Complete nuclear ribosomal DNA sequence analyses of the black-footed abalone Haliotis iris     

Zhansheng Guo  Leng Han 《新西兰海洋与淡水研究杂志》2018,52(2):232-246

The black-footed abalone Haliotis iris is an economically important shellfish species in New Zealand. We successfully amplified, sequenced and analysed the complete nuclear ribosomal DNA (nrDNA) of H. iris. The length of the nrDNA was determined to be around 9.6?kb and included, in order, small subunit ribosomal RNA (nrSSU, 1858bp), internal transcribed spacer (ITS, 749?bp), large subunit ribosomal RNA (nrLSU, 3412bp) and an intergenic spacer (IGS, 3560–3662?bp). The nrLSU genes were identical in two individuals, whereas the nrSSU and ITS regions existed at three and four base differences, respectively. The IGS was more variable than the other nrDNA regions. A phylogenetic tree was constructed based on the ITS sequence datasets, which revealed that Haliotidae has two major subclades, mainly distributed in the North Pacific, Europe and Australia. The complete nrDNA sequence will be useful for the classification, phylogeny and breeding of this shellfish.  相似文献   

不同饲养方式对乌鳢(Ophiocephalus argus)肠道微生物群落结构差异及种类多样性的影响     

盛鹏程  周冬仁  韩新荣  胡晓波  叶雪平  徐磊  周聃  吴琦芳  郝贵杰 《海洋与湖沼》2020,51(1):148-155

以乌鳢(Ophiocephalus argus)为研究对象,采用不同日粮饲喂,试验W1组饲喂冰鲜鱼,试验W2组饲喂畜禽内脏。12周后,取肠道内容物,利用16S rDNA技术研究投喂不同饲粮的乌鳢肠道生物群落结构差异和微生物多样性,分别获得W1组和W2组乌鳢肠道细菌有效序列51124和39298条。结果分析表明;W1组和W2组物种注释(operational taxonomic unit,OTU)数目分别为2631和4114条,分类地位明确的细菌种类分别隶属5个属和49个属,W1组和W2组乌鳢肠道细菌种类差异很大。W1组乌鳢肠道细菌的优势类群是邻单胞菌属(Plesiomonas)、狭义梭菌属(Clostridium sensu stricto)、鲸蜡菌属(Cetobacterium);W2组乌鳢肠道细菌的优势类群是狭义梭菌属(Clostridium sensu stricto)、邻单胞菌属(Plesiomonas)、Spartobacteria、甲基副球菌属(Methyloparacoccus)、杆菌属(Alsobacter)、Saccharibacteria、分支杆菌属(Mycobacterium)。W2组乌鳢肠道细菌香农指数高于W1组乌鳢肠道细菌,表明前者肠道细菌多样性大于后者。本实验揭示了畜禽内脏饲喂乌鳢肠道细菌的群落种类多样性、OTU丰富度和物种总数均高于冰鲜鱼饲喂乌鳢;W1组肠道有益菌OTU丰富度大于W2组,且W2组还存在一些潜在致病菌。本研究为乌鳢的健康养殖和后续肠道微生物资源的挖掘提供了理论依据。  相似文献   

Feeding intensity and molecular prey identification of the mantis shrimp,Oratosquilla oratoria (De Haan, 1844), in the Tianjin coastal zone of Bohai Bay     

Qi-Kang Bo  Yun-Zhao Lu  Hui-Jing Mi  Yan-Guang Yu  De-Xian Gu  Hong-Zheng You  Shuang Hao 《Marine Ecology》2020,41(4):e12594

Bohai Bay, a representative semi-enclosed bay of China, has been severely impacted in recent decades by rapid human development. Although the mantis shrimp Oratosquilla oratoria plays an important role in the Bohai Bay ecosystem and fishery, its feeding ecology and the impact of habitat changes on its feeding habits are poorly known. In this study, we sought to identify its feeding strategy through the separation of stomach contents, and to describe its trophic ecology during maturation in the Tianjin coastal zone of Bohai Bay by the DNA barcoding method using a fragment (about 690 bp) of the mitochondrial cytochrome oxidase I (CO I) gene. A total of 594 specimens were collected from March to July 2018, and 347 (58.42%) stomachs were found to have food remains. More than half of the O. oratoria individuals had poor feeding activity, and the degree of feeding of females was higher than that of males, but there was no significant difference in the visual fullness index and the fullness weight index (FWI) between sexes for each month. In addition, the feeding activity of O. oratoria was consistent across the months, suggesting in artificial breeding programs it is not worried too much about the accessional diet supplied to the female bloodstocks except maintaining their normal food. A total of 167 retrieved prey items yielded 187 readable sequences; 86.63% of these sequences could be assigned to the species level. Consequently, 25 different prey taxa covering all readable sequences were identified, showing O. oratoria is a generalist predator. In terms of percent composition by frequency of occurrences (%N), crustaceans and fishes accounted for the same and highest percentage (35.83%) in the mantis shrimp diet, followed by mollusks (24.59%) and the remaining marine organisms (3.73%) including Polychaeta (2.67%), Sagittoidea (0.53%), and Chromadorea (0.53%). The result shows the benthic fish Oxudercidae (family) appears to be an especially important food supply for O. oratoria during maturation. The degree of cannibalism decreased with an increase in diet species and the frequencies of cannibalism in this study was noticeably higher than that in previous studies, suggesting that cannibalism may be a significant feeding strategy in the mantis shrimp O. oratoria in the Tianjin coastal zone of Bohai Bay, and because of the frequently cannibalistic behavior, the high stocking density of broodstocks should be avoided.  相似文献   

