为探讨抗球虫药物地克珠利和马杜拉霉素对柔嫩艾美球虫18 S rDNA的影响,分别对人工诱导的柔嫩艾美球虫地克珠利抗药株(ETAD)、马杜拉霉素抗药株(ETAM)和药物敏感株 (ETDS)孢子化卵囊的18 S rDNA基因进行了克隆测序,并通过生物信息软件...为探讨抗球虫药物地克珠利和马杜拉霉素对柔嫩艾美球虫18 S rDNA的影响,分别对人工诱导的柔嫩艾美球虫地克珠利抗药株(ETAD)、马杜拉霉素抗药株(ETAM)和药物敏感株 (ETDS)孢子化卵囊的18 S rDNA基因进行了克隆测序,并通过生物信息软件进行对比差异分析。结果显示,ETAM株有3个碱基发生突变(T170突变为C,T646突变为C,G694突变为C); ETAD株有1个碱基发生突变(T646突变为C)。经进一步分析比较,发现ETAM株18 S rRNA 的二级结构与ETDS株的差异很大,而ETAD株18 S rRNA的二级结构则与ETDS株的完全相同。这些碱基的突变有可能是导致E．tenella产生抗药性的原因之一。展开更多
Sequences from a region of the nuclear ribosomal 18S rDNA gene of approximately 1 912 base pairs （bp） were used to generate a molecular phylogeny for the Pentatomomorpha based on 53 species representing 21 putative ...Sequences from a region of the nuclear ribosomal 18S rDNA gene of approximately 1 912 base pairs （bp） were used to generate a molecular phylogeny for the Pentatomomorpha based on 53 species representing 21 putative families. Phylogenetic analyses using the most parsimony method （MP）, maximum likelihood method （ML）, and neighbor joining method （NJ） showed strong support that the Pentatomomorpha lineage is a monophyly and the superfamily Aradoidea is a sister group to the remainder of the Pentatomomorpha （Trichophora）. The Trichophora could be divided into two clades ： one clade consisted of the monophyletic superfamilies Pentatomoidea and Pyrrhocoroidea; the other was mainly the polyphyletic superfamilies Lygaeoidea, Coreoidea and Idiostoloidea. The superfamilies Lygaeoidea and Coreoidea were both polyphyletic. Within Lygaeoidea, Piesmatidae was sister to Berytidae. They formed a clade locating at the basal of the Trichophora and distantly related to the other two families Lygaeidae and Rhyparochromidae. This research suggested that 18S rDNA was a proper marker to reconstruct the phylogeny of Pentatomomorpha that was accordant to morphological studies and the research of Li et al （2005）. The Pyrrhocoroidea was further divided from the Coreoidea （s./at ）. It was suggested that the Piesmatidae might be assigned as a superfamily of Pentatomomorpha rather than a family in Lygaeoidea.展开更多
应用PCR技术对在鸭粪中发现的疑似环孢子虫的18 S rDNA部分基因和ITS-1+基因进行了扩增,将扩增出的片段纯化后连接至pMD-18T载体上,选取阳性克隆进行序列测定,并利用NCBI在线BLAST程序和MEGA 4软件对测序结果进行了同源性比较和系统发...应用PCR技术对在鸭粪中发现的疑似环孢子虫的18 S rDNA部分基因和ITS-1+基因进行了扩增,将扩增出的片段纯化后连接至pMD-18T载体上,选取阳性克隆进行序列测定,并利用NCBI在线BLAST程序和MEGA 4软件对测序结果进行了同源性比较和系统发育树构建。结果显示,测得的18 SrDNA序列与环孢子虫的相似性最高(98%),且在系统树中位于同一分支上;测得的ITS-1序列高度特异,在GenBank中未发现同源性序列,可以确定其为环孢子虫的一个新种,暂命名为鸭源环孢子虫。展开更多
Chlorophyta species are common in the southern and northern coastal areas of China. In recent years, frequent green tide incidents in Chinese coastal waters have raised concerns and attracted the attention of scientis...Chlorophyta species are common in the southern and northern coastal areas of China. In recent years, frequent green tide incidents in Chinese coastal waters have raised concerns and attracted the attention of scientists. In this paper, we sequenced the 18S rDNA genes, the internal transcribed spacer （ITS） regions and the rbcL genes in seven organisms and obtained 536-566 bp long ITS sequences, 1 377-I 407 bp long rbcL sequences and 1 718-1 761 bp long partial 18S rDNA sequences. The GC base pair content was highest in the ITS regions and lowest in the rbcL genes. The sequencing results showed that the three Ulvaprolifera （or U. pertusa） gene sequences from Qingdao and Nan＇ao Island were identical. The ITS, 18S rDNA and rbcL genes in U. prolifera and U. pertusa from different sea areas in China were unchanged by geographic distance. U.flexuosa had the least evolutionary distance from U. californica in both the ITS regions （0.009） and the 18S rDNA （0.002）. These data verified that Ulva and Enteromorpha are not separate genera.展开更多
