕囊藻聚在同一大分支上, 与其他海域来源的球形棕囊藻遗传距离为0.0000~0.0071, 其中北部湾WZS3-1株与墨西哥湾株CCMP627、苏里南株CCMP628、厄瓜多尔株CCMP1528、南非株P162、中国海株RCC:K1398及汕头株Santou97的球形棕囊藻亲缘关系最近, 遗传距离为0.0000, 而北部湾WZS1、WZS2、WZS4、WZS5株与香港株SKLMP_T005和渤海株BOHAI1亲缘关系最近, 遗传距离为0.0000。球形棕囊藻的种内遗传距离(0.0000~0.0073)明显小于种间遗传距离(0.0084~0.0440), 因此可确定来自北部湾不同海域的9株棕囊藻均为球形棕囊藻。此外, 球形棕囊藻各藻株间的亲缘关系远近与其地理位置分布不能完全对应。本研究结果将为我国棕囊藻藻华藻种库构建、棕囊藻北部湾株生理生态研究和北部湾棕囊藻藻华发生机理研究等提供参考。  相似文献   

藻类类胡萝卜素合成通路基因的系统发育分析     

王珊珊  张磊  池珊  王国良  王绪敏  刘涛  唐学玺 《海洋学报(英文版)》2018,37(4):89-101

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北部湾涠洲岛红色赤潮藻的分子鉴定     

徐轶肖  何喜林  张腾  赵志娟  韦光领 《海洋科学》2020,44(9):63-73

为了弄清北部湾涠洲岛6株疑似红色赤潮藻（Akashiwo sanguinea）株的种类，作者采用光学显微镜和荧光显微镜对其进行形态学初步鉴定；并对藻株SSU rDNA、LSU rDNA和ITS序列测序，利用最大似然法构建系统发育树。结果表明，北部湾涠洲岛6株藻与红色赤潮藻形态特征基本符合；3种序列系统发育树分析均发现北部湾涠洲岛6株藻与不同海域来源的红色赤潮藻聚在同一大分支上，自展值高达99、100、100；与来自亚洲海域的韩国安山株、新加坡株、中国厦门港株序列差异最小，亲缘关系最近，而与其他地理来源的红色赤潮藻序列差异大，亲缘关系较远。红色赤潮藻SSU、LSU、ITS种内遗传距离分别为0.001~0.008、0.003~0.025和0.045~0.406，明显小于该藻与其他裸甲藻科（Gymnodiniaceae）藻属下的种间遗传距离0.032~0.072、0.165~0.222和0.589~1.559，因此可确定北部湾涠洲岛6株藻均为红色赤潮藻。研究结果将为北部湾海域赤潮生物来源与组成、赤潮的发生与管理提供基础信息。  相似文献   

环境16S rDNA和16S rcDNA序列分析湖光岩玛珥湖的浮游细菌组成     

秦青英  曾永辉  郭倩茹  简纪常  鲁义善  吴灶和 《广东海洋大学学报》2013,(3):1-9

通过提取环境总16S rDNA和总16S rRNA分别构建DNA克隆文库和反转录cDNA文库,并进行克隆测序和序列分析,探讨湖光岩玛珥湖浮游细菌和浮游活性细菌的遗传多样性。结果表明:构建两个水层的4个克隆文库,即1 m和10 m水层总菌的16S rDNA文库和总活性菌的16S rcDNA文库,共获得413条序列,分属15门、32目、52科;1 m水层的rDNA文库与rcDNA文库中Verrucomicrobia类群所占比例最大(36.8%和32.1%),其次为Alphaproteobacteri(a 15.1%和16%)和Betaproteobacteri(a 17.9%和16%);在10 m水层的2个文库中,Alphaproteobacteria类群均占绝对优势,分别为63.5%(rDNA)和43.8%(rcDNA),其次为Verrucomicrobia(11.5%和14.3%),其他细菌类群包括Acidobacteria、Chloroflexi、Firmicutes、待定门OD1、Planctomycetes、Spirochetes和Deltaproteobacteria,比例在0.8%~3.8%之间;在科的水平上,SAR11为湖光岩玛珥湖最为丰富的类群,占总克隆数的26.9%,其中在10 m水层的比例高达51.5%。序列同源性分析表明,绝大多数序列(89.8%)来源于新种,其中19.6%的序列可能来自于新属,69%的序列可能来自于全新的科。湖光岩玛珥湖浮游细菌群落结构较为独特,有大量的浮游细菌种类尚未获得相应的纯培养物,蕴含着丰富而新颖的微生物资源。  相似文献   

浙江镇海潮间带沉积物中可培养微生物初步研究     

郑莹  霍颖异 《海洋学研究》2012,30(4):65-71

针对浙江镇海潮间带沉积物样 品,采用纯培养法分离培养海洋微生物,并基于16S rRNA基因序列,开展系统发育学研究,分析沉积物细菌群落结构及多样性。分离获得细菌39株,16S rRNA基因序列分析表明,这些菌株分别属于厚壁菌门Firmicutes(51. 3%)、变形杆菌门Proteobacteria(30.8%)、拟杆菌门Bacteroidetes(15. 4%)和放线菌门Actinobacteria(2. 6%)4个类群。厚壁菌门和变形杆菌门的菌株主要归属于芽孢杆菌纲Bacilli和a-变形杆菌纲Alphaproteobacteria,它们可能在近海海洋生态系统的元素地球化学循环中发挥了重要作用。此外,部分菌株16S rRNA基因序列与已报道物种的相似性较低,可能代表了新的分类单元。研究丰富了浙江近海微生物种质资源,并拓展了对浙江近海可培养细菌多样性的认识,为今后开发利用海洋微生物资源积累了资料。  相似文献