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Comparative analysis of expressed sequence tags from tissues in ripening stages of peach (Prunus persica L. Batsch)

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Abstract

Expressed sequence tag (EST) represents a resource for gene discovery, genome annotation and comparative genomics in plants. ESTs were derived by sequencing clones from five libraries created from two different fruit tissues (skin and mesocarp), at four ripening stages (from post-allegation to post-climacteric) in three different genotypes of peach (OroA, Bolero and Suncrest). A total of 10,847 EST sequences were produced (dataset A); in addition, 21,857 peach ESTs (dataset B) were obtained from public databases. Clustering and assembly of both datasets gave 17,858 unigenes. Analysis of the sequences allowed the assignment of a putative function to 70.8% of the ESTs. In order to define the relationship among fruit tissues transcriptome, a gene ontology analysis was performed. Differences among organs and among different maturation stages of the same organs were identified in organelle, signal transducer and antioxidant activity. A distance matrix of pairwise correlation coefficients analysis was applied between the libraries. Shoot appeared to outgroup and our analysis proved to be an efficient tool to parallel and complement gene expression studies (for example, based on microarray analysis). We conducted an analysis of the frequency of genes putatively involved in the metabolism of some volatiles, which pointed to a predominant presence of those transcripts in the skin. The metabolic pathways of esters and lactones were selected for further isolation and cloning of key genes. The EST database is available at the web site www.itb.cnr.it/estree.

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Acknowledgments

This work was financed by MIUR project 2004079422 and by FIRB project RBNE01SFXY. We are greatly thankful to Prof. Daniele Bassi (University of Milan) for his collaboration in maintaining the plants. We wish to thank Prof. Francesco Salamini, Dr. John Williams and Dr. Fabio Nocito for critical reading of the manuscript.

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Authors and Affiliations

  1. Fondazione Parco Tecnologico Padano, via Einstein Loc. C.na Codazza, 26900, Lodi, Italy

    A. Vecchietti, B. Lazzari, R. Malinverni, A. Caprera & C. Pozzi

  2. Dipartimento di Produzione Vegetale, Università degli Studi di Milano, via Celoria 2, 20133, Milan, Italy

    C. Ortugno, F. Bianchi & I. Mignani

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  1. A. Vecchietti
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  2. B. Lazzari
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  3. C. Ortugno
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  5. R. Malinverni
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  6. A. Caprera
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  7. I. Mignani
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Correspondence to A. Vecchietti.

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Communicated by: R. Velasco

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ESM Figure A

(JPG 472 KB)

ESM Table A

Resistance to penetration (Newton), Brix degree (°Bx), and fruit weight of the four ripening stages (s1, s2, s3 and s4). (DOC 295 KB)

ESM Table B

Transcripts distribution in Gene Ontology-based functional categories (DOC 535 KB)

ESM Table C

Putative function of the most abundant transcripts in libraries. (DOC 685 KB)

ESM Table D

EST frequency analysis results and classification in clusters and classes (see Text for further details). Numbers in columns 2–5 refer to ESTs representing every given annotated contig, reported in column 1. s3, s4, skin and shoot refer, respectively, to s3 libraries pool, s4 libraries pool, skin library and shoot library, see “Materials and methods” section EST frequency analysis (EFA) paragraph. (DOC 492 KB)

ESM Table E

Statistics on occurrence and distribution on SSR motif (DOC 690 KB)

ESM Table F

Library distribution of putative genes in ESTreeDB coding for aroma key enzymes (DOC 505 KB)

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Vecchietti, A., Lazzari, B., Ortugno, C. et al. Comparative analysis of expressed sequence tags from tissues in ripening stages of peach (Prunus persica L. Batsch). Tree Genetics & Genomes 5, 377–391 (2009). https://doi.org/10.1007/s11295-008-0193-6

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