The sequences of the ITS(internal transcribed spacer) and 5.8S rDNA of three cultivated strains of Porphyra haitanensis thalli(NB,PT and ST) were amplified,sequenced and analyzed.In addition,the phylogenic relationshi...The sequences of the ITS(internal transcribed spacer) and 5.8S rDNA of three cultivated strains of Porphyra haitanensis thalli(NB,PT and ST) were amplified,sequenced and analyzed.In addition,the phylogenic relationships of the sequences identified in this study with those of other Porphyra retrieved from GenBank were evaluated.The results are as follows:the sequences of the ITS and 5.8S rDNA were essentially identical among the three strains.The sequences of ITS1 were 331 bp to 334 bp,while those of the 5.8S rDNA were 158 bp and the sequences of ITS2 ranged from 673 bp to 681 bp.The sequences of the ITS had a high level of homology(up to 99.5%) with that of P.haitanensis(DQ662228) retrieved from GenBank,but were only approximately 50% homologous with those of other species of Porphyra.The results obtained when a phylogenetic tree was constructed coincided with the results of the homology analysis.These results suggest that the three cultivated strains of P.haitanensis evolved conservatively and that the ITS showed evolutionary consistency.However,the sequences of the ITS and 5.8S rDNA of different Porphyra species showed great variations.Therefore,the relationship of Porphyra interspecies phyletic evolution could be judged,which provides the proof for Porphyra identification study.However,proper classifications of the subspecies and the populations of Porphyra should be determined through the use of other molecular techniques to determine the genetic variability and rational phylogenetic relationships.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
Restriction fragment length polymorphism （RFLP） profiles of the amplified products of Internal Transcribed Spacer （ITS） region of rDNA using four restriction enzymes （Alul, Rsal, HinfI and HhaI） revealed distinc...Restriction fragment length polymorphism （RFLP） profiles of the amplified products of Internal Transcribed Spacer （ITS） region of rDNA using four restriction enzymes （Alul, Rsal, HinfI and HhaI） revealed distinctness of six Indian isolates of Steinernema one each from Maharashtra （IARI-EPN-mh）, Himachal Pradesh （IARI-EPN-hp）, Dehradun （IARI-EPN-dhdl）, Jharkhand （IARI-EPN-jhl） and two from Madhya Pradesh （IARI-EPN-bpll ＆ IARI-EPN-gwll）, when compared with the only native species Steinernema thermophilum. One of the restriction enzyme, Rsal could differentiate all the six species/strains from one another. The three restriction enzymes yielded patterns which were of diagnostic value but Rsal appeared to be the best diagnostic marker for differentiating these isolates. A tree constructed based upon the band sharing amongst the isolates, produced trichotomy which placed strains from Madhya Pradesh and Jharkhand in one group showing 94% homology, one strain from Bhopal （M.P） formed separate clade along with S. thermophilum with 72% similarity. These isolates, from Maharashtra, Himachal Pradesh and Dehradun, showed only 51% similarity with the S. thermophilum by forming separate clade.展开更多
Prostomates and haptorians are two basal groups of ciliates with limited morphological characteristics available for tax- onomy. Morphologically, the structures used to identify prostomates and haptorians are similar ...Prostomates and haptorians are two basal groups of ciliates with limited morphological characteristics available for tax- onomy. Morphologically, the structures used to identify prostomates and haptorians are similar or even identical, which generate heavy taxonomic and phylogenetic confusion. In present work, phylogenetic positions lineage of two rare genera, Plagiopogon and Askenasia, were investigated. Three genes including small subunit ribosomal RNA gene （hereafter SSU rDNA）, internal transcribed spacer region （ITS region）, and large subunit ribosomal RNA gene （LSU rDNA） were analyzed, 10 new sequences five species each. Our findings included 1） class Prostomatea and order Haptorida are multiphyletic; 2） it may not be appropriate to place order Cyclotriehiida in subclass Haptoria, and the systematic lineage of order Cyclotrichiida needs to be verified further; 3） genus Plagio- pogon branches consistently within a clade covering most prostomes and is basal of clade Colepidae, implying its close lineage to Prostomatea; and 4） Askenasia is phylogenetically distant from the subclass Haptoria but close to classes Prostomatea, Plagiopylea and Oligohymenophorea. We supposed that the toxicyst of Askenasia may be close to taxa of prostomes instead of haptorians, and the dorsal brush is a more typical morphological characteristics of haptorians than toxicysts.展开更多
Nannochloropsis is a genus of marine eukaryotic unicellular algae,which belongs to class Eustigmatophyceae.The spe-cies of Nannochloropsis which are fine rotifer feed and rich in eicosapentaenoic acid(EPA)are economic...Nannochloropsis is a genus of marine eukaryotic unicellular algae,which belongs to class Eustigmatophyceae.The spe-cies of Nannochloropsis which are fine rotifer feed and rich in eicosapentaenoic acid(EPA)are economically important.Species in this genus are usually 2-5μm in size and are morphologically similar,which makes their identification difficult.We obtained a monoclone of Nannochloropsis with plating method in this study.DNA was extracted and the quality was determined by restriction enzyme digestion and spectrophotometer analysis.The DNA extracted was used to amplify the sequences of 18S ribosomal RNA gene,ITS region of ribosomal RNA transcription unit and rbcL gene.The phylogenetic analysis was carried out by constructing the neighbor-joining trees with Tamura-Nei distances.The phylogenetic analysis showed that the monoclone is N.oceanica.展开更多
