PavyPauleParsonsEtAl2005

Référence

Pavy, N., Paule, C., Parsons, L., Crow, J.A., Morency, M.J., Cooke, J., Johnson, J.E., Noumen, E., Guillet-Claude, C., Butterfield, Y., Barber, S., Yang, G., Liu, J., Stott, J., Kirkpatrick, R., Siddiqui, A., Holt, R., Marra, M., Seguin, A., Retzel, E., Bousquet, J., MacKay, J. (2005) Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters. BMC Genomics, 6:144.

Résumé

Background: The sequencing and analysis of ESTs is for now the only practical approach for large-scale gene discovery and annotation in conifers because their very large genomes are unlikely to be sequenced in the near future. Our objective was to produce extensive collections of ESTs and cDNA clones to support manufacture of cDNA microarrays and gene discovery in white spruce (Picea glauca [Moench] Voss). Results: We produced 16 cDNA libraries from different tissues and a variety of treatments, and partially sequenced 50,000 cDNA clones. High quality 3' and 5' reads were assembled into 16,578 consensus sequences, 45% of which represented full length inserts. Consensus sequences derived from 5' and 3' reads of the same cDNA clone were linked to define 14,471 transcripts. A large proportion (84%) of the spruce sequences matched a pine sequence, but only 68% of the spruce transcripts had homologs in Arabidopsis or rice. Nearly all the sequences that matched the Populus trichocarpa genome (the only sequenced tree genome) also matched rice or Arabidopsis genomes. We used several sequence similarity search approaches for assignment of putative functions, including blast searches against general and specialized databases (transcription factors, cell wall related proteins), Gene Ontology term assignation and Hidden Markov Model searches against PFAM protein families and domains. In total, 70% of the spruce transcripts displayed matches to proteins of known or unknown function in the Uniref100 database (blastx e-value < 1e-10). We identified multigenic families that appeared larger in spruce than in the Arabidopsis or rice genomes. Detailed analysis of translationally controlled tumour proteins and S-adenosylmethionine synthetase families confirmed a twofold size difference. Sequences and annotations were organized in a dedicated database, SpruceDB. Several search tools were developed to mine the data either based on their occurrence in the cDNA libraries or on functional annotations. Conclusion: This report illustrates specific approaches for large-scale gene discovery and annotation in an organism that is very distantly related to any of the fully sequenced genomes. The ArboreaSet sequences and cDNA clones represent a valuable resource for investigations ranging from plant comparative genomics to applied conifer genetics.

Format EndNote

Vous pouvez importer cette référence dans EndNote.

Format BibTeX-CSV

Vous pouvez importer cette référence en format BibTeX-CSV.

Format BibTeX

Vous pouvez copier l'entrée BibTeX de cette référence ci-bas, ou l'importer directement dans un logiciel tel que JabRef .

@ARTICLE { PavyPauleParsonsEtAl2005,
    AUTHOR = { Pavy, N. and Paule, C. and Parsons, L. and Crow, J.A. and Morency, M.J. and Cooke, J. and Johnson, J.E. and Noumen, E. and Guillet-Claude, C. and Butterfield, Y. and Barber, S. and Yang, G. and Liu, J. and Stott, J. and Kirkpatrick, R. and Siddiqui, A. and Holt, R. and Marra, M. and Seguin, A. and Retzel, E. and Bousquet, J. and MacKay, J. },
    TITLE = { Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters },
    JOURNAL = { BMC Genomics },
    YEAR = { 2005 },
    VOLUME = { 6 },
    PAGES = { 144 },
    NOTE = { Times Cited: 3 Article English Cited References Count: 55 980yz },
    ABSTRACT = { Background: The sequencing and analysis of ESTs is for now the only practical approach for large-scale gene discovery and annotation in conifers because their very large genomes are unlikely to be sequenced in the near future. Our objective was to produce extensive collections of ESTs and cDNA clones to support manufacture of cDNA microarrays and gene discovery in white spruce (Picea glauca [Moench] Voss). Results: We produced 16 cDNA libraries from different tissues and a variety of treatments, and partially sequenced 50,000 cDNA clones. High quality 3' and 5' reads were assembled into 16,578 consensus sequences, 45% of which represented full length inserts. Consensus sequences derived from 5' and 3' reads of the same cDNA clone were linked to define 14,471 transcripts. A large proportion (84%) of the spruce sequences matched a pine sequence, but only 68% of the spruce transcripts had homologs in Arabidopsis or rice. Nearly all the sequences that matched the Populus trichocarpa genome (the only sequenced tree genome) also matched rice or Arabidopsis genomes. We used several sequence similarity search approaches for assignment of putative functions, including blast searches against general and specialized databases (transcription factors, cell wall related proteins), Gene Ontology term assignation and Hidden Markov Model searches against PFAM protein families and domains. In total, 70% of the spruce transcripts displayed matches to proteins of known or unknown function in the Uniref100 database (blastx e-value < 1e-10). We identified multigenic families that appeared larger in spruce than in the Arabidopsis or rice genomes. Detailed analysis of translationally controlled tumour proteins and S-adenosylmethionine synthetase families confirmed a twofold size difference. Sequences and annotations were organized in a dedicated database, SpruceDB. Several search tools were developed to mine the data either based on their occurrence in the cDNA libraries or on functional annotations. Conclusion: This report illustrates specific approaches for large-scale gene discovery and annotation in an organism that is very distantly related to any of the fully sequenced genomes. The ArboreaSet sequences and cDNA clones represent a valuable resource for investigations ranging from plant comparative genomics to applied conifer genetics. },
    KEYWORDS = { wood-forming tissues pinus-pinaster ait. gene-expression loblolly-pine functional annotation nucleotide diversity information resource arabidopsis-thaliana lignin content tumor protein },
    OWNER = { brugerolles },
    TIMESTAMP = { 2007.12.05 },
}

********************************************************** *************************** FRQNT ************************ **********************************************************

Un regroupement stratégique du

********************************************************** ***************** Facebook Twitter *********************** **********************************************************

Abonnez-vous à
l'Infolettre du CEF!

********************************************************** ***************** Pub - ABC CBA 2020 ****************** **********************************************************

31 mai au 4 juin 2020

********************************************************** ***************** Pub - Symphonies_Boreales ****************** **********************************************************

********************************************************** ***************** Boîte à trucs *************** **********************************************************

CEF-Référence
La référence vedette !

Jérémie Alluard (2016) Les statistiques au moments de la rédaction 

  • Ce document a pour but de guider les étudiants à intégrer de manière appropriée une analyse statistique dans leur rapport de recherche.

Voir les autres...