PavyLarocheBousquetEtAl2005

Référence

Pavy, N., Laroche, J., Bousquet, J., MacKay, J. (2005) Large-scale statistical analysis of secondary xylem ESTs in pine. Plant Molecular Biology, 57(2):203-224.

Résumé

A computational analysis of pine transcripts was conducted to contribute to the functional annotation of conifer sequences. A statistical analysis of expressed sequential tags(ESTs) belonging the 7732 contigs in the TIGR Pinus Gene Index (PGI1.0) identified 260 differentially represented gene sequences across six cDNA libraries from loblolly pine secondary xylem. Cluster analysis of this subset of contigs resulted in five groups representing genes preferentially represented in one of the xylem samples (compression wood, plannings, root xylem, latewood) and one group containing mostly genes simultaneously present in compression and side wood libraries. To complement the sequence annotation, 27 cDNA clones representing selected transcripts were completely sequenced. Several genes were identified that could represent putative markers for xylem from different organs, at different stages of development. Several sequences encoding regulatory proteins were over-represented in root xylem as opposed to the other xylem samples. Some of them belonged to known families of plant transcription factors, but two genes were previously uncharacterized in plants. One transcript was homologous to the gene encoding the Smad4 interacting factor, a key co-activator in TGF beta (transforming growth factor) signalling in animals. Thus, the digital analysis of pine ESTs highlighted a putative gene function of potentially broad interest but that has yet to be investigated in plants. More generally, this study showed that the application of numerical approaches to EST databases should be helpful in establishing priorities among genes to consider for targeted functional studies. Thus, we illustrated the potential of extracting information from conifer sequences already accessible through well-structured public databases.

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@ARTICLE { PavyLarocheBousquetEtAl2005,
    AUTHOR = { Pavy, N. and Laroche, J. and Bousquet, J. and MacKay, J. },
    TITLE = { Large-scale statistical analysis of secondary xylem ESTs in pine },
    JOURNAL = { Plant Molecular Biology },
    YEAR = { 2005 },
    VOLUME = { 57 },
    PAGES = { 203-224 },
    NUMBER = { 2 },
    NOTE = { Times Cited: 5 Article English Cited References Count: 50 915fy },
    ABSTRACT = { A computational analysis of pine transcripts was conducted to contribute to the functional annotation of conifer sequences. A statistical analysis of expressed sequential tags(ESTs) belonging the 7732 contigs in the TIGR Pinus Gene Index (PGI1.0) identified 260 differentially represented gene sequences across six cDNA libraries from loblolly pine secondary xylem. Cluster analysis of this subset of contigs resulted in five groups representing genes preferentially represented in one of the xylem samples (compression wood, plannings, root xylem, latewood) and one group containing mostly genes simultaneously present in compression and side wood libraries. To complement the sequence annotation, 27 cDNA clones representing selected transcripts were completely sequenced. Several genes were identified that could represent putative markers for xylem from different organs, at different stages of development. Several sequences encoding regulatory proteins were over-represented in root xylem as opposed to the other xylem samples. Some of them belonged to known families of plant transcription factors, but two genes were previously uncharacterized in plants. One transcript was homologous to the gene encoding the Smad4 interacting factor, a key co-activator in TGF beta (transforming growth factor) signalling in animals. Thus, the digital analysis of pine ESTs highlighted a putative gene function of potentially broad interest but that has yet to be investigated in plants. More generally, this study showed that the application of numerical approaches to EST databases should be helpful in establishing priorities among genes to consider for targeted functional studies. Thus, we illustrated the potential of extracting information from conifer sequences already accessible through well-structured public databases. },
    KEYWORDS = { computational analysis est gene discovery pine xylem expressed sequence tags wood-forming tissues gene-expression loblolly-pine differential expression arabidopsis-thaliana protein patterns plant cdna },
    OWNER = { brugerolles },
    TIMESTAMP = { 2007.12.05 },
}

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