Journal Title
Title of Journal: Funct Integr Genomics
|
Abbravation: Functional & Integrative Genomics
|
Publisher
Springer-Verlag
|
|
|
|
|
|
Authors: C Moser C Segala P Fontana I Salakhudtinov P Gatto M Pindo E Zyprian R Toepfer M S Grando R Velasco
Publish Date: 2005/04/22
Volume: 5, Issue: 4, Pages: 208-217
Abstract
Expressed sequence tags ESTs are providing a valuable approach to sampling organismexpressed genomes especially when studying large genomes such as those of many plants We report on the comparison of 8647 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 4203 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 IASMAgrape database freely available at the address http//genomicsiasmaitWe wish to thank Claudio Varotto for his critical evaluation of the manuscript and Anita Zamboni and Marco Stefanini for providing technical support This work was supported by the ‘Advanced Biology’ project funded by the Fondazione delle Casse di Risparmio di Trento e Rovereto Trento Italy PG and MP are recipients of fellowships granted by the Fondo Unico of the Province of Trento ‘Resveratrol’ and ‘BACco’ respectively IS was supported by the research circle of German Viticulture Forschungsring des Deutschen Weinbaues FDW of the German Society for Agriculture Bernhard Korn RZPD German Resource for Genome Research was helpful in the initial phases of cDNA cloning
Keywords:
.
|
Other Papers In This Journal:
- Control of flowering time and spike development in cereals: the earliness per se Eps-1 region in wheat, rice, and Brachypodium
- The R2R3-MYB, bHLH, WD40, and related transcription factors in flavonoid biosynthesis
- miRNA-based drought regulation in wheat
- Comparative genomics and functional analysis of the NiaP family uncover nicotinate transporters from bacteria, plants, and mammals
- Integrated protein network and microarray analysis to identify potential biomarkers after myocardial infarction
- Genome-wide analysis of intronless genes in rice and Arabidopsis
- Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes
- Identification of candidate genes JcARF19 and JcIAA9 associated with seed size traits in Jatropha
- Genome-wide expression profiling in Geobacter sulfurreducens : identification of Fur and RpoS transcription regulatory sites in a rel Gsu mutant
- Empirical Bayes estimation of gene-specific effects in micro-array research
- Phytoremediation and phytosensing of chemical contaminants, RDX and TNT: identification of the required target genes
- Os11Gsk gene from a wild rice, Oryza rufipogon improves yield in rice
- Genomic sequencing reveals gene content, genomic organization, and recombination relationships in barley
|