Morphological and molecular evidence supports the first occurrence of two fishes,Siganus sutor(Valenciennes, 1835)and Seriolina nigrofasciata(Rüppell, 1829)(Actinopterygii:Perciformes), from marine waters of Odisha coast,Bay of Bengal,India     

Barik Tapan K.  Swain Surya N.  Sahu Bijayalaxmi  Tripathy Bibarani  Acharya Usha R. 《海洋学报(英文版)》2020,39(6):26-35

Marine ecosystems provide a wide variety of diverse habitats that frequently promote migration and ecological adaptation. The extent to which the geographic distribution of marine organism has reshaped by human activities remains underappreciated. The limitations intrinsic to morphology-based identification systems have engendered an urgent need for reliable genetic methods that enable the unequivocal recognition of fish species,particularly those that are prone to overexploitation and/or market substitution. In the present study, however, an attempt has been taken to identify two locally adapted fish species, Siganus sutor(Valenciennes, 1835) and Seriolina nigrofasciata(Rüppell, 1829) of order Perciformes, which happens to be the first record in Odisha coast,Bay of Bengal. The diagnostic characteristics of Siganus sutor are: dorsal fin XIII-10, anal fin VII-9, pectoral fin 15,pelvic fin II-3, while that of Seriolina nigrofasciata dorsal fin VI-I-35, anal fin I-17, pectoral fin 16, pelvic fin 5. All COI barcodes generated in this study were matched with reference sequences of expected species, according to morphological identification. Bayesian and likelihood phylogenetic trees were drawn based on DNA barcodes and all the specimens clustered in agreement with their taxonomic classification at the species level. The phylogeographic studies based on haplotype network and migration rates suggest that both the species were not panmitic and the high-frequency population distribution indicates successful migration. The result of this study provides an important validation of the use of DNA barcode sequences for monitoring species diversity and changes within a complex marine ecosystem.  相似文献   

基于SLAF测序分析3个塔形马蹄螺群体的遗传结构和多样性*     

黄景  欧泽奎  刘文广  何毛贤 《热带海洋学报》2020,39(5):1-18

塔形马蹄螺(Tectus pyramis), 海洋软体动物, 广泛分布于中国深圳大鹏湾、海南岛、西沙和南沙群岛的珊瑚礁生态系统中。文章采用特异性位点扩增片段简化基因组测序技术(SLAF-seq)对来自深圳(SZ)、三亚(SY)和西沙(XS)的塔形马蹄螺群体的遗传多样性和结构进行分析。通过测序共获得115.74Mb读长数据, 平均测序深度为337.87倍, 测序质量值(Q₃₀)平均为94.07%。研究获得118679个多态性SLAF标签, 获得846502个高度一致的群体单核苷酸多态性位点(SNPs), 其中有155个显著差异SNPs。3个群体的平均观察杂合度(H_o)和期望杂合度(H_e)值分别为0.1441~0.1611和0.2537~0.2695。平均多态性信息含量(PIC)为0.2048~0.2176。通过系统发育树分析、主成分分析和聚类分析, 将45个个体大致分为3个类群, 每个群体的所有个体都可以聚类成一个类群。SZ和SY群体的遗传结构相似, 遗传距离最低(0.2510), 遗传分化系数F_st值最低(0.0818)。但XS与其他两个群体间的遗传分化明显, 尤其是XS和SZ群体(F_st=0.1868)。3个群体的遗传分化可能与海流和地理位置有关。  相似文献   

虾夷扇贝TET基因在配子发生和早期发育中的表达模式     

李仰平  张玲玲  李若佼  刘甜  郭振义  李婉茹  包振民 《中国海洋大学学报(自然科学版)》2020,50(4):54-62

DNA甲基化参与调节动物配子发生和胚胎发育过程,TET基因负责DNA主动去甲基化,在基因印迹去除和细胞全能性获得中起重要作用。为了解海洋贝类配子发生和胚胎发育过程中DNA去甲基化如何发生,本研究以虾夷扇贝为研究对象,鉴定了其TET基因,并分析了该基因在性腺和胚胎幼虫发育中的表达变化。结果表明,虾夷扇贝基因组中含有1个TET基因(PyTET),该基因长39127 bp,包含10个外显子,编码1592个氨基酸,其蛋白具有完整的2OGFeDO超家族的加氧酶结构域。在性腺发育过程中,PyTET基因表达峰值出现在休止期精巢和增殖期卵巢,原位杂交结果显示其在精原细胞、精母细胞中均有表达,在卵母细胞中的表达明显高于卵原细胞;在早期发育过程中,其峰值出现在囊胚期。以上结果提示虾夷扇贝配子发生和胚胎发育过程中均发生了DNA主动去甲基化,这将有助于系统了解表观调控在贝类发育中的作用。  相似文献   