The wild Porphyra yezoensis collected from the Qingdao coast was used to prepare protoplasts by enzyme digestion. The pure line was constructed by cultivating the protoplasts. The 18S rDNA of the P. yezoensis pure lin...The wild Porphyra yezoensis collected from the Qingdao coast was used to prepare protoplasts by enzyme digestion. The pure line was constructed by cultivating the protoplasts. The 18S rDNA of the P. yezoensis pure line was cloned and sequenced. Sequence analysis was executed for this sequence and other 22 sequences retrieved from GenBank. A phylogenetic tree was constructed using the neighbor joining method. The results revealed a high diversity of 18S rDNA sequences in genus Porphyra and the considerable variation of 18S rDNA sequences in different strains of the same species P. yezoensis and P. tenera. Significant difference of 18S rDNA sequence was observed between P. yezoensis from Qingdao, China, and the two strains of P. yezoensis from Japan, but the three strains of P. yezoensis formed a stable clade in the phylogenetic tree. These results indicate the possibility of interspecies and intraspecies discrimination of Porphyra using the 18S rDNA sequences.展开更多
The nuclear-encoded small subunit ribosomal RNA gene （18S rDNA） of 16 isolates of Chondrus from 8 countries were sequenced. A total of 1796 nucleotides were obtained and aligned with the phylogenetic analysis conduc...The nuclear-encoded small subunit ribosomal RNA gene （18S rDNA） of 16 isolates of Chondrus from 8 countries were sequenced. A total of 1796 nucleotides were obtained and aligned with the phylogenetic analysis conducted. The results suggest that the entity from Dalian, China, regarded as C. spl is C. pinnulatus. The C. sp2 previously depicted as C. yendoi or Mazzaellajaponica may belong to genus Chondrus. So, 4 Chondrus species, i.e.C. ocellatus, C. nipponicus, C. armatus, and C. pinnulatus are distributed in China. However, the entity from Connemara, Ireland, named C. crispus, is not a Chondrus species but that ofMastocarpus stellatus, although it is morphologically similar to C. crispus. Phylogenetic analysis based on complete 18S rDNA sequence data shows that genus Chondrus includes 3 main lineages： the Northern Pacific lineage, containing C. ocellatus, C. yendoi, and C, nipponicus; C, armatus, and C. pinnulatus form the sub-North Pacific lineage; and the Northern Atlantic Ocean lineage, comprising samples of C. crispus from Canada, Portugal, Ireland, Germany and France. The phylogenetic relationships indicate that genus Chondrus might have a North Pacific ancestral origin, radiated to North Atlantic area, and then formed the species C. crispus.展开更多
[Objective] The paper was to measure and analyze pathogen of 18S rDNA sequence of the pathogen of melon powdery mildew from lands overlaid with sands. [Method]The melon powdery mildew was isolated from infected plants...[Objective] The paper was to measure and analyze pathogen of 18S rDNA sequence of the pathogen of melon powdery mildew from lands overlaid with sands. [Method]The melon powdery mildew was isolated from infected plants of ＂Yujinxiang＂, a major melon variety cultivated in lands overlaid with sands in the middle arid area of Ningxia. Genome DNA was extracted from its conidia using Chelex-100 method. 18S rDNA sequence was amplified by PCR, which was analyzed by Blast after sequencing, and the phylogenetic tree was constructed. [Result] 18S rDNA sequence analysis showed that the pathogen of melon powdery mildew belonged to Podosphaera. [Conclusion] The study provided reference for biocontrol and disease-resistance breeding against melon powdery mildew.展开更多
