We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using t...We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using this measure transcriptomes from different species were evaluated by mapping them to gene families and integrating the mapping results with expression data. Statistical tests were applied to the transcriptome evaluation results to identify differentially expressed families. A Perl program named Pro-Diff was compiled to im- plement this method. To evaluate the method and provide an example of its use, two liver EST transcriptomes from two closely related fish that live in different temperature zones were compared. One EST library was from a recent sequencing project of Dissosticus maw- soni, a fish that lives in cold Antarctic sea waters, while the other was newly sequenced data （available at： http：//www.fishgenome.org/ polarbank/） from Notothenia angustata, a species that lives in temperate near-shore water of southern New Zealand. Results from the com- parison were consistent with results inferred from phenotype differences and also with our previously published Gene Ontology-based method. The Pro-Diffprogram and operation manual can be downloaded from： http：//www.fishgenome.org/download/Prodiff.rar.展开更多
A cDNA library was constructed from the liver of Lampetra japonica.10077 ESTs were obtained by random selecting clones for sequencing.The results demonstrated that 8515 ESTs were assembled into 648 consensus sequences...A cDNA library was constructed from the liver of Lampetra japonica.10077 ESTs were obtained by random selecting clones for sequencing.The results demonstrated that 8515 ESTs were assembled into 648 consensus sequences,represented 2210 unique transcripts,47.06%of which were predicted as full length cDNAs.In addition,1562 ESTs were singlets.Using the BLAST to align the assembled ESTs,we found that 93.9%(2053)transcripts shared similarity to sequences published in GenBank databases.The functional annotations to assembled ESTs showed that the genes,involved in immu-nology,blood coagulation and metabolism of jawed vertebrates,were highly expressed in the liver of L.japonica.Furthermore,8 potential novel genes were identified.Further comparing liver transcriptome of L.japonica with Fundulus heteroclitus,Mus musculus,Bos Taurus,and Homo sapiens revealed that the genes of Chitinase and Polysaccharides metabolism were more highly expressed in L.japonica than the others,which implied that they may play an important role in immunity of L.japonica.In addi-tion,using the TargetScan,we marked microRNA target within 3′UTR of L.japonica liver transcriptome.The data indicated that some microRNA targets were homology with the targets embeded in human cancer genes.The result seems to provide a useful clue to the treatment of human cancer.Therefore,the present work will be an important resource for investigating the functional genomics and pro-teomics of L.japonica as well as evolution of vertebrates.展开更多
基金supported by the grants from the Ministry of Science and Technology of China (No.2006AA02Z331 and 2004CB117404)the Key Project of Chinese Academy of Sciences (No.KSCX2-YW-N-020) to Liangbiao ChenNSF OPP 0636696 to C-H CC
文摘We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using this measure transcriptomes from different species were evaluated by mapping them to gene families and integrating the mapping results with expression data. Statistical tests were applied to the transcriptome evaluation results to identify differentially expressed families. A Perl program named Pro-Diff was compiled to im- plement this method. To evaluate the method and provide an example of its use, two liver EST transcriptomes from two closely related fish that live in different temperature zones were compared. One EST library was from a recent sequencing project of Dissosticus maw- soni, a fish that lives in cold Antarctic sea waters, while the other was newly sequenced data （available at： http：//www.fishgenome.org/ polarbank/） from Notothenia angustata, a species that lives in temperate near-shore water of southern New Zealand. Results from the com- parison were consistent with results inferred from phenotype differences and also with our previously published Gene Ontology-based method. The Pro-Diffprogram and operation manual can be downloaded from： http：//www.fishgenome.org/download/Prodiff.rar.
基金Supported by the National High-Tech R&D Program(863 Program)(Grant No.2007AA09Z428)the National Natural Science Foundation of China(Grant Nos.60305001 and 60575005)+1 种基金the Key Project of Science and Technology of the Educa-tional Ministry of China(Grant No.206032)the Science and Technology Pro-ject of Dalian,China(Grant No.2006E11SF068)
文摘A cDNA library was constructed from the liver of Lampetra japonica.10077 ESTs were obtained by random selecting clones for sequencing.The results demonstrated that 8515 ESTs were assembled into 648 consensus sequences,represented 2210 unique transcripts,47.06%of which were predicted as full length cDNAs.In addition,1562 ESTs were singlets.Using the BLAST to align the assembled ESTs,we found that 93.9%(2053)transcripts shared similarity to sequences published in GenBank databases.The functional annotations to assembled ESTs showed that the genes,involved in immu-nology,blood coagulation and metabolism of jawed vertebrates,were highly expressed in the liver of L.japonica.Furthermore,8 potential novel genes were identified.Further comparing liver transcriptome of L.japonica with Fundulus heteroclitus,Mus musculus,Bos Taurus,and Homo sapiens revealed that the genes of Chitinase and Polysaccharides metabolism were more highly expressed in L.japonica than the others,which implied that they may play an important role in immunity of L.japonica.In addi-tion,using the TargetScan,we marked microRNA target within 3′UTR of L.japonica liver transcriptome.The data indicated that some microRNA targets were homology with the targets embeded in human cancer genes.The result seems to provide a useful clue to the treatment of human cancer.Therefore,the present work will be an important resource for investigating the functional genomics and pro-teomics of L.japonica as well as evolution of vertebrates.
