The complete genome sequence of transmissible Gastroenteritis virus (TGEV) strain TS, previously isolated from Gansu province, was cloned and compared with published sequence data from other TGEV strains. Phylogenetic...The complete genome sequence of transmissible Gastroenteritis virus (TGEV) strain TS, previously isolated from Gansu province, was cloned and compared with published sequence data from other TGEV strains. Phylogenetic tree analysis based on the amino acid and nucleotide sequences of the S gene showed that the TGEV strains were divided into 3 clusters. TGEV TS showed a close evolutionary relationship to the American Miller cluster but had a 5' non-translated region (NTR) sequence closely related to the American Purdue cluster. Continued culture in different cell types indicated that TGEV TS virulence could be attenuated after fifty passages in Porcine kidney (PK-15) cells, and that the Porcine kidney cell line IB-RS-2 (IBRS) was not suitable for culture of the TGEV strain TS.展开更多
To investigate molecular epidemiology of DuCV in Cherry Valley ducks in China, the complete genomes of six DuCV strains, which were detected from Cherry Valley ducks in China between 2007 and 2008, were sequenced. Seq...To investigate molecular epidemiology of DuCV in Cherry Valley ducks in China, the complete genomes of six DuCV strains, which were detected from Cherry Valley ducks in China between 2007 and 2008, were sequenced. Sequence and phylogenetic analysis were carried out to compare these six strains with another 27 DuCV strains from Mulard duck, Muscovy duck, Pekin ducks and Mule duck. The analysis showed that the six DuCV strains exhibited typical genetic features of the family of DuCV, such as a stem-loop structure, three major open reading frames (Rep, Cap and ORF3), four intergenic repeats and the conserved motifs for rolling circle replication and for the dNTP binding domain located in the Rep protein. Phylogenetic analysis of the nucleotide sequences of the complete genome and Cap gene of these strains together with those that have been previously published demonstrated two distinct DuCV genotypes. The DuCV strains with complete genomes containing 1988 and 1989 nucleotides clustered in genotype A, whereas the strains with complete genomes containing 1991, 1992, 1995 and 1996 nucleotides lay in genotype B. The six DuCV strains from Cherry Valley ducks were divided into the two groups. The results of the study provides some insight into the variation of DuCVs in Cherry Valley ducks.展开更多
The fruit flies of the Bactrocera （Diptera： Tephritidae） are one of the major economically important insects in Asia. So far, there are at least seven species found in Chongqing, China. By using mitochondrial 16s r...The fruit flies of the Bactrocera （Diptera： Tephritidae） are one of the major economically important insects in Asia. So far, there are at least seven species found in Chongqing, China. By using mitochondrial 16s rDNA sequences, the phylogenetic relationships among seven Bactrocera species, Bactrocera cucurbitae （Coquillett）, B. tau （Walker）, B. diaphora （Hendel）, B. caudata （Fabricius）, B. scutellata （Hendel）, B. dorsalis （Hendel）, and B. minax （Enderlein） were investigated. Nucleotide diversity within species ranged from 0.3% to 10.9%. According to the result, B. cucurbitae （Coquillett）, B. tau （Walker）, B. diaphora （Hendel）, and B. caudata （Fabricius） have no enough sites to be distinguished among the other species in the 347bp nucleotide sequences of the 16s rDNA gene. At the same time, excluding B. scutellata （Hendel） and B. minax （Enderlein）, the other species recognition sites are not only too little but also discontinuous. Phylogenetic trees calculated from both maximum parsimony and neighbor-joining phylogenetic analysis methods showed that B. cucurbitae and B. tau were closely related, B. diaphora （Hendel） and B. caudata （Fabricius） also had a close relationship. B. minax （Enderlein） has a furthest relationship from the other 6 species. From the results, we can infer that the our data supports previous classification of Bactrocera based on morphological characters in other words, but the Bactrocera subgenera, Zeugodacus is polyphyletic.展开更多
Evolutionary studies have been of prime importance to life scientists since ancient times. The advancements in technology has made it possible to make available the massive amounts of genomic data. The abundance of ge...Evolutionary studies have been of prime importance to life scientists since ancient times. The advancements in technology has made it possible to make available the massive amounts of genomic data. The abundance of genomic data poses new challenges for biologists, computer scientists and mathematicians to develop approaches for discovery of new relationships in data and evolutionary networks. In this work, nucleotide sequences are converted into binary sequences to explore the network among different species. A new approach based on binary sequences has been proposed to reconstruct the accurate phylogenetic network. The algorithm developed is validated by comparing the results with those obtained by already existing method of network construction. A program is also coded in C language on the Intel Core i3 Dell inspiron machine to obtain the evolutionary network. The new approach developed also provides the fast solutions as there is no need of aligning the sequences.展开更多
基金National Basic Research Program(2004CCA00500)National High-tech Development Research Program of China (2006AA02Z440)
文摘The complete genome sequence of transmissible Gastroenteritis virus (TGEV) strain TS, previously isolated from Gansu province, was cloned and compared with published sequence data from other TGEV strains. Phylogenetic tree analysis based on the amino acid and nucleotide sequences of the S gene showed that the TGEV strains were divided into 3 clusters. TGEV TS showed a close evolutionary relationship to the American Miller cluster but had a 5' non-translated region (NTR) sequence closely related to the American Purdue cluster. Continued culture in different cell types indicated that TGEV TS virulence could be attenuated after fifty passages in Porcine kidney (PK-15) cells, and that the Porcine kidney cell line IB-RS-2 (IBRS) was not suitable for culture of the TGEV strain TS.