目的基于核糖体18S r DNA基因对基氏蠊螨进行分子鉴定。方法采集和分离储藏物样本,进行螨类的形态学鉴定。提取单个螨的基因组DNA,经PCR扩增、克隆和测序获得COⅠ基因和18S r DNA基因,将所获序列进行Blast对比。检索Gen Bank数据库中蠊...目的基于核糖体18S r DNA基因对基氏蠊螨进行分子鉴定。方法采集和分离储藏物样本,进行螨类的形态学鉴定。提取单个螨的基因组DNA,经PCR扩增、克隆和测序获得COⅠ基因和18S r DNA基因,将所获序列进行Blast对比。检索Gen Bank数据库中蠊螨属18S r DNA基因序列,利用Clustal X 1.83软件进行多序列比对,基于MEGA X软件进行序列分析并以邻接法(Neighbor-Joining,NJ)构建系统发育树。结果采集的样本经形态和COⅠ基因双重鉴定为基氏蠊螨。同时,所选取的10个基氏蠊螨的18S r DNA基因序列完全一致,均表现出A/T碱基偏向性,与同属的Blattisocius tarsalis和Blattisocius everti分别有98.73%和98.94%的同源性。基于18S r DNA基因序列的系统进化树显示,基氏蠊螨与Blattisocius tarsalis和Blattisocius everti聚为一支。结论本研究建立了基氏蠊螨基于18S r DNA基因序列的分子鉴定方法,为基氏蠊螨的准确鉴定奠定基础。展开更多
Nucleotide sequences from 18S rDNA of 11 ostracodes, which represent four suborders and six superfamilies of podocopidan, were determined. The phylogenetic relationships were analyzed based on three kinds of methods (...Nucleotide sequences from 18S rDNA of 11 ostracodes, which represent four suborders and six superfamilies of podocopidan, were determined. The phylogenetic relationships were analyzed based on three kinds of methods (maximum-likelihood, maximum-parsimony, and neighbor-joining), and the three topologies gained were basically similar. The results have showed that (1) a monophyletic Podocopida was supported strongly; (2) the phylogenetic relationships of four suborders were (Darwinulocopina plus (Bairdiocopina plus (Cytherocopina plus Cypridocopina))), which indicated that a close relationship between Cytherocopina and Cypridocopina, and Darwinulocopina had separated early from the main podocopinan; (3) Cypridocopinan formed a monophyletic group, among which the phylogenetic relationship of three superfamilies was (Cypridoidea plus (Macrocypridoidea plus Pontocypridoidea)).展开更多
Pelagic copepods play an important role in the marine food web. However, a full understanding of the ecological status of this zooplankton group depends on the careful study of their natural diets. In previous PCR-bas...Pelagic copepods play an important role in the marine food web. However, a full understanding of the ecological status of this zooplankton group depends on the careful study of their natural diets. In previous PCR-based copepod diet studies, we found many apostome ciliates that live symbiotically under the exoskeleton of the copepods, and their sequences were often over-represented in the 18S rRNA gene （18S rDNA） libraries. As a first step to address this issue, we designed three apostome ciliate 18S rDNA blocking primers, and tested their blocking efficiency against apostome ciliate 18S rDNA under various PCR conditions. Using a semi-quantitative PCR method, we optimized the conditions to efficiently amplify the 18S rDNA of the prey while simultaneously excluding the symbiotic apostome ciliates. This technique will facilitate PCR-based diet studies of copepods and other zooplankton in their natural environments.展开更多
It has been reported that there was a linkage of 5S rRNA gene to 18S-5.8S-25S rRNA gene in a few of species in Ochrophyta.In regard to the usual two positions of linked 5S rDNA to the 3′end of 25S rDNA,two pairs of p...It has been reported that there was a linkage of 5S rRNA gene to 18S-5.8S-25S rRNA gene in a few of species in Ochrophyta.In regard to the usual two positions of linked 5S rDNA to the 3′end of 25S rDNA,two pairs of primers were designed for amplification to verify this linkage of two genes in a kelp cultivar of Saccharina japonica,one of species in Ochrophyta.This result supplemented the previous report that 5S rDNA was unlinked to 25S rDNA in this kelp.In order to simultaneously visualize this unlinkage of two genes,dual-color fluorescence in situ hybridization(FISH)technique was applied to the cytogenetics of S.japonica.Dual-color FISH images showed that two and four hybridization signals were present in the kelp gametophyte and sporophyte,respectively,metaphase nuclei hybridized simultaneously with the labeled probes of 18S rDNA and 5S rDNA.Both haploid and diploid karyotypes