红藻DNA条形码分析技术研究进展     

茅云翔  吴菲菲  杜国英 《中国海洋大学学报(自然科学版)》2014,44(8):48-53

DNA条形码是指利用一段相对较短的标准DNA片段,对物种进行识别和鉴定。目前该技术在动物、植物物种鉴定领域已经得到了广泛的研究和应用。在藻类的研究中,尚未确定一条统一的标准条形码基因,现阶段都是使用2条或2条以上基因序列来完成物种鉴定。对于形态多样、种类繁多的海洋红藻,常用的DNA条形码基因有COI基因(Partial cytochrome c oxidase I gene)、UPA基因(Partial 23SrRNA gene,universal plastid amplicon)、LSU基因(Partial 28SrRNA gene)和rbcL基因(The large subunit of ribulose-1,5-bisphosphate carboxylase)等,这些基因中2个或3个基因的互补运用准确有效地提高了红藻的鉴定准确率,尤其是COI基因的种间差异大足够区分相近物种。本文在概述条形码的原理及其标准的基础上,阐述了红藻DNA条形码鉴定研究的新进展以及常用几种基因片段的优缺点,并对条形码在红藻鉴定中存在的问题进行了分析,对其应用前景进行了展望。  相似文献   

Association of triacylglyceride content and transcript abundance of genes involving in lipid synthesis of nitrogen deficient Phaeodactylum tricornutum     

张琳  韩吉昌  杨官品  朱葆华  潘克厚 《中国海洋湖沼学报》2014,32(2):397-402

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溶藻弧菌acfA基因克隆与生物信息学分析     

程海燕  庞欢瑛  鲁义善  简纪常  吴灶和  蔡双虎 《广东海洋大学学报》2014,(1):9-14

溶藻弧菌引起海水养殖产业弧菌病的主要病原,附着定植因子基因acfA是溶藻弧菌重要毒力基因之一,其表达产物是溶藻弧菌有效定植在宿主肠道上所必需的蛋白。根据弧菌属细菌acfA基因基因保守区设计引物,采用Touchdown PCR扩增acfA基因部分序列,Inverse PCR和Nested PCR扩增已知序列侧翼序列,成功克隆了溶藻弧菌acfA基因全长。克隆的acfA基因序列全长为743 bp,开放阅读框长度为648 bp组成,共编码215个氨基酸,在5′端上游未发现-35区和-10区序列。演绎的ACFA蛋白N端有18个氨基酸信号肽序列,表明该蛋白是分泌型蛋白;蛋白结构分析表明主要由α螺旋和不规则卷曲构成。BLAST分析表明,该蛋白氨基酸序列与其他弧菌相应蛋白同源性较高,是较保守的外膜蛋白。  相似文献   

鳗鲡目鱼类线粒体蛋白质编码基因易位及系统演化关系分析     

申欣  田美  孟学平  程汉良  阎斌伦 《海洋学报》2014,36(4):73-81

鳗鲡目鱼类线粒体基因组的基因组成较为保守,在58个线粒体基因组中,仅有3个物种存在基因数量的差异。在19个鳗鲡目鱼类线粒体基因组中存在主编码基因的重排。主编码基因的变异位点分析结果支持nad5、nad4和nad2基因作为cox1和lrRNA基因辅助的分子标记。鳗鲡科Anguillidae的20个种(亚种)聚在一起,强烈支持鳗鲡科为单系群(BPP=100)。鳗鲡科下属的3个类群(大洋洲类群、大西洋类群和印度洋-太平洋类群)也同时得到有力的验证(BPP均为100)。线鳗科Nemichthyidae和锯齿鳗科Serrivomeridae亲缘关系最近,二者聚类后,与鳗鲡科Anguillidae构成姊妹群(BPP=100)。在囊喉鱼亚目Saccopharyngoidei中,宽咽鱼科Eurypharyngidae与囊鳃鳗科Saccopharyngidae聚类(BPP=100),同时,单颌鳗科Monognathidae与月尾鳗科Cyematidae聚类(BPP=100),4个科聚在一支,支持囊喉鱼亚目为单系群(BPP=100)。在囊喉鱼亚目线粒体基因组中,3个物种(吞鳗Eurypharynx pelecanoides、拉文囊鳃鳗Saccopharynx lavenbergi和杰氏单颌鳗Monognathus jesperseni)存在主编码基因的重排。16种鳗鲡(细美体鳗Ariosoma shiroanago、短吻颈鳗Derichthys serpentinus、凯氏短尾康吉鳗Coloconger cadenati、鸭颈鳗Nessorhamphus ingolfianus、龟草鳗Thalassenchelys sp.、粗犁齿海鳗Cynoponticus ferox、百吉海鳗Muraenesox bagio、巨斑花蛇鳗Myrichthys maculosus、大吻沙蛇鳗Ophisurus macrorhynchos、几内亚副康吉鳗Paraconger notialis、哈氏异康吉鳗Heteroconger hassi、小头鸭嘴鳗Nettastoma parviceps、弱头鳗Leptocephalus sp.、斑点长犁齿鳗Hoplunnis punctata、尖吻小鸭嘴鳗Facciolella oxyrhyncha和星康吉鳗Conger myriaster),与鳗鲡目线粒体主编码基因的原始排列相比,共享nad6基因的易位。同时,基于线粒体基因组13个蛋白质编码基因构建的系统演化树,强烈支持这16个物种聚为一支(BPP=100)。然而,由此而带来的海鳗科Muraenesocidae、拟鯙科Chlopsidae和糯鳗科Congridae是否为单系群的问题,值得今后深入探究。  相似文献   

