Mitochondrial gene fragments of 16S rRNA gene of four species （Rhacophorus rhodopus, R. reinwardtii, Philautus albopunctatus and P. rhododiscus ） from 11 populations were sequenced in this study. Homologous sequence...Mitochondrial gene fragments of 16S rRNA gene of four species （Rhacophorus rhodopus, R. reinwardtii, Philautus albopunctatus and P. rhododiscus ） from 11 populations were sequenced in this study. Homologous sequences of R. bipunctatus, Theloderma asperum, T. corticale and Buergeria japonica were obtained by screening the GenBank database. After excluding all gaps and ambiguous positions, aligned sequences were 500 bp in length with 115 variable sites and 92 parsimony-informative sites. Using B .japonica as an outgroup, phylogenetic relationships were analyzed using Bayesian inference, maximum parsimony and maximum likelihood methods. Our results indicated that neither of R. rhodopus and P. albopunctatus were monophyletic at the species level. The population of R. rhodopus from Hainan Island was more close to R. bipunctatus than to populations of R. rhodopus from Yunnan Province. Furthermore, the populations of R. rhodopus from Yunnan Province can be divided into two main lineages. Theloderma corticale and P.rhododiscus were clustered together and T. asperum was nested in P.albopunctatus. We considered that P. albopunctatus Liu and Hu, 1962, was the synonymy of T. asperum Boulenger, 1886, and suggested removing P. rhododiscus from Philautus into the genus Theloderma.展开更多
[Objective] The aim was to provide molecular biological basis for the researches on the genetic resources,genetic relationship among species and phyletic evolution of S.barcoo.[Method] PCR amplification and sequencing...[Objective] The aim was to provide molecular biological basis for the researches on the genetic resources,genetic relationship among species and phyletic evolution of S.barcoo.[Method] PCR amplification and sequencing were used to study the 16S rRNA and COI gene fragments.[Result] As for 16S rRNA gene fragments,nucleotide sequences of 791 bp were obtained,and the A,T,G and C contents in this fragment were 31.6%,21.4%,20.4% and 26.7%respectively.As for the COI gene fragments,the size was 631 bp and the A,T,G And C contents were 27.7%,23.6%,29.8% and 18.9% respectively.Among these two gene fragments,the content of GC was lower than AT,and AT/GC of these two fragments was 1.13 and 1.05 respectively.[Conclusion] The genetic characteristics of gene fragments of 16S rRNA and COI of S.barcoo suggested that the variation in the same species was relatively low.The sequences of 16S rRNA gene in three samples the same,while the sequences of COI gene was also the same,indicating that these two gene of S.barcoo were conservative.展开更多
Partial sequences of the mitochondrial 16S rRNA gene were determined for two Sesarma species （S. haematocheir and S. pficata）, and the length of sequence of S. haematocheir and S. plicata was the same. Of the 533 nu...Partial sequences of the mitochondrial 16S rRNA gene were determined for two Sesarma species （S. haematocheir and S. pficata）, and the length of sequence of S. haematocheir and S. plicata was the same. Of the 533 nucleotides obtained, the A, T, G and C contents were similar, which were 198 bp （37.1%）, 206 bp （38.6%）, 84 bp （15.8%）, 45 bp （8.4%） and 200 bp （37.5%）, 205 bp （38.5%）, 81 bp （15.2%）, 47 bp （8.8%） respectively. There were 49 different sites between the two species, including 21 transition sites, 22 transversion sites and 6 deletion/insertion sites. Furthermore, 361 bp homologous fragment was analyzed to discuss the phylogenetic relationship of 20 Sesarma species. The results showed that AT content （78.6% - 82.9%） was higher than GC content and there were 91 vadable positions of 16S rRNA sequences among the 20 species. Among 3 Sesarma species in China, S. dehaani and S. haematocheir were closely related （d=0.0151）; and there were greater genetic distances between S. pficata and S. dehaani I S. haematocheir （d=0.0924/0.0923）. The average genetic distances of S. plicata , S. dehaani and S. haematocheir with the North American crabs of genus Sesarma were respectively 0.103 2 ± 0.008 9, 0.0783±0.0105 and 0.072 0± 0.011, which indicated that there were greater genetic differences between China and North American Sesarma crabs and they were monophyletic each other.展开更多
To clarify cuttlefish phylogeny, mitochondrial cytochrome c oxidase subunit I (COI) gene and partial 16S rRNA geneare sequenced for 13 cephalopod species. Phylogenetic trees are constructed, with the neighbor-joining ...To clarify cuttlefish phylogeny, mitochondrial cytochrome c oxidase subunit I (COI) gene and partial 16S rRNA geneare sequenced for 13 cephalopod species. Phylogenetic trees are constructed, with the neighbor-joining method.Coleoids are divided into two main lineages, Decabrachia and Octobrachia. The monophyly of the order Sepioidea,which includes the families Sepiidae, Sepiolidae and Idiosepiidae , is not supported. From the two families ofSepioidea examined, the Sepiolidae are polyphyletic and are excluded from the order. On the basis of 16S rRNA andamino acid of COI gene sequences data, the two genera (Sepiella and Sepia) from the Sepiidae can be distinguished, butdo not have a visible boundary using COI gene sequences. The reason is explained. This suggests that the 16S rDNAof cephalopods is a precious tool to analyze taxonomic relationships at the genus level, and COI gene is fitter at ahigher taxonomic level (i.e., family).展开更多