in decreasing length of chromosomes showed that 18S-5.8S-25S rDNA was localized at the interstitial region of Chromosome 23,whereas 5S rDNA resided at the sub-telomeric region of Chromosome 27.These karyotypes suggested that the kelp nuclear genome had only one locus of each rRNA gene,and their loci on different chromosomes indicated the physical unlinkage of 5S rDNA to 18S-5.8S-25S rDNA in this kelp.Therefore,dual-color FISH seems to be a powerful technique for the discrimination and pairing of chromosomes featured in both small size and nearly identical shape in S.japonica.展开更多
Phyllosphere algae are common in tropical rainforests,forming visible biofilms or spots on plant leaf surfaces.However,knowledge of phyllosphere algal diversity and the environmental factors that drive that diversity ...Phyllosphere algae are common in tropical rainforests,forming visible biofilms or spots on plant leaf surfaces.However,knowledge of phyllosphere algal diversity and the environmental factors that drive that diversity is limited.The aim of this study is to identify the environmental factors that drive phyllosphere algal community composition and diversity in rainforests.For this purpose,we used single molecule real-time sequencing of full-length 18S rDNA to characterize the composition of phyllosphere microalgal communities growing on four host tree species(Ficus tikoua,Caryota mitis,Arenga pinnata,and Musa acuminata) common to three types of forest over four months at the Xishuangbanna Tropical Botanical Garden,Yunnan Province,China.Environmental 18S rDNA sequences revealed that the green algae orders Watanabeales and Trentepohliales were dominant in almost all algal communities and that phyllosphere algal species richness and biomass were lower in planted forest than in primeval and reserve rainforest.In addition,algal community composition differed significantly between planted forest and primeval rainforest.We also found that algal communities were affected by soluble reactive phosphorous,total nitrogen,and ammonium contents.Our findings indicate that algal community structure is significantly related to forest type and host tree species.Furthermore,this study is the first to identify environmental factors that affect phyllosphere algal communities,significantly contributing to future taxonomic research,especially for the green algae orders Watanabeales and Trentepohliales.This research also serves as an important reference for molecular diversity analysis of algae in other specific habitats,such as epiphytic algae and soil algae.展开更多
Quantitative evaluation of the copepod feeding process is critical for understanding the functioning of marine food webs, as this provides a major link between primary producers and higher trophic levels. In this stud...Quantitative evaluation of the copepod feeding process is critical for understanding the functioning of marine food webs, as this provides a major link between primary producers and higher trophic levels. In this study, a molecular protocol based on quantitative polymerase chain reaction(qPCR) targeting 18S rDNA was developed and used to investigate the feeding and digestion rates of the copepod Acartia erythraea in a laboratory experiment using microalgae Thalassiosira weissflogii, Prorocentrum shikokuense, and Alexandrium catenella as prey. Although offered an equal encounter rate based on biovolume, prey uptake varied substantially among the three algal species, with the ingestion rate(IR) and digestion rate(DR) of A. erythraea differing significantly(P <0.001) based on both cell counting and qPCR detection. Acartia erythraea showed the highest IR(2.79×10~4 cells/(ind.·h)) and DR(2.43×10~4 cells/(ind.