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
本文介绍了第三代DNA测序的技术原理及应用现状,并对相关的生物信息学技术进行了综述。第三代测序技术以单分子测序为主要特点,目前已广泛应用于食品科学及生命科学研究的各个领域,其代表有Heliscope Bio Science公司的SMS技术、Pacific...本文介绍了第三代DNA测序的技术原理及应用现状,并对相关的生物信息学技术进行了综述。第三代测序技术以单分子测序为主要特点,目前已广泛应用于食品科学及生命科学研究的各个领域,其代表有Heliscope Bio Science公司的SMS技术、Pacific Bio Sciences公司的SMRT技术等。本文同时归纳总结了基因组学相关的生物信息学发展状况及常用的数据库。展开更多
为建立用于二代测序技术的最适细菌DNA提取方法。分别用磁珠法、热裂解法、试剂盒法(有溶菌酶处理和无溶菌酶处理)、超声波法、超声+热裂解法共6种方法提取等量混合的细菌DNA,特异性扩增其16S r RNA的V3-V4高变区基因,经二代测序并分析...为建立用于二代测序技术的最适细菌DNA提取方法。分别用磁珠法、热裂解法、试剂盒法(有溶菌酶处理和无溶菌酶处理)、超声波法、超声+热裂解法共6种方法提取等量混合的细菌DNA,特异性扩增其16S r RNA的V3-V4高变区基因,经二代测序并分析结果中的细菌种类及其相对含量分布。6种方法的测序结果中,细菌种类鉴定结果无明显差异;而在磁珠法和试剂盒法(有溶菌酶处理)结果中,不同细菌的含量分布最为接近样品中的真实情况。在6种方法中,磁珠法和试剂盒法(有溶菌酶处理)适合于二代测序技术中混合细菌DNA的提取。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.
文摘本文介绍了第三代DNA测序的技术原理及应用现状,并对相关的生物信息学技术进行了综述。第三代测序技术以单分子测序为主要特点,目前已广泛应用于食品科学及生命科学研究的各个领域,其代表有Heliscope Bio Science公司的SMS技术、Pacific Bio Sciences公司的SMRT技术等。本文同时归纳总结了基因组学相关的生物信息学发展状况及常用的数据库。
文摘为建立用于二代测序技术的最适细菌DNA提取方法。分别用磁珠法、热裂解法、试剂盒法(有溶菌酶处理和无溶菌酶处理)、超声波法、超声+热裂解法共6种方法提取等量混合的细菌DNA,特异性扩增其16S r RNA的V3-V4高变区基因,经二代测序并分析结果中的细菌种类及其相对含量分布。6种方法的测序结果中,细菌种类鉴定结果无明显差异;而在磁珠法和试剂盒法(有溶菌酶处理)结果中,不同细菌的含量分布最为接近样品中的真实情况。在6种方法中,磁珠法和试剂盒法(有溶菌酶处理)适合于二代测序技术中混合细菌DNA的提取。
