The complete mitochondrial cytochrome oxidase subunit Ⅱ （COⅡ） gene of Penaeinae shrimp Fenneropenaeus chinensis was cloned and sequenced. The gene is 688 bp in length and codes for 229 amino acids. It shows 83.2%,...The complete mitochondrial cytochrome oxidase subunit Ⅱ （COⅡ） gene of Penaeinae shrimp Fenneropenaeus chinensis was cloned and sequenced. The gene is 688 bp in length and codes for 229 amino acids. It shows 83.2%, 87.0% and 83.8% sequence similarity to Marsupenaeus Japonicus, Penaeus monodon and Farfantepenaeus notialis, respectively. The A＋T content of the whole gene and that at the third position of codons are 64.7% and 78.2%, respectively. The phylogenetic relationship between F. chinensis and three other species representing genera Farfanatepenaeus, Marsupenaeus and Penaeus was analyzed. Results showed that the genetic distances among the four taxa ranged from 0.144 0 to 0.200 5, exceeding those estimated with COⅠ and partial 16S rRNA gene sequences among Marsupenaeus, Litopenaeus and Melicertus, and being therefore larger than the value among subgenera. It has been suggested that the COⅡ gene has a faster evolutionary rate than that of the COⅠ gene and partial 16S rRNA gene and could be used for phylogenetic analysis at genus or species level. The results of the present study indicated that Farfantepenaeus, Fenneropenaeus, Marsupenaeus and Penaeus are at a higher phylogenetic level than subgenus, which supports the opinion of the elevation of phylogenetic status of the four subgenera to genus level.展开更多
De novo transcriptome assembly is an important approach in RNA-Seq data analysis and it can help us to reconstruct the transcriptome and investigate gene expression profiles without reference genome sequences.We carri...De novo transcriptome assembly is an important approach in RNA-Seq data analysis and it can help us to reconstruct the transcriptome and investigate gene expression profiles without reference genome sequences.We carried out transcriptome assemblies with two RNA-Seq datasets generated from human brain and cell line,respectively.We then determined an efficient way to yield an optimal overall assembly using three different strategies.We first assembled brain and cell line transcriptome using a single k-mer length.Next we tested a range of values of k-mer length and coverage cutoff in assembling.Lastly,we combined the assembled contigs from a range of k values to generate a final assembly.By comparing these assembly results,we found that using only one k-mer value for assembly is not enough to generate good assembly results,but combining the contigs from different k-mer values could yield longer contigs and greatly improve the overall assembly.展开更多
The HASM(high accuracy surface modeling) technique is based on the fundamental theory of surfaces,which has been proved to improve the interpolation accuracy in surface fitting.However,the integral iterative solution ...The HASM(high accuracy surface modeling) technique is based on the fundamental theory of surfaces,which has been proved to improve the interpolation accuracy in surface fitting.However,the integral iterative solution in previous studies resulted in high temporal complexity in computation and huge memory usage so that it became difficult to put the technique into application,especially for large-scale datasets.In the study,an innovative model(HASM-AD) is developed according to the sequential least squares on the basis of data adjustment theory.Sequential division is adopted in the technique,so that linear equations can be divided into groups to be processed in sequence with the temporal complexity reduced greatly in computation.The experiment indicates that the HASM-AD technique surpasses the traditional spatial interpolation methods in accuracy.Also,the cross-validation result proves the same conclusion for the spatial interpolation of soil PH property with the data sampled in Jiangxi province.Moreover,it is demonstrated in the study that the HASM-AD technique significantly reduces the computational complexity and lessens memory usage in computation.展开更多
文摘The complete mitochondrial cytochrome oxidase subunit Ⅱ （COⅡ） gene of Penaeinae shrimp Fenneropenaeus chinensis was cloned and sequenced. The gene is 688 bp in length and codes for 229 amino acids. It shows 83.2%, 87.0% and 83.8% sequence similarity to Marsupenaeus Japonicus, Penaeus monodon and Farfantepenaeus notialis, respectively. The A＋T content of the whole gene and that at the third position of codons are 64.7% and 78.2%, respectively. The phylogenetic relationship between F. chinensis and three other species representing genera Farfanatepenaeus, Marsupenaeus and Penaeus was analyzed. Results showed that the genetic distances among the four taxa ranged from 0.144 0 to 0.200 5, exceeding those estimated with COⅠ and partial 16S rRNA gene sequences among Marsupenaeus, Litopenaeus and Melicertus, and being therefore larger than the value among subgenera. It has been suggested that the COⅡ gene has a faster evolutionary rate than that of the COⅠ gene and partial 16S rRNA gene and could be used for phylogenetic analysis at genus or species level. The results of the present study indicated that Farfantepenaeus, Fenneropenaeus, Marsupenaeus and Penaeus are at a higher phylogenetic level than subgenus, which supports the opinion of the elevation of phylogenetic status of the four subgenera to genus level.
基金supported by the National Basic Research Program of China (Grant Nos. 2010CB945401, 2007CB108800)National Natural Science Foundation of China (Grant Nos. 30870575, 31071162,31000590)the Science and Technology Commission of Shanghai Municipality (Grant No. 11DZ2260300)
文摘De novo transcriptome assembly is an important approach in RNA-Seq data analysis and it can help us to reconstruct the transcriptome and investigate gene expression profiles without reference genome sequences.We carried out transcriptome assemblies with two RNA-Seq datasets generated from human brain and cell line,respectively.We then determined an efficient way to yield an optimal overall assembly using three different strategies.We first assembled brain and cell line transcriptome using a single k-mer length.Next we tested a range of values of k-mer length and coverage cutoff in assembling.Lastly,we combined the assembled contigs from a range of k values to generate a final assembly.By comparing these assembly results,we found that using only one k-mer value for assembly is not enough to generate good assembly results,but combining the contigs from different k-mer values could yield longer contigs and greatly improve the overall assembly.
基金Supported by the National Science Fund for Distinguished Young Scholars (No. 40825003)the Major Directivity Projects of Chinese Academy of Science (No. kzcx2-yw-429)the National High-tech R&D Program of China (No. 2006AA12Z219)
文摘The HASM(high accuracy surface modeling) technique is based on the fundamental theory of surfaces,which has been proved to improve the interpolation accuracy in surface fitting.However,the integral iterative solution in previous studies resulted in high temporal complexity in computation and huge memory usage so that it became difficult to put the technique into application,especially for large-scale datasets.In the study,an innovative model(HASM-AD) is developed according to the sequential least squares on the basis of data adjustment theory.Sequential division is adopted in the technique,so that linear equations can be divided into groups to be processed in sequence with the temporal complexity reduced greatly in computation.The experiment indicates that the HASM-AD technique surpasses the traditional spatial interpolation methods in accuracy.Also,the cross-validation result proves the same conclusion for the spatial interpolation of soil PH property with the data sampled in Jiangxi province.Moreover,it is demonstrated in the study that the HASM-AD technique significantly reduces the computational complexity and lessens memory usage in computation.