·h)) on T. weissflogii, and the lowest amounts of ingested P. shikokuense were detected. The highest assimilation rate(~90.64%, IR/DR) was observed in copepods fed with P. shikokuense. The qPCR method used here can help determine the digestion rate and assimilation rate of copepods by detecting cells remaining in the gut hence providing the possibility to examine trophic links involving key species in the marine ecosystem. Our results indicate that A. erythraea has diet-specific feeding performance in different processes, and a quantitative assessment of copepod feeding is needed to accurately determine its functional role in the energy and matter uptake from marine food webs.展开更多
文摘为探讨抗球虫药物地克珠利和马杜拉霉素对柔嫩艾美球虫18 S rDNA的影响,分别对人工诱导的柔嫩艾美球虫地克珠利抗药株(ETAD)、马杜拉霉素抗药株(ETAM)和药物敏感株 (ETDS)孢子化卵囊的18 S rDNA基因进行了克隆测序,并通过生物信息软件进行对比差异分析。结果显示,ETAM株有3个碱基发生突变(T170突变为C,T646突变为C,G694突变为C); ETAD株有1个碱基发生突变(T646突变为C)。经进一步分析比较,发现ETAM株18 S rRNA 的二级结构与ETDS株的差异很大,而ETAD株18 S rRNA的二级结构则与ETDS株的完全相同。这些碱基的突变有可能是导致E．tenella产生抗药性的原因之一。
文摘Sequences from a region of the nuclear ribosomal 18S rDNA gene of approximately 1 912 base pairs （bp） were used to generate a molecular phylogeny for the Pentatomomorpha based on 53 species representing 21 putative families. Phylogenetic analyses using the most parsimony method （MP）, maximum likelihood method （ML）, and neighbor joining method （NJ） showed strong support that the Pentatomomorpha lineage is a monophyly and the superfamily Aradoidea is a sister group to the remainder of the Pentatomomorpha （Trichophora）. The Trichophora could be divided into two clades ： one clade consisted of the monophyletic superfamilies Pentatomoidea and Pyrrhocoroidea; the other was mainly the polyphyletic superfamilies Lygaeoidea, Coreoidea and Idiostoloidea. The superfamilies Lygaeoidea and Coreoidea were both polyphyletic. Within Lygaeoidea, Piesmatidae was sister to Berytidae. They formed a clade locating at the basal of the Trichophora and distantly related to the other two families Lygaeidae and Rhyparochromidae. This research suggested that 18S rDNA was a proper marker to reconstruct the phylogeny of Pentatomomorpha that was accordant to morphological studies and the research of Li et al （2005）. The Pyrrhocoroidea was further divided from the Coreoidea （s./at ）. It was suggested that the Piesmatidae might be assigned as a superfamily of Pentatomomorpha rather than a family in Lygaeoidea.
文摘应用PCR技术对在鸭粪中发现的疑似环孢子虫的18 S rDNA部分基因和ITS-1+基因进行了扩增,将扩增出的片段纯化后连接至pMD-18T载体上,选取阳性克隆进行序列测定,并利用NCBI在线BLAST程序和MEGA 4软件对测序结果进行了同源性比较和系统发育树构建。结果显示,测得的18 SrDNA序列与环孢子虫的相似性最高(98%),且在系统树中位于同一分支上;测得的ITS-1序列高度特异,在GenBank中未发现同源性序列,可以确定其为环孢子虫的一个新种,暂命名为鸭源环孢子虫。
基金Supported by the National Natural Science Foundation of China (No.30570125)the Key Construction Laboratory of Marine Biotechnology of Jiangsu Province (No. 2010HS03)
文摘Chlorophyta species are common in the southern and northern coastal areas of China. In recent years, frequent green tide incidents in Chinese coastal waters have raised concerns and attracted the attention of scientists. In this paper, we sequenced the 18S rDNA genes, the internal transcribed spacer （ITS） regions and the rbcL genes in seven organisms and obtained 536-566 bp long ITS sequences, 1 377-I 407 bp long rbcL sequences and 1 718-1 761 bp long partial 18S rDNA sequences. The GC base pair content was highest in the ITS regions and lowest in the rbcL genes. The sequencing results showed that the three Ulvaprolifera （or U. pertusa） gene sequences from Qingdao and Nan＇ao Island were identical. The ITS, 18S rDNA and rbcL genes in U. prolifera and U. pertusa from different sea areas in China were unchanged by geographic distance. U.flexuosa had the least evolutionary distance from U. californica in both the ITS regions （0.009） and the 18S rDNA （0.002）. These data verified that Ulva and Enteromorpha are not separate genera.