基金the grant of Shandong Province Higher Educational Science and Technology Program (J08LF07)Shandong Provincial Natural Sciences Fund (Q2006D04)
文摘To investigate molecular epidemiology of DuCV in Cherry Valley ducks in China, the complete genomes of six DuCV strains, which were detected from Cherry Valley ducks in China between 2007 and 2008, were sequenced. Sequence and phylogenetic analysis were carried out to compare these six strains with another 27 DuCV strains from Mulard duck, Muscovy duck, Pekin ducks and Mule duck. The analysis showed that the six DuCV strains exhibited typical genetic features of the family of DuCV, such as a stem-loop structure, three major open reading frames (Rep, Cap and ORF3), four intergenic repeats and the conserved motifs for rolling circle replication and for the dNTP binding domain located in the Rep protein. Phylogenetic analysis of the nucleotide sequences of the complete genome and Cap gene of these strains together with those that have been previously published demonstrated two distinct DuCV genotypes. The DuCV strains with complete genomes containing 1988 and 1989 nucleotides clustered in genotype A, whereas the strains with complete genomes containing 1991, 1992, 1995 and 1996 nucleotides lay in genotype B. The six DuCV strains from Cherry Valley ducks were divided into the two groups. The results of the study provides some insight into the variation of DuCVs in Cherry Valley ducks.
文摘The fruit flies of the Bactrocera （Diptera： Tephritidae） are one of the major economically important insects in Asia. So far, there are at least seven species found in Chongqing, China. By using mitochondrial 16s rDNA sequences, the phylogenetic relationships among seven Bactrocera species, Bactrocera cucurbitae （Coquillett）, B. tau （Walker）, B. diaphora （Hendel）, B. caudata （Fabricius）, B. scutellata （Hendel）, B. dorsalis （Hendel）, and B. minax （Enderlein） were investigated. Nucleotide diversity within species ranged from 0.3% to 10.9%. According to the result, B. cucurbitae （Coquillett）, B. tau （Walker）, B. diaphora （Hendel）, and B. caudata （Fabricius） have no enough sites to be distinguished among the other species in the 347bp nucleotide sequences of the 16s rDNA gene. At the same time, excluding B. scutellata （Hendel） and B. minax （Enderlein）, the other species recognition sites are not only too little but also discontinuous. Phylogenetic trees calculated from both maximum parsimony and neighbor-joining phylogenetic analysis methods showed that B. cucurbitae and B. tau were closely related, B. diaphora （Hendel） and B. caudata （Fabricius） also had a close relationship. B. minax （Enderlein） has a furthest relationship from the other 6 species. From the results, we can infer that the our data supports previous classification of Bactrocera based on morphological characters in other words, but the Bactrocera subgenera, Zeugodacus is polyphyletic.
文摘Evolutionary studies have been of prime importance to life scientists since ancient times. The advancements in technology has made it possible to make available the massive amounts of genomic data. The abundance of genomic data poses new challenges for biologists, computer scientists and mathematicians to develop approaches for discovery of new relationships in data and evolutionary networks. In this work, nucleotide sequences are converted into binary sequences to explore the network among different species. A new approach based on binary sequences has been proposed to reconstruct the accurate phylogenetic network. The algorithm developed is validated by comparing the results with those obtained by already existing method of network construction. A program is also coded in C language on the Intel Core i3 Dell inspiron machine to obtain the evolutionary network. The new approach developed also provides the fast solutions as there is no need of aligning the sequences.
