Document Detail


Comparative analysis of expressed sequence tags from different organs of Vitis vinifera L.
MedLine Citation:
PMID:  15856347     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Expressed sequence tags (ESTs) are providing a valuable approach to sampling organism-expressed genomes, especially when studying large genomes such as those of many plants. We report on the comparison of 8,647 ESTs generated from six different grape (Vitis vinifera L.) organs: berry, root, leaf, bud, shoot and inflorescence. Clustering and assembly of these ESTs resulted in 4,203 unique sequences and revealed that at this level of EST sampling, each organ shares a low percentage of transcripts with the others. To define organ relationships based on EST counts, we calculated a distance matrix of pairwise correlation coefficients between the libraries which indicated bud, inflorescence and shoot as a group distinct from the other organs considered in this study. A putative function was identified for about 85% of the unique sequences. By assigning them to specific functional classes, we were able to highlight strong differences between organs in the metabolism, protein biosynthesis and photosynthesis categories. This grape EST collection has also proven to be a valuable source for the development of 'functional' simple sequence repeats (SSRs) markers: a total of 405 SSRs have been identified. EST sequences and annotation results have been organised in the IASMA-grape database, freely available at the address http://genomics.iasma.it.
Authors:
C Moser; C Segala; P Fontana; I Salakhudtinov; P Gatto; M Pindo; E Zyprian; R Toepfer; M S Grando; R Velasco
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Publication Detail:
Type:  Comparative Study; Journal Article; Research Support, Non-U.S. Gov't     Date:  2005-04-22
Journal Detail:
Title:  Functional & integrative genomics     Volume:  5     ISSN:  1438-793X     ISO Abbreviation:  Funct. Integr. Genomics     Publication Date:  2005 Oct 
Date Detail:
Created Date:  2005-09-21     Completed Date:  2006-01-24     Revised Date:  2006-11-15    
Medline Journal Info:
Nlm Unique ID:  100939343     Medline TA:  Funct Integr Genomics     Country:  Germany    
Other Details:
Languages:  eng     Pagination:  208-17     Citation Subset:  IM    
Affiliation:
Istituto Agrario San Michele all'Adige, S. Michele a/Adige, 38010 Trento, Italy. claudio.moser@iasma.it
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MeSH Terms
Descriptor/Qualifier:
DNA, Complementary
Expressed Sequence Tags*
Microsatellite Repeats / genetics
Polymorphism, Genetic
Vitis / genetics*
Chemical
Reg. No./Substance:
0/DNA, Complementary

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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