文摘The wild Porphyra yezoensis collected from the Qingdao coast was used to prepare protoplasts by enzyme digestion. The pure line was constructed by cultivating the protoplasts. The 18S rDNA of the P. yezoensis pure line was cloned and sequenced. Sequence analysis was executed for this sequence and other 22 sequences retrieved from GenBank. A phylogenetic tree was constructed using the neighbor joining method. The results revealed a high diversity of 18S rDNA sequences in genus Porphyra and the considerable variation of 18S rDNA sequences in different strains of the same species P. yezoensis and P. tenera. Significant difference of 18S rDNA sequence was observed between P. yezoensis from Qingdao, China, and the two strains of P. yezoensis from Japan, but the three strains of P. yezoensis formed a stable clade in the phylogenetic tree. These results indicate the possibility of interspecies and intraspecies discrimination of Porphyra using the 18S rDNA sequences.
基金Shandong Agriculture Seedstocks Project, and Knowledge Innovation Program of Chinese Academy of Sciences (kscx2-yw-n-47-02) the Key Laboratory of Experimental Marine Biology, Institute of Oceanology, CAS.
文摘The nuclear-encoded small subunit ribosomal RNA gene （18S rDNA） of 16 isolates of Chondrus from 8 countries were sequenced. A total of 1796 nucleotides were obtained and aligned with the phylogenetic analysis conducted. The results suggest that the entity from Dalian, China, regarded as C. spl is C. pinnulatus. The C. sp2 previously depicted as C. yendoi or Mazzaellajaponica may belong to genus Chondrus. So, 4 Chondrus species, i.e.C. ocellatus, C. nipponicus, C. armatus, and C. pinnulatus are distributed in China. However, the entity from Connemara, Ireland, named C. crispus, is not a Chondrus species but that ofMastocarpus stellatus, although it is morphologically similar to C. crispus. Phylogenetic analysis based on complete 18S rDNA sequence data shows that genus Chondrus includes 3 main lineages： the Northern Pacific lineage, containing C. ocellatus, C. yendoi, and C, nipponicus; C, armatus, and C. pinnulatus form the sub-North Pacific lineage; and the Northern Atlantic Ocean lineage, comprising samples of C. crispus from Canada, Portugal, Ireland, Germany and France. The phylogenetic relationships indicate that genus Chondrus might have a North Pacific ancestral origin, radiated to North Atlantic area, and then formed the species C. crispus.
基金Supported by Natural Science Foundation of Ningxia Hui Autonomous Region(NZ0958)
文摘[Objective] The paper was to measure and analyze pathogen of 18S rDNA sequence of the pathogen of melon powdery mildew from lands overlaid with sands. [Method]The melon powdery mildew was isolated from infected plants of ＂Yujinxiang＂, a major melon variety cultivated in lands overlaid with sands in the middle arid area of Ningxia. Genome DNA was extracted from its conidia using Chelex-100 method. 18S rDNA sequence was amplified by PCR, which was analyzed by Blast after sequencing, and the phylogenetic tree was constructed. [Result] 18S rDNA sequence analysis showed that the pathogen of melon powdery mildew belonged to Podosphaera. [Conclusion] The study provided reference for biocontrol and disease-resistance breeding against melon powdery mildew.