Phylogenomic analysis of transcriptomic sequences of mitochondria and chloroplasts for marine red algae (Rhodophyta) in China   总被引：1，自引：1，他引：0  

JIA Shangang  WANG Xumin  QIAN Hao  LI Tianyong  SUN Jing  WANG Liang  YU Jun  LI Xingang  YIN Jinlong  LIU Tao  WU Shuangxiu 《海洋学报(英文版)》2014,33(2):86-93

The chloroplast and mitochondrion of red algae （Phylum Rhodophyta） may have originated from different endosymbiosis. In this study, we carried out phylogenomic analysis to distinguish their evolutionary lin-eages by using red algal RNA-seq datasets of the 1 000 Plants （1KP） Project and publicly available complete genomes of mitochondria and chloroplasts of Rhodophyta. We have found that red algae were divided into three clades of orders, Florideophyceae, Bangiophyceae and Cyanidiophyceae. Taxonomy resolution for Class Florideophyceae showed that Order Gigartinales was close to Order Halymeniales, while Order Graci-lariales was in a clade of Order Ceramials. We confirmed Prionitis divaricata （Family Halymeniaceae） was closely related to the clade of Order Gracilariales, rather than to genus Grateloupia of Order Halymeniales as reported before. Furthermore, we found both mitochondrial and chloroplastic genes in Rhodophyta under negative selection （Ka/Ks〈1）, suggesting that red algae, as one primitive group of eukaryotic algae, might share joint evolutionary history with these two organelles for a long time, although we identified some dif-ferences in their phylogenetic trees. Our analysis provided the basic phylogenetic relationships of red algae, and demonstrated their potential ability to study endosymbiotic events.  相似文献   

西南印度洋深海热液硫化物区沉积物微生物群落结构和固氮基因多样性   总被引：1，自引：0，他引：1  

吴月红  曹佚  王春生  吴敏  Aharon Oren  许学伟 《海洋学报(英文版)》2014,33(10):94-104

A sediment sample was collected from a deep-sea hydrothermal vent field located at a depth of 2 951 m on the Southwest Indian Ridge. Phylogenetic analyses were performed on the prokaryotic community using polymerase chain reaction（PCR） amplification of the 16 S rRNA and nifH genes. Within the Archaea, the dominant clones were from marine benthic group E（MBGE） and marine group I（MGI） belonging to the phyla Euryarchaeota and Thaumarchaeota, respectively. More than half of the bacterial clones belonged to the Proteobacteria, and most fell within the Gammaproteobacteria. No epsilonproteobacterial sequence was observed. Additional phyla were detected including the Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Nitrospirae, Chloroflexi, Chlorobi, Chlamydiae, Verrucomicrobia, and candidate divisions OD1, OP11, WS3 and TM6, confirming their existence in hydrothermal vent environments. The detection of nifH gene suggests that biological nitrogen fixation may occur in the hydrothermal vent field of the Southwest Indian Ridge. Phylogenetic analysis indicated that only Clusters I and III NifH were present. This is consistent with the phylogenetic analysis of the microbial 16 S rRNA genes, indicating that Bacteria play the main role in nitrogen fixation in this hydrothermal vent environment.  相似文献   

Cloning and expression analysis of the chloroplast fructose- 1,6-bisphosphatase gene from Pyropia haitanensis     

XIAO Haidong  CHEN Changsheng  XU Yan  JI Dehu  XIE Chaotian 《海洋学报(英文版)》2014,33(4):92-100

Fructose-1,6-bisphosphatase(FBPase) is one of the key enzymes in Calvin circle and starch biosynthesis. In this study, the full-length of cpFBPase gene from Pyropia haitanensis was cloned by using rapid amplification of cDNA ends(RACE) technology. The nucleotide sequence of PhcpFBPase consists of 1 400 bp, including a 5′ untranslated region(UTR) of 92 bp, a 3′?UTR of 69 bp, and an open reading frame(ORF) of 1 236 bp, which can be translated into a 412-amino-acid putative peptides with a molecular weight of 44.3 kDa and a theoretical pI of 5.23. Multiple sequence alignment indicated that the protein belonged to the chloroplast FBPase enzyme. Phylogenetic analysis showed that the protein assembled with the cpFBPase of a thermal tolerant unicellular red micro-algae Galdieria sulphuraria. Expression patterns analyzed by qRT-PCR revealed that the expression of PhcpFBPase gene in the thallus phage was 7-fold higher than in the conchocelis phage, which suggested the different mechanisms of inorganic carbon utilization among the different life phages of P. haitanensis. And the different response modes of PhcpFBPase mRNA levels to high temperature and desiccation stress indicated that PhcpFBPase played an important role in responsing to abiotic stress.  相似文献   