A 605 bp section of mitochondrial 16S rRNA gene from Paralichthys olivaceus, Pseudorhombus cinnamomeus, Psetta maxima and Kareius bicoloratus, which represent 3 families of Order Pleuronectiformes was amplified by PCR...A 605 bp section of mitochondrial 16S rRNA gene from Paralichthys olivaceus, Pseudorhombus cinnamomeus, Psetta maxima and Kareius bicoloratus, which represent 3 families of Order Pleuronectiformes was amplified by PCR and sequenced to show the molecular systematics of Pleuronectiformes for comparison with related gene sequences of other 6 flatfish downloaded from GenBank. Phylogenetic analysis based on ge- netic distance from related gene sequences of 10 flatfish showed that this method was ideal to explore the rela- tionship between species, genera and families. Phylogenetic trees set-up is based on neighbor-joining, maximum parsimony and maximum likelihood methods that accords to the general rule of Pleuronectiformes evolution. But they also resulted in some confusion. Unlike data from morphological characters, P. olivaceus clustered with K. bicoloratus, but P. cinnamomeus did not cluster with P. olivaceus, which is worth further studying.展开更多
This study aimed to reveal the microbial diversity in the fecal samples of bactrian camels using the 16 S r RNA sequencing analysis on the Illumina Mi Seq platform. Three fecal samples were collected from two geograph...This study aimed to reveal the microbial diversity in the fecal samples of bactrian camels using the 16 S r RNA sequencing analysis on the Illumina Mi Seq platform. Three fecal samples were collected from two geographical regions in China. Operational taxonomic unit（OTU） clustering was performed by identifying an OTU at 97% sequence identity. The alpha and beta diversities were applied to estimate the differences in microbial diversity among the three fecal samples. Totally, 4409, 3151 and 4075 OTUs in the fecal samples were identified in the Lop Nor wild camel（Camelus ferus）, the domestic camel（C. bactrianus） and Dunhuang wild camel（C. ferus）, respectively. The majority of bactreria were affiliated with phylum Firmicutes and Bacteroidetes in the three samples. The wild camels had higher gastrointestinal tract microbial diversity than the domestic one, while the microbial composition of the Lop Nor wild camel shared higher similarity with domestic camel at the genus and family levels than that of the Dunhuang wild camel did. Our results may provide a theoretical basis for assessing their health conditions and may thus be useful for protecting the critically endangered species of C. ferus.展开更多
基金Supported by the National Natural Science Foundation of China (30670243)
文摘Mitochondrial gene fragments of 16S rRNA gene of four species （Rhacophorus rhodopus, R. reinwardtii, Philautus albopunctatus and P. rhododiscus ） from 11 populations were sequenced in this study. Homologous sequences of R. bipunctatus, Theloderma asperum, T. corticale and Buergeria japonica were obtained by screening the GenBank database. After excluding all gaps and ambiguous positions, aligned sequences were 500 bp in length with 115 variable sites and 92 parsimony-informative sites. Using B .japonica as an outgroup, phylogenetic relationships were analyzed using Bayesian inference, maximum parsimony and maximum likelihood methods. Our results indicated that neither of R. rhodopus and P. albopunctatus were monophyletic at the species level. The population of R. rhodopus from Hainan Island was more close to R. bipunctatus than to populations of R. rhodopus from Yunnan Province. Furthermore, the populations of R. rhodopus from Yunnan Province can be divided into two main lineages. Theloderma corticale and P.rhododiscus were clustered together and T. asperum was nested in P.albopunctatus. We considered that P. albopunctatus Liu and Hu, 1962, was the synonymy of T. asperum Boulenger, 1886, and suggested removing P. rhododiscus from Philautus into the genus Theloderma.
基金Supported by Agricultural Seed Project of Shandong Province~~
文摘[Objective] The aim was to provide molecular biological basis for the researches on the genetic resources,genetic relationship among species and phyletic evolution of S.barcoo.[Method] PCR amplification and sequencing were used to study the 16S rRNA and COI gene fragments.[Result] As for 16S rRNA gene fragments,nucleotide sequences of 791 bp were obtained,and the A,T,G and C contents in this fragment were 31.6%,21.4%,20.4% and 26.7%respectively.As for the COI gene fragments,the size was 631 bp and the A,T,G And C contents were 27.7%,23.6%,29.8% and 18.9% respectively.Among these two gene fragments,the content of GC was lower than AT,and AT/GC of these two fragments was 1.13 and 1.05 respectively.[Conclusion] The genetic characteristics of gene fragments of 16S rRNA and COI of S.barcoo suggested that the variation in the same species was relatively low.The sequences of 16S rRNA gene in three samples the same,while the sequences of COI gene was also the same,indicating that these two gene of S.barcoo were conservative.