文摘目的基于核糖体18S r DNA基因对基氏蠊螨进行分子鉴定。方法采集和分离储藏物样本,进行螨类的形态学鉴定。提取单个螨的基因组DNA,经PCR扩增、克隆和测序获得COⅠ基因和18S r DNA基因,将所获序列进行Blast对比。检索Gen Bank数据库中蠊螨属18S r DNA基因序列,利用Clustal X 1.83软件进行多序列比对,基于MEGA X软件进行序列分析并以邻接法(Neighbor-Joining,NJ)构建系统发育树。结果采集的样本经形态和COⅠ基因双重鉴定为基氏蠊螨。同时,所选取的10个基氏蠊螨的18S r DNA基因序列完全一致,均表现出A/T碱基偏向性,与同属的Blattisocius tarsalis和Blattisocius everti分别有98.73%和98.94%的同源性。基于18S r DNA基因序列的系统进化树显示,基氏蠊螨与Blattisocius tarsalis和Blattisocius everti聚为一支。结论本研究建立了基氏蠊螨基于18S r DNA基因序列的分子鉴定方法,为基氏蠊螨的准确鉴定奠定基础。
基金supported by the Major Project of the National Natural Science Foundation of China under contract No.30130040the Cultivation Fund of the Key Scientific and Technical hmovation Project,Ministry of Education of China under contract No.704023+2 种基金E-institute of Shanghai Municipal Education Commission under contract No.E03009the Program of Shanghai Subject Chief Scientist under contract No.05XD14005 to Chen Liqiaothe PhD Program Scholarship Fund of ECNU 2005.
文摘Nucleotide sequences from 18S rDNA of 11 ostracodes, which represent four suborders and six superfamilies of podocopidan, were determined. The phylogenetic relationships were analyzed based on three kinds of methods (maximum-likelihood, maximum-parsimony, and neighbor-joining), and the three topologies gained were basically similar. The results have showed that (1) a monophyletic Podocopida was supported strongly; (2) the phylogenetic relationships of four suborders were (Darwinulocopina plus (Bairdiocopina plus (Cytherocopina plus Cypridocopina))), which indicated that a close relationship between Cytherocopina and Cypridocopina, and Darwinulocopina had separated early from the main podocopinan; (3) Cypridocopinan formed a monophyletic group, among which the phylogenetic relationship of three superfamilies was (Cypridoidea plus (Macrocypridoidea plus Pontocypridoidea)).
基金Supported by the National Natural Science Foundation of China(No.41076085)
文摘Pelagic copepods play an important role in the marine food web. However, a full understanding of the ecological status of this zooplankton group depends on the careful study of their natural diets. In previous PCR-based copepod diet studies, we found many apostome ciliates that live symbiotically under the exoskeleton of the copepods, and their sequences were often over-represented in the 18S rRNA gene （18S rDNA） libraries. As a first step to address this issue, we designed three apostome ciliate 18S rDNA blocking primers, and tested their blocking efficiency against apostome ciliate 18S rDNA under various PCR conditions. Using a semi-quantitative PCR method, we optimized the conditions to efficiently amplify the 18S rDNA of the prey while simultaneously excluding the symbiotic apostome ciliates. This technique will facilitate PCR-based diet studies of copepods and other zooplankton in their natural environments.