Sensitive and rapid detection of two toxic microalgae Alexandrium by loop-mediated isothermal amplification     

ZHANG Fengying  SHI Yanhong  JIANG Keji  XU Zhaoli  MA Lingbo 《海洋学报(英文版)》2018,37(2):139-146

A loop-mediated isothermal amplification (LAMP) assay was designed and evaluated for rapid detection of the toxic microalgae Alexandrium catenella and A. minutum, which can produce paralytic shellfish poisoning (PSP). Two sets of four specific primers targeting these two species were derived from the sequence of internal transcribed spacer (ITS) of ribosomal DNA. The method worked well in less than an hour under isothermal conditions of 65℃. LAMP specificity was validated in closely related algae as a comparison, suggesting the strict specificity of the LAMP primers. Two visual inspection approaches were feasible to interpret the positive or negative results. The detection limits of A. catenella and A. minutum samples using the LAMP assay were found to be 5.6 and 4.5 pg DNA, respectively. The sensitivity of this LAMP assay was 10 or 100-fold higher than Polymerase Chain Reaction (PCR) method in detecting the two microalgae. These characteristics of species specificity, sensitivity, and rapidity suggest that this method has the potentiality in the monitoring of red tide caused by A. catenella and A. minutum.  相似文献   

Biotic drivers of river and floodplain geomorphology – New molecular methods for assessing present‐day and past biota          下载免费PDF全文

Annegret Larsen  Nadir Alvarez  Christoph Sperisen  Stuart N. Lane 《地球表面变化过程与地形》2018,43(1):333-338

Geomorphology has increasingly considered the role of biotic factors as controls upon geomorphic processes across a wide range of spatial and temporal scales. Where timescales are long (centennial and longer), it has been possible to quantify relationships between geomorphic processes and vegetation using, for example, the pollen record. However, where the biotic agents are fauna, longer term reconstruction of the impacts of biological activity upon geomorphic processes is more challenging. Here, we review the prospect of using environmental DNA as a molecular proxy to decipher the presence and nature of faunal influences on geomorphic processes in both present and ancient deposits. When used appropriately, this method has the potential to improve our understanding of biotic drivers of geomorphic processes, notably fauna, over long timescales and so to reconstruct how such drivers might explain the landscape as we see it today. Copyright © 2017 John Wiley & Sons, Ltd.  相似文献   

ATS藻板与自然礁石上藻群生物多样性的比较     

王欢欢  谭斯尹  王慧  杜虹  侯涛  陈贤建  黎俊珺  黄莹 《热带海洋学报》2019,38(1):43-48

ATS(algal turf scrubber)系统是一种利用潮间带藻类高效去除富营养化水体中氮(N)、磷(P)元素的水质净化系统, 藻类是支持整个系统最重要的组成部分, 其群落结构与水质净化效果密切相关。该研究基于Illumina MiSeq平台的高通量测序技术对海水水族缸的ATS系统中藻板样品和自然礁石上的藻类进行多样性分析。18S rDNA研究结果表明, ATS系统中经筛选得到藻类优化序列21390条, 其中对丝藻属Antithamnion占主要地位, 占序列总数的22.79%, 其次19.07%序列归入斜纹藻属Psammodictyon; 宋井、展南亭、后宅3个地区的藻类经筛选分别得到88435、87129、106458条优化序列, 主要为分枝色指藻属Chroodactylon、宽果藻属Mastocarpus和日本马泽藻属Mazzaella。ATS系统和自然环境样品共有的优势藻为骨条藻属Skeletonema和仙菜属Ceramium。本实验在研究ATS系统与自然礁石上的藻类群落相似性的同时, 深入探究了其群落结构的差异性, 为进一步优化ATS系统的功能提供了理论依据。  相似文献   

南海沉积物细菌胞外蛋白酶在家族水平上的多样性   总被引：2，自引：0，他引：2  

杨金玉  冯阳阳  陈秀兰  解彬彬  张玉忠  石梅  张熙颖 《海洋学报(英文版)》2019,38(12):73-83

海洋产蛋白酶细菌及其分泌的胞外蛋白酶在降解有机氮以推动海洋氮循环进行方面发挥着重要作用，但目前对这二者多样性的认识非常有限。本研究自南海沉积物中筛选得到90株产蛋白酶细菌，并通过N-端氨基酸序列，分析了其胞外蛋白酶在家族水平上的多样性。16S rRNA基因序列分析的结果表明，筛选的产蛋白酶细菌均属于Gammaproteobacteria纲，且大多数属于Alteromonadales目和Vibrionales目的不同属。对其中14株菌株的14个胞外蛋白酶的N-端氨基酸序列分析表明，所有这些蛋白酶属于金属蛋白酶的M4家族或丝氨酸蛋白酶的S8家族。本研究提供了海洋沉积物产蛋白酶细菌在类群及其胞外蛋白酶在类型上的新细节，这将有助于全面了解微生物酶促降解海洋沉积物有机氮的过程和机理。  相似文献