基金supported by the special grant of Chongqing University of Arts and Sciences for the person with ability
文摘Partial sequences of the mitochondrial 16S rRNA gene were determined for two Sesarma species （S. haematocheir and S. pficata）, and the length of sequence of S. haematocheir and S. plicata was the same. Of the 533 nucleotides obtained, the A, T, G and C contents were similar, which were 198 bp （37.1%）, 206 bp （38.6%）, 84 bp （15.8%）, 45 bp （8.4%） and 200 bp （37.5%）, 205 bp （38.5%）, 81 bp （15.2%）, 47 bp （8.8%） respectively. There were 49 different sites between the two species, including 21 transition sites, 22 transversion sites and 6 deletion/insertion sites. Furthermore, 361 bp homologous fragment was analyzed to discuss the phylogenetic relationship of 20 Sesarma species. The results showed that AT content （78.6% - 82.9%） was higher than GC content and there were 91 vadable positions of 16S rRNA sequences among the 20 species. Among 3 Sesarma species in China, S. dehaani and S. haematocheir were closely related （d=0.0151）; and there were greater genetic distances between S. pficata and S. dehaani I S. haematocheir （d=0.0924/0.0923）. The average genetic distances of S. plicata , S. dehaani and S. haematocheir with the North American crabs of genus Sesarma were respectively 0.103 2 ± 0.008 9, 0.0783±0.0105 and 0.072 0± 0.011, which indicated that there were greater genetic differences between China and North American Sesarma crabs and they were monophyletic each other.
文摘To clarify cuttlefish phylogeny, mitochondrial cytochrome c oxidase subunit I (COI) gene and partial 16S rRNA geneare sequenced for 13 cephalopod species. Phylogenetic trees are constructed, with the neighbor-joining method.Coleoids are divided into two main lineages, Decabrachia and Octobrachia. The monophyly of the order Sepioidea,which includes the families Sepiidae, Sepiolidae and Idiosepiidae , is not supported. From the two families ofSepioidea examined, the Sepiolidae are polyphyletic and are excluded from the order. On the basis of 16S rRNA andamino acid of COI gene sequences data, the two genera (Sepiella and Sepia) from the Sepiidae can be distinguished, butdo not have a visible boundary using COI gene sequences. The reason is explained. This suggests that the 16S rDNAof cephalopods is a precious tool to analyze taxonomic relationships at the genus level, and COI gene is fitter at ahigher taxonomic level (i.e., family).
基金Supported by Natural Science Fund of China (No. 30271036) and Natural Science Fund of Shandong Province of China
文摘A 605 bp section of mitochondrial 16S rRNA gene from Paralichthys olivaceus, Pseudorhombus cinnamomeus, Psetta maxima and Kareius bicoloratus, which represent 3 families of Order Pleuronectiformes was amplified by PCR and sequenced to show the molecular systematics of Pleuronectiformes for comparison with related gene sequences of other 6 flatfish downloaded from GenBank. Phylogenetic analysis based on ge- netic distance from related gene sequences of 10 flatfish showed that this method was ideal to explore the rela- tionship between species, genera and families. Phylogenetic trees set-up is based on neighbor-joining, maximum parsimony and maximum likelihood methods that accords to the general rule of Pleuronectiformes evolution. But they also resulted in some confusion. Unlike data from morphological characters, P. olivaceus clustered with K. bicoloratus, but P. cinnamomeus did not cluster with P. olivaceus, which is worth further studying.
基金supported by the Xinjiang Lop Nur Wild Camels National Reserve Comprehensive Scientific Research Projects by The Environmental Protection Agency of China (20100228)
文摘This study aimed to reveal the microbial diversity in the fecal samples of bactrian camels using the 16 S r RNA sequencing analysis on the Illumina Mi Seq platform. Three fecal samples were collected from two geographical regions in China. Operational taxonomic unit（OTU） clustering was performed by identifying an OTU at 97% sequence identity. The alpha and beta diversities were applied to estimate the differences in microbial diversity among the three fecal samples. Totally, 4409, 3151 and 4075 OTUs in the fecal samples were identified in the Lop Nor wild camel（Camelus ferus）, the domestic camel（C. bactrianus） and Dunhuang wild camel（C. ferus）, respectively. The majority of bactreria were affiliated with phylum Firmicutes and Bacteroidetes in the three samples. The wild camels had higher gastrointestinal tract microbial diversity than the domestic one, while the microbial composition of the Lop Nor wild camel shared higher similarity with domestic camel at the genus and family levels than that of the Dunhuang wild camel did. Our results may provide a theoretical basis for assessing their health conditions and may thus be useful for protecting the critically endangered species of C. ferus.
