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://www.genomics.iasma.it.

Moser, C.; Segala, C.; Fontana, P.; Salakhutdinov, I.; Gatto, P.; Pindo, M.; Zyprian, E.; Toepfer, R.; Grando, M.S.; Velasco, R. (2005). Comparative analysis of expressed sequence tags from different organs of Vitis vinifera L.. FUNCTIONAL & INTEGRATIVE GENOMICS, 5 (4): 208-217. doi: 10.1007/s10142-005-0143-4 handle: http://hdl.handle.net/10449/17860

Comparative analysis of expressed sequence tags from different organs of Vitis vinifera L.

Moser, Claudio;Segala, Cinzia;Fontana, Paolo;Gatto, Pamela;Pindo, Massimo;Grando, Maria Stella;Velasco, Riccardo
2005-01-01

Abstract

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://www.genomics.iasma.it.
Vitis vinifera
ESTs
Organ specificity of gene expression
Microsatellites
Settore AGR/07 - GENETICA AGRARIA
2005
Moser, C.; Segala, C.; Fontana, P.; Salakhutdinov, I.; Gatto, P.; Pindo, M.; Zyprian, E.; Toepfer, R.; Grando, M.S.; Velasco, R. (2005). Comparative analysis of expressed sequence tags from different organs of Vitis vinifera L.. FUNCTIONAL & INTEGRATIVE GENOMICS, 5 (4): 208-217. doi: 10.1007/s10142-005-0143-4 handle: http://hdl.handle.net/10449/17860
File in questo prodotto:
File Dimensione Formato  
2005_Moser et al_Functional&Integrative Genomics.pdf

solo utenti autorizzati

Licenza: Tutti i diritti riservati (All rights reserved)
Dimensione 1.46 MB
Formato Adobe PDF
1.46 MB Adobe PDF   Visualizza/Apri   Richiedi una copia

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10449/17860
Citazioni
  • ???jsp.display-item.citation.pmc??? 15
  • Scopus 44
  • ???jsp.display-item.citation.isi??? ND
social impact