基金Supported by the National Natural Science Foundation of China(Nos.41376136,31201992)the Double First-Class Discipline of Fisheries Science in China。
文摘It has been reported that there was a linkage of 5S rRNA gene to 18S-5.8S-25S rRNA gene in a few of species in Ochrophyta.In regard to the usual two positions of linked 5S rDNA to the 3′end of 25S rDNA,two pairs of primers were designed for amplification to verify this linkage of two genes in a kelp cultivar of Saccharina japonica,one of species in Ochrophyta.This result supplemented the previous report that 5S rDNA was unlinked to 25S rDNA in this kelp.In order to simultaneously visualize this unlinkage of two genes,dual-color fluorescence in situ hybridization(FISH)technique was applied to the cytogenetics of S.japonica.Dual-color FISH images showed that two and four hybridization signals were present in the kelp gametophyte and sporophyte,respectively,metaphase nuclei hybridized simultaneously with the labeled probes of 18S rDNA and 5S rDNA.Both haploid and diploid karyotypes in decreasing length of chromosomes showed that 18S-5.8S-25S rDNA was localized at the interstitial region of Chromosome 23,whereas 5S rDNA resided at the sub-telomeric region of Chromosome 27.These karyotypes suggested that the kelp nuclear genome had only one locus of each rRNA gene,and their loci on different chromosomes indicated the physical unlinkage of 5S rDNA to 18S-5.8S-25S rDNA in this kelp.Therefore,dual-color FISH seems to be a powerful technique for the discrimination and pairing of chromosomes featured in both small size and nearly identical shape in S.japonica.
基金supported by the National Natural Science Foundation of China (Grant no.31870189 and 32000168)。
文摘Phyllosphere algae are common in tropical rainforests,forming visible biofilms or spots on plant leaf surfaces.However,knowledge of phyllosphere algal diversity and the environmental factors that drive that diversity is limited.The aim of this study is to identify the environmental factors that drive phyllosphere algal community composition and diversity in rainforests.For this purpose,we used single molecule real-time sequencing of full-length 18S rDNA to characterize the composition of phyllosphere microalgal communities growing on four host tree species(Ficus tikoua,Caryota mitis,Arenga pinnata,and Musa acuminata) common to three types of forest over four months at the Xishuangbanna Tropical Botanical Garden,Yunnan Province,China.Environmental 18S rDNA sequences revealed that the green algae orders Watanabeales and Trentepohliales were dominant in almost all algal communities and that phyllosphere algal species richness and biomass were lower in planted forest than in primeval and reserve rainforest.In addition,algal community composition differed significantly between planted forest and primeval rainforest.We also found that algal communities were affected by soluble reactive phosphorous,total nitrogen,and ammonium contents.Our findings indicate that algal community structure is significantly related to forest type and host tree species.Furthermore,this study is the first to identify environmental factors that affect phyllosphere algal communities,significantly contributing to future taxonomic research,especially for the green algae orders Watanabeales and Trentepohliales.This research also serves as an important reference for molecular diversity analysis of algae in other specific habitats,such as epiphytic algae and soil algae.
基金The National Natural Science Foundation of China under contract Nos 41806188 and 42176118the Science and Technology Planning Project of Guangdong Province,China under contract No. 2020B1212060058the Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) under contract No.GML2019ZD0404。
文摘Quantitative evaluation of the copepod feeding process is critical for understanding the functioning of marine food webs, as this provides a major link between primary producers and higher trophic levels. In this study, a molecular protocol based on quantitative polymerase chain reaction(qPCR) targeting 18S rDNA was developed and used to investigate the feeding and digestion rates of the copepod Acartia erythraea in a laboratory experiment using microalgae Thalassiosira weissflogii, Prorocentrum shikokuense, and Alexandrium catenella as prey. Although offered an equal encounter rate based on biovolume, prey uptake varied substantially among the three algal species, with the ingestion rate(IR) and digestion rate(DR) of A. erythraea differing significantly(P <0.001) based on both cell counting and qPCR detection. Acartia erythraea showed the highest IR(2.79×10~4 cells/(ind.·h)) and DR(2.43×10~4 cells/(ind.·h)) on T. weissflogii, and the lowest amounts of ingested P. shikokuense were detected. The highest assimilation rate(~90.64%, IR/DR) was observed in copepods fed with P. shikokuense. The qPCR method used here can help determine the digestion rate and assimilation rate of copepods by detecting cells remaining in the gut hence providing the possibility to examine trophic links involving key species in the marine ecosystem. Our results indicate that A. erythraea has diet-specific feeding performance in different processes, and a quantitative assessment of copepod feeding is needed to accurately determine its functional role in the energy and matter uptake from marine food webs.