Microbial decomposers,especially a fungal group called aquatic hyphomycetes,play a critical role in processing plant litter in freshwaters by increasing its palatability to invertebrate shredders.Traditionally,communi...Microbial decomposers,especially a fungal group called aquatic hyphomycetes,play a critical role in processing plant litter in freshwaters by increasing its palatability to invertebrate shredders.Traditionally,communities of aquatic hyphomycetes have been assessed through the identification of spores,which misses non-sporulating taxa.Among new technologies,454 pyrosequencing stands out as most promising for large-scale species identification.However,very few attempts have been made to validate its effectiveness for assessing the diversity of stream-dwelling fungal communities.We attempted to gain greater insight into the diversity of aquatic fungal communities in streams exposed to various degrees of eutrophication by using the 454 pyrosequencing technology.A total of 173,889 ITS2 pyrosequencing reads with hits for fungi were obtained from the 5 investigated streams.The majority of operational taxonomic units(OTUs)belonged to Ascomycota and the identification to the genus level was achieved for 169 OTUs.Of the total,135,257 reads(ca.78%)showed close affinities to aquatic hyphomycete species.Pyrosequencing showed declining fungal diversity in the most eutrophic streams,which was congruent with a reduced diversity found through spore identification.Dominance patterns revealed by connecting representative OTUs to ITS sequences from aquatic hyphomycetes were similar to those determined by traditional spore identification techniques.However,454 pyrosequencing provided a more comprehensive view of fungal diversity;it captured almost twice as many taxa as spore counts.This study vali-dates the effectiveness of 454 pyrosequencing for surveying the diversity of stream-dwelling fungal decomposer communities.Its application may accelerate the use of these communities for monitoring the integrity of freshwaters.展开更多
基金Supported by the National Natural Science Foundation of China (No 40576074)the Key Laboratory of Experimental Marine Biology,Institute of Oceanology,Chinese Academy of Sciences (No KFN92007NO1)
文摘The sequences of the ITS(internal transcribed spacer) and 5.8S rDNA of three cultivated strains of Porphyra haitanensis thalli(NB,PT and ST) were amplified,sequenced and analyzed.In addition,the phylogenic relationships of the sequences identified in this study with those of other Porphyra retrieved from GenBank were evaluated.The results are as follows:the sequences of the ITS and 5.8S rDNA were essentially identical among the three strains.The sequences of ITS1 were 331 bp to 334 bp,while those of the 5.8S rDNA were 158 bp and the sequences of ITS2 ranged from 673 bp to 681 bp.The sequences of the ITS had a high level of homology(up to 99.5%) with that of P.haitanensis(DQ662228) retrieved from GenBank,but were only approximately 50% homologous with those of other species of Porphyra.The results obtained when a phylogenetic tree was constructed coincided with the results of the homology analysis.These results suggest that the three cultivated strains of P.haitanensis evolved conservatively and that the ITS showed evolutionary consistency.However,the sequences of the ITS and 5.8S rDNA of different Porphyra species showed great variations.Therefore,the relationship of Porphyra interspecies phyletic evolution could be judged,which provides the proof for Porphyra identification study.However,proper classifications of the subspecies and the populations of Porphyra should be determined through the use of other molecular techniques to determine the genetic variability and rational phylogenetic relationships.
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Restriction fragment length polymorphism （RFLP） profiles of the amplified products of Internal Transcribed Spacer （ITS） region of rDNA using four restriction enzymes （Alul, Rsal, HinfI and HhaI） revealed distinctness of six Indian isolates of Steinernema one each from Maharashtra （IARI-EPN-mh）, Himachal Pradesh （IARI-EPN-hp）, Dehradun （IARI-EPN-dhdl）, Jharkhand （IARI-EPN-jhl） and two from Madhya Pradesh （IARI-EPN-bpll ＆ IARI-EPN-gwll）, when compared with the only native species Steinernema thermophilum. One of the restriction enzyme, Rsal could differentiate all the six species/strains from one another. The three restriction enzymes yielded patterns which were of diagnostic value but Rsal appeared to be the best diagnostic marker for differentiating these isolates. A tree constructed based upon the band sharing amongst the isolates, produced trichotomy which placed strains from Madhya Pradesh and Jharkhand in one group showing 94% homology, one strain from Bhopal （M.P） formed separate clade along with S. thermophilum with 72% similarity. These isolates, from Maharashtra, Himachal Pradesh and Dehradun, showed only 51% similarity with the S. thermophilum by forming separate clade.
