The Yellow Sea Cold Water Mass(YSCWM)is a distinct hydrographic phenomenon of the Yellow Sea,and the distribution pattern of meio-and macrobenthos diff ers inside and outside of the YSCWM.However,such a pattern has ne...The Yellow Sea Cold Water Mass(YSCWM)is a distinct hydrographic phenomenon of the Yellow Sea,and the distribution pattern of meio-and macrobenthos diff ers inside and outside of the YSCWM.However,such a pattern has never been observed in the microbenthic ciliate communities.Therefore,we hypothesized that benthic ciliates followed a similar distribution pattern as meio-and macrobenthos,but this pattern has not been uncovered by morphological methods.We evaluated the diversity and distribution of benthic ciliates at fi ve stations along hydrographic gradients across the YSCWM and adjacent shallow water by using morphology and DNA and complementary DNA(cDNA)high-throughput sequencing of the V4 region of 18S rRNA gene.Results showed that the diversity of benthic ciliates detected by DNA(303 OTUs),and the cDNA(611 OTUs)sequencing was much higher than that detected by the morphological method(79 species).Morphological method detected roughly diff erent ciliate communities inside and outside of the YSCWM,but without statistical signifi cance.No clear pattern was obtained by DNA sequencing.In contrast,cDNA sequencing revealed a distinct distribution pattern of benthic ciliate communities like meioand macrobenthos,which coincided well with the results of the environmental parameter analysis.More than half of the total sequences detected by DNA sequencing belonged to planktonic ciliates,most(if not all)of which were recovered from historic DNA originating through the sedimentation of pelagic forms because none of them were observed morphologically.The irrelevant historic DNA greatly infl uenced the recovery of rare species and thus limited the understanding of the benthic ciliate diversity and distribution.Our research indicates that the methods used have signifi cant eff ects on the investigation of benthic ciliate communities and highlights that cDNA sequencing has great advantages in estimating the diversity and distribution of benthic ciliates,as well as the potential for benthic environmental assessments.展开更多
To construct a directional cDNA library from Chinese giant salamander Andrias davidianus liver by SMART(switching mechanism at 5′ end of RNA transcript)technique, we purified the mRNA from Andrias davidianus liver an...To construct a directional cDNA library from Chinese giant salamander Andrias davidianus liver by SMART(switching mechanism at 5′ end of RNA transcript)technique, we purified the mRNA from Andrias davidianus liver and the first strand cDNA was synthesized through reverse transcription by using a modified oligo(dT)primer(contained sfi ⅠB site). We used the SMART oligonucleotide (contained sfi ⅠA site) as a template so that the first strand cDNA could be extended over the 5′ end of mRNA. The double strand cDNA was amplified by LD PCR (long distance PCR) with the above two primers and then digested by sfi Ⅰ (ⅠA and ⅠB) restriction enzyme. After cDNA fractionation through CHROMA SPIN column, the double strand cDNA was ligated into the sfi Ⅰ digested λtripIEx2 vector and then the recombinant DNA was packaged in vitro . The content of the unamplified Andrias davidianus liver cDNA library is 1 5×10 6 in which the percentage of recombinant clones is about 98 9%. The titer of the amplified cDNA library is 1 0×10 10 pfu/ml and the average exogenous inserts of the recombinants is 1 25 kb. These results show that the Andrias davidianus liver cDNA library has excellent quality.展开更多
基金Supported by the National Natural Science Foundation of China(Nos.41876171,41506167,41476144)。
文摘The Yellow Sea Cold Water Mass(YSCWM)is a distinct hydrographic phenomenon of the Yellow Sea,and the distribution pattern of meio-and macrobenthos diff ers inside and outside of the YSCWM.However,such a pattern has never been observed in the microbenthic ciliate communities.Therefore,we hypothesized that benthic ciliates followed a similar distribution pattern as meio-and macrobenthos,but this pattern has not been uncovered by morphological methods.We evaluated the diversity and distribution of benthic ciliates at fi ve stations along hydrographic gradients across the YSCWM and adjacent shallow water by using morphology and DNA and complementary DNA(cDNA)high-throughput sequencing of the V4 region of 18S rRNA gene.Results showed that the diversity of benthic ciliates detected by DNA(303 OTUs),and the cDNA(611 OTUs)sequencing was much higher than that detected by the morphological method(79 species).Morphological method detected roughly diff erent ciliate communities inside and outside of the YSCWM,but without statistical signifi cance.No clear pattern was obtained by DNA sequencing.In contrast,cDNA sequencing revealed a distinct distribution pattern of benthic ciliate communities like meioand macrobenthos,which coincided well with the results of the environmental parameter analysis.More than half of the total sequences detected by DNA sequencing belonged to planktonic ciliates,most(if not all)of which were recovered from historic DNA originating through the sedimentation of pelagic forms because none of them were observed morphologically.The irrelevant historic DNA greatly infl uenced the recovery of rare species and thus limited the understanding of the benthic ciliate diversity and distribution.Our research indicates that the methods used have signifi cant eff ects on the investigation of benthic ciliate communities and highlights that cDNA sequencing has great advantages in estimating the diversity and distribution of benthic ciliates,as well as the potential for benthic environmental assessments.
文摘To construct a directional cDNA library from Chinese giant salamander Andrias davidianus liver by SMART(switching mechanism at 5′ end of RNA transcript)technique, we purified the mRNA from Andrias davidianus liver and the first strand cDNA was synthesized through reverse transcription by using a modified oligo(dT)primer(contained sfi ⅠB site). We used the SMART oligonucleotide (contained sfi ⅠA site) as a template so that the first strand cDNA could be extended over the 5′ end of mRNA. The double strand cDNA was amplified by LD PCR (long distance PCR) with the above two primers and then digested by sfi Ⅰ (ⅠA and ⅠB) restriction enzyme. After cDNA fractionation through CHROMA SPIN column, the double strand cDNA was ligated into the sfi Ⅰ digested λtripIEx2 vector and then the recombinant DNA was packaged in vitro . The content of the unamplified Andrias davidianus liver cDNA library is 1 5×10 6 in which the percentage of recombinant clones is about 98 9%. The titer of the amplified cDNA library is 1 0×10 10 pfu/ml and the average exogenous inserts of the recombinants is 1 25 kb. These results show that the Andrias davidianus liver cDNA library has excellent quality.
