本研究旨在阐明鸡蛔虫分离株线粒体细胞色素c氧化酶第Ⅰ亚基(cox1)基因部分序列(pcox1)的遗传变异情况,并用pcox1序列构建其与其他蛔虫的进化关系。应用聚合酶链反应(PCR)扩增鸡蛔虫虫株的pcox1,将测定获得序列应用Clustal X 1.81程序...本研究旨在阐明鸡蛔虫分离株线粒体细胞色素c氧化酶第Ⅰ亚基(cox1)基因部分序列(pcox1)的遗传变异情况,并用pcox1序列构建其与其他蛔虫的进化关系。应用聚合酶链反应(PCR)扩增鸡蛔虫虫株的pcox1,将测定获得序列应用Clustal X 1.81程序进行比对,然后用Phylip 3.67程序MP法和Mega 4.0程序NJ法绘制种系发育树,并用Puzzle 5.2程序构建最大似然树。所获得的pcox1序列长度一致,均为250bp,种内变异在0～2.5%之间。种系发育分析表明,8个鸡蛔虫分离株位于同一分枝。由于鸡蛔虫pcox1序列种内相对保守,种间差异较大(6.9%～15.3%),故可作为种间遗传变异研究的标记,研究结果为进一步研究鸡蛔虫的群体遗传结构奠定了基础。展开更多
Objective This study aims to investigate the infection of Clonorchis sinensis(C.sinensis)in highincidence areas of Hunan Province,China.The phylogenetic analysis of the C.sinensis species in the highly infected areas ...Objective This study aims to investigate the infection of Clonorchis sinensis(C.sinensis)in highincidence areas of Hunan Province,China.The phylogenetic analysis of the C.sinensis species in the highly infected areas was carried out.Method Infection of the definitive human host and intermediate fish host by C.sinensis was investigated,and the mitochondrial genes cox1 and Nad1 were used as genetic markers for phylogenetic analysis.Results In 2016–2020,the average population infection rate of Hunan was 1.38%,while in Tongdao County the rate was up to 26.90%,and the highest fish infection rate was detected in Qiyang County(99.44%in the dorsal fin of crucian carp).High genetic sequence similarity was observed in the samples from Qiyang and Lengshuitan which exhibited high homology with those from Guangdong and Gansu,whereas the parasitic species from Tongdao was highly homologous with those located in high-latitude areas.Moreover,no significant difference was found in the gene sequence of the parasitic species in definitive hosts dogs and cats.Conclusion The systematically study of C.sinensis infection in the high-incidence areas will contribute greatly to the prevention and effectively controlling the spread of Clonorchis sinensis in Hunan Province The endemic of C.sinensis infection in Hunan Province is the result of co-action of local and foreign parasite species.展开更多
DNA barcoding provides accurate identification of zooplankton species through all life stages. Single-gene-targeted metagenomic analysis based on DNA barcode databases can facilitate longterm monitoring of zooplankton...DNA barcoding provides accurate identification of zooplankton species through all life stages. Single-gene-targeted metagenomic analysis based on DNA barcode databases can facilitate longterm monitoring of zooplankton communities. With the help of the available zooplankton databases, the zooplankton community of the Changjiang(Yangtze) River estuary was studied using a single-gene-targeted metagenomic method to estimate the species richness of this community. A total of 856 mitochondrial cytochrome oxidase subunit 1(cox1) gene sequences were determined. The environmental barcodes were clustered into 70 molecular operational taxonomic units(MOTUs). Forty-two MOTUs matched barcoded marine organisms with more than 90% similarity and were assigned to either the species(similarity>96%) or genus level(similarity<96%). Sibling species could also be distinguished. Many species that were overlooked by morphological methods were identified by molecular methods, especially gelatinous zooplankton and merozooplankton that were likely sampled at different life history phases. Zooplankton community structures differed significantly among all of the samples. The MOTU spatial distributions were infl uenced by the ecological habits of the corresponding species. In conclusion, single-gene-targeted metagenomic analysis is a useful tool for zooplankton studies, with which specimens from all life history stages can be identified quickly and effectively with a comprehensive database.展开更多
Few studies have explored the differences between Sanger and HTS methods in the results of mitogenome sequencing. We used a single individual of insect to study the differences between the sequences given by Sanger an...Few studies have explored the differences between Sanger and HTS methods in the results of mitogenome sequencing. We used a single individual of insect to study the differences between the sequences given by Sanger and PCR-free HTS methods. Here we provided evidence for biased results of sequencing due to different methods in the mitochondrial genes of atp6, atp8, cox1, cox2, cox3, Cytb, nad2, nad3, nad4, nad5, rrn S, rrnL, trnH, trn I, and control region at various degrees. Especially, in cox1, the differently sequenced nucleotides account for 2.6% of the complete length. Furthermore, the highest value of the intraspecific genetic distance based on K2 P accounts for 2.5% using a barcode fragment size of cox1（651 bp, Sanger）, while the maximum distance of the corresponding cox1 fragment obtained by the two sequencing methods was 5.0%. We revealed that the methods of Sanger and HTS may give different sequencing results of mitochondrial genes, which may reflect the heteroplasmy of mitogenomes within an insect individual. Therefore, researchers should be very cautious in using the mixed data of a gene given by different methods of sequencing.展开更多