基金supported by the National Natural Science Foundation of China(Nos.31222050,41376141,3112041,and 31471973)the international research projects from King Saud University(Nos.RGP-VPP-083,IRG14-22)
文摘Prostomates and haptorians are two basal groups of ciliates with limited morphological characteristics available for tax- onomy. Morphologically, the structures used to identify prostomates and haptorians are similar or even identical, which generate heavy taxonomic and phylogenetic confusion. In present work, phylogenetic positions lineage of two rare genera, Plagiopogon and Askenasia, were investigated. Three genes including small subunit ribosomal RNA gene （hereafter SSU rDNA）, internal transcribed spacer region （ITS region）, and large subunit ribosomal RNA gene （LSU rDNA） were analyzed, 10 new sequences five species each. Our findings included 1） class Prostomatea and order Haptorida are multiphyletic; 2） it may not be appropriate to place order Cyclotriehiida in subclass Haptoria, and the systematic lineage of order Cyclotrichiida needs to be verified further; 3） genus Plagio- pogon branches consistently within a clade covering most prostomes and is basal of clade Colepidae, implying its close lineage to Prostomatea; and 4） Askenasia is phylogenetically distant from the subclass Haptoria but close to classes Prostomatea, Plagiopylea and Oligohymenophorea. We supposed that the toxicyst of Askenasia may be close to taxa of prostomes instead of haptorians, and the dorsal brush is a more typical morphological characteristics of haptorians than toxicysts.
基金the National High Technology Research and Development Program of China (2010AA10A403)the National Natural Science Foundation of China (No.40976076)+1 种基金the Major State Basic Research Development Program of China (973 Program) (2011CB200901)the Basic Research Program of Municipal Bureau of Science and Technology of Qingdao (09-1-3-22-jch)
文摘Nannochloropsis is a genus of marine eukaryotic unicellular algae,which belongs to class Eustigmatophyceae.The spe-cies of Nannochloropsis which are fine rotifer feed and rich in eicosapentaenoic acid(EPA)are economically important.Species in this genus are usually 2-5μm in size and are morphologically similar,which makes their identification difficult.We obtained a monoclone of Nannochloropsis with plating method in this study.DNA was extracted and the quality was determined by restriction enzyme digestion and spectrophotometer analysis.The DNA extracted was used to amplify the sequences of 18S ribosomal RNA gene,ITS region of ribosomal RNA transcription unit and rbcL gene.The phylogenetic analysis was carried out by constructing the neighbor-joining trees with Tamura-Nei distances.The phylogenetic analysis showed that the monoclone is N.oceanica.
基金Fund–Operational Competitiveness Programme(FEDER-POFC-COMPETE)(FCOMP-01-0124-FEDER-013954)the Portuguese Foundation for Science and Technology supported this study(PEst-OE/BIA/UI4050/2014 and PTDC/AACAMB/113746/2009)S.Duarte(SFRH/BPD/47574/2008).
文摘Microbial decomposers,especially a fungal group called aquatic hyphomycetes,play a critical role in processing plant litter in freshwaters by increasing its palatability to invertebrate shredders.Traditionally,communities of aquatic hyphomycetes have been assessed through the identification of spores,which misses non-sporulating taxa.Among new technologies,454 pyrosequencing stands out as most promising for large-scale species identification.However,very few attempts have been made to validate its effectiveness for assessing the diversity of stream-dwelling fungal communities.We attempted to gain greater insight into the diversity of aquatic fungal communities in streams exposed to various degrees of eutrophication by using the 454 pyrosequencing technology.A total of 173,889 ITS2 pyrosequencing reads with hits for fungi were obtained from the 5 investigated streams.The majority of operational taxonomic units(OTUs)belonged to Ascomycota and the identification to the genus level was achieved for 169 OTUs.Of the total,135,257 reads(ca.78%)showed close affinities to aquatic hyphomycete species.Pyrosequencing showed declining fungal diversity in the most eutrophic streams,which was congruent with a reduced diversity found through spore identification.Dominance patterns revealed by connecting representative OTUs to ITS sequences from aquatic hyphomycetes were similar to those determined by traditional spore identification techniques.However,454 pyrosequencing provided a more comprehensive view of fungal diversity;it captured almost twice as many taxa as spore counts.This study vali-dates the effectiveness of 454 pyrosequencing for surveying the diversity of stream-dwelling fungal decomposer communities.Its application may accelerate the use of these communities for monitoring the integrity of freshwaters.