长江口沉积物-水界面砷的迁移转化机制与微生物调控分析     

张玉婷  段丽琴  宋金明  张乃星  尹美玲  李学刚  袁华茂 《地学前缘》2022,29(4):144-155

为探析长江口沉积物-水界面砷的迁移转化机制,本文分析了2019年夏季长江口4个站位上覆水和间隙水中总As浓度及形态的剖面变化特征,耦合氧化还原敏感元素(Fe、Mn和S)的剖面变化剖析了沉积物-水界面砷循环的Fe-Mn-S控制机制,同时结合砷相关功能基因探讨了沉积物-水界面砷迁移转化的微生物调控过程,估算了沉积物-水界面总As的扩散通量。结果表明,除A7-4站位外,长江口其他3个站位间隙水总As以As³⁺为主要存在形态,且总As浓度均在上覆水中为最低值(0.748~1.57 μg·L^-1),而在间隙水中随着深度增加而逐渐增加并在6~9 cm深度达到峰值(7.14~26.9 μg·L^-1)。间隙水总As及As³⁺浓度的剖面变化趋势与溶解态Fe²⁺、Mn²⁺相似,其均在中间层出现高值,说明沉积物Fe/Mn还原带砷的释放可能是随固相Fe(Ⅲ)或Mn(Ⅳ)的还原而转移到间隙水中的。氧化层和Fe/Mn还原带过渡区间隙水砷浓度与砷异化还原菌功能基因arrA和arsC丰度存在对应关系(除A1-3站外),说明砷异化还原菌将溶解As⁵⁺或固相As⁵⁺还原为溶解As³⁺可能是该过渡层砷迁移转化的另一重要过程。硫酸盐还原带的间隙水总As和As³⁺浓度降低,但由于间隙水的低S^2-浓度不利于砷硫化物生成,因此深层间隙水砷可能与铁硫矿物结合而被移除。底层环境氧化还原条件是影响沉积物-水界面砷迁移转化的重要因素,随底层水DO浓度的降低,砷迁移转化更倾向于微生物还原控制。长江口沉积物-水界面总As的扩散通量为1.18×10^-7~2.07×10^-7 μmol·cm^-2·s^-1,均表现为沉积物间隙水中总As向上覆水释放,即沉积物是研究区域水体总As的来源之一。  相似文献   

Genetic study of Kelp “901” strain     

夏鹏王秀良  李晓捷赵玉山姚琳  段德麟 《中国海洋湖沼学报》2005,23(2):152-157

Based on DNA extraction and optimization of random amplified reaction (RAPD) to the gametophytes and sporophytes of Kelp “901” strain, genetic study on variation was conducted to its parents and offsprings of F6, F7,Fs, and F9 generation. RAPD results have shown that among 30 selected primers for gametophytes, 297 loci ranging from 200 to 3 000 bp were obtained in the average of 9,9 loci for each primer, This indicated a high polymorphic rate with RAPD detection. UPGMA (unweighted pair-group method arithmetic average) analysis showed that each male and female gametophyte of a generation could be clustered into one pair separately. The genetic distances of the Kelp 901 generation were 0.321 2-0.476 7, and the maximum was between F7 and Fs (0.476 7). Identity analysis showed that F6 generation was more close to the female parent (0.659 3), and F7 generation was more close to the male parent (0.5788). To the sporophytes study in 24 selected primers for RAPD amplification, 191 loci ranging from 230-2 800 bp were obtained, in the average to each primer of 8.0 loci. The heterozygosity to six populations were male parent (0.223 9),female parent (0.107 2), F6 (0.216 4), F7 (0.228 6), F8 (0.229 6) and F9 (0.317 2). The nearest genetic distance was 0.083 5 (Fs, F9). Total heterozygosity (HT) ofF6, F7, F8 and F9 generations was 0.318 6, the average heterozygosity (Hs) for F6,F7, F8 and F9 generations was 0.248 0, and deduced coefficient of population differentiation (Gst) was 22.2%. Six sequence characterized amplified regions (SCAR) were preliminary screened through RAPD analysis. It needed to be verified in detail as they are significant for molecular marker assistance in breeding and selecting Laminaria.  相似文献   

基因间隔序列（ITS）在水产动物种质鉴定和遗传多样性分析中的应用   总被引：1，自引：0，他引：1  

徐田军  刘楚吾刘丽董秋芬  杨叶欣 《广东海洋大学学报》2006,26(1):84-88

近年来，由于国内外市场对水产品的需求不断增长，水产业因此获得了长足的发展，许多水产种类的养殖量有了大幅度的增加，在给我国国民经济的增长作出贡献的同时，已经不可避免的带来了许多弊端，一些方面甚至在一定程度上会影响未来水产业的发展。其中最应该引起关注的是由于目前捕捞强度的增加、生态环境的恶化等，导致许多种群的数量大量减少，产量也随之降低，种质资源遭到前所未有的破坏和衰退。因此，种质鉴定、种群分析及保护和遗传多样性的研究已经成为当前水产研究的当务之急。  相似文献