基金supported by the National Natural Science Foundation of China(31100482,31411140034)the Scientific Research Fund of Hunan Provincial Education Department(16B119)
文摘Objective This study aims to investigate the infection of Clonorchis sinensis(C.sinensis)in highincidence areas of Hunan Province,China.The phylogenetic analysis of the C.sinensis species in the highly infected areas was carried out.Method Infection of the definitive human host and intermediate fish host by C.sinensis was investigated,and the mitochondrial genes cox1 and Nad1 were used as genetic markers for phylogenetic analysis.Results In 2016–2020,the average population infection rate of Hunan was 1.38%,while in Tongdao County the rate was up to 26.90%,and the highest fish infection rate was detected in Qiyang County(99.44%in the dorsal fin of crucian carp).High genetic sequence similarity was observed in the samples from Qiyang and Lengshuitan which exhibited high homology with those from Guangdong and Gansu,whereas the parasitic species from Tongdao was highly homologous with those located in high-latitude areas.Moreover,no significant difference was found in the gene sequence of the parasitic species in definitive hosts dogs and cats.Conclusion The systematically study of C.sinensis infection in the high-incidence areas will contribute greatly to the prevention and effectively controlling the spread of Clonorchis sinensis in Hunan Province The endemic of C.sinensis infection in Hunan Province is the result of co-action of local and foreign parasite species.
基金Supported by the National Natural Science Foundation of China(No.41230963)the National Basic Research Program of China(973 Program)(No.2011CB403604)+2 种基金the"135"Fund of Institute of Oceanology,Chinese Academy of Sciences(No.2012I0060102)the Innovative Research Group Funding of the National Natural Science Foundation of China(No.41121064)the Strategic Priority Research Program of Chinese Academy of Sciences(No.XDA11020305)
文摘DNA barcoding provides accurate identification of zooplankton species through all life stages. Single-gene-targeted metagenomic analysis based on DNA barcode databases can facilitate longterm monitoring of zooplankton communities. With the help of the available zooplankton databases, the zooplankton community of the Changjiang(Yangtze) River estuary was studied using a single-gene-targeted metagenomic method to estimate the species richness of this community. A total of 856 mitochondrial cytochrome oxidase subunit 1(cox1) gene sequences were determined. The environmental barcodes were clustered into 70 molecular operational taxonomic units(MOTUs). Forty-two MOTUs matched barcoded marine organisms with more than 90% similarity and were assigned to either the species(similarity>96%) or genus level(similarity<96%). Sibling species could also be distinguished. Many species that were overlooked by morphological methods were identified by molecular methods, especially gelatinous zooplankton and merozooplankton that were likely sampled at different life history phases. Zooplankton community structures differed significantly among all of the samples. The MOTU spatial distributions were infl uenced by the ecological habits of the corresponding species. In conclusion, single-gene-targeted metagenomic analysis is a useful tool for zooplankton studies, with which specimens from all life history stages can be identified quickly and effectively with a comprehensive database.
基金supported by the National Natural Science Foundation of China(31222051)
文摘Few studies have explored the differences between Sanger and HTS methods in the results of mitogenome sequencing. We used a single individual of insect to study the differences between the sequences given by Sanger and PCR-free HTS methods. Here we provided evidence for biased results of sequencing due to different methods in the mitochondrial genes of atp6, atp8, cox1, cox2, cox3, Cytb, nad2, nad3, nad4, nad5, rrn S, rrnL, trnH, trn I, and control region at various degrees. Especially, in cox1, the differently sequenced nucleotides account for 2.6% of the complete length. Furthermore, the highest value of the intraspecific genetic distance based on K2 P accounts for 2.5% using a barcode fragment size of cox1（651 bp, Sanger）, while the maximum distance of the corresponding cox1 fragment obtained by the two sequencing methods was 5.0%. We revealed that the methods of Sanger and HTS may give different sequencing results of mitochondrial genes, which may reflect the heteroplasmy of mitogenomes within an insect individual. Therefore, researchers should be very cautious in using the mixed data of a gene given by different methods of sequencing.
