Tree Genetics & Genomes

, Volume 5, Issue 3, pp 377–391 | Cite as

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

  • A. Vecchietti
  • B. Lazzari
  • C. Ortugno
  • F. Bianchi
  • R. Malinverni
  • A. Caprera
  • I. Mignani
  • C. Pozzi
Original Paper


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


Peach EST Tissue and stage specificity of gene expression SSR Aroma 

Supplementary material

11295_2008_193_Fig4_ESM.jpg (47 kb)
ESM Figure A

(JPG 472 KB)

11295_2008_193_MOESM1_ESM.doc (30 kb)
ESM Table AResistance to penetration (Newton), Brix degree (°Bx), and fruit weight of the four ripening stages (s1, s2, s3 and s4). (DOC 295 KB)
11295_2008_193_MOESM2_ESM.doc (54 kb)
ESM Table BTranscripts distribution in Gene Ontology-based functional categories (DOC 535 KB)
11295_2008_193_MOESM3_ESM.doc (68 kb)
ESM Table CPutative function of the most abundant transcripts in libraries. (DOC 685 KB)
11295_2008_193_MOESM4_ESM.doc (492 kb)
ESM Table DEST 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)
11295_2008_193_MOESM5_ESM.doc (69 kb)
ESM Table EStatistics on occurrence and distribution on SSR motif (DOC 690 KB)
11295_2008_193_MOESM6_ESM.doc (50 kb)
ESM Table FLibrary distribution of putative genes in ESTreeDB coding for aroma key enzymes (DOC 505 KB)


  1. Abbott A, Georgi L, Yvergniaux D, Inigo M, Sosinski B, Wang Y, Blenda A, Reighard G (2002) Peach: the model genome for Rosaceae. Acta Hortic 575:145–155Google Scholar
  2. Ablett E, Seaton G, Scott K, Shelton D, Graham MW, Baverstock P, Lee LS, Henry R (2000) Analysis of grape ESTs: global gene expression pattern in leaf and berry. Plant Sci 159:87–95PubMedCrossRefGoogle Scholar
  3. Aharoni A, Keizer LC, Bouwmeester HJ, Sun Z, Alvarez-Huerta M, Verhoeven HA, Blaas J, van Houwelingen AM, De Vos RC, van der Voet H, Jansen RC, Guis M, Mol J, Davis RW, Schena M, van Tunen AJ, O’Connell AP (2000) Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays. Plant Cell 12:647–662PubMedCrossRefGoogle Scholar
  4. Aubert C, Gunata Z, Ambid C, Baumes R (2003) Changes in physicochemical characteristics and volatile constituents of yellow- and white-fleshed nectarines during maturation and artificial ripening. J Agric Food Chem 51:3083–3091PubMedCrossRefGoogle Scholar
  5. Bausher M, Shatters R, Chaparro J, Dang P, Hunter W, Niedz R (2003) An expressed sequence tag (EST) set from Citrus sinensis L. Osbeck whole seedlings and the implications of further perennial source investigations. Plant Sci 165:415–422CrossRefGoogle Scholar
  6. Bhalerao R, Keskitalo J, Sterky F, Erlandsson R, Björkbacka H, Birve SJ, Karlsson J, Gardeström P, Gustafsson P, Lundeberg J, Jansson S (2003) Gene expression in autumn leaves. Plant Physiol 131:430–442PubMedCrossRefGoogle Scholar
  7. Bogs J, Ebadi A, McDavid D, Robinson SP (2006) Identification of the flavonoid hydroxylases from grapevine and their regulation during fruit development. Plant Physiol 140:279–291PubMedCrossRefGoogle Scholar
  8. Botton A, De Franceschi F, Ramina A, Tonutti P (2005) Evolution of the allergenic potential in peach and nectarine fruits during ripening. Acta Hort 682:469–474Google Scholar
  9. Brummell DA, Harpster MH (2001) Cell wall metabolism in fruit softening and quality and its manipulation in transgenic plants. Plant Mol Biol 47:311–340PubMedCrossRefGoogle Scholar
  10. Brummell DA, Dal Cin V, Crisosto CH, Labavitch JM (2004) Cell wall metabolism during maturation, ripening and senescence of peach fruit. J Exp Bot 55:2029–2039PubMedCrossRefGoogle Scholar
  11. Cakir B, Agasse A, Gaillard C, Saumonneau A, Delrot S, Atanassova R (2003) A grape ASR protein involved in sugar and abscisic acid signalling. Plant Cell 15:2165–2180PubMedCrossRefGoogle Scholar
  12. Chen F, Tholl D, D’Auria JC, Farooq A, Pichersky E, Gershenzon J (2003) Biosynthesis and emission of terpenoid volatiles from Arabidopsis flowers. Plant Cell 15:481–494PubMedCrossRefGoogle Scholar
  13. Chernys JT, Zeevaart JAD (2000) Characterization of the 9-cis-epoxycarotenoid dioxygenase gene family and the regulation of abscisic acid biosynthesis in avocado. Plant Physiol 124:343–353PubMedCrossRefGoogle Scholar
  14. Chou HH, Holmes MH (2001) DNA sequence quality trimming and vector removal. Bioinformatics 17:1093–1104PubMedCrossRefGoogle Scholar
  15. Dirlewanger E, Graziano E, Joobeur T, Garriga-Caldere F, Cosson P, Howad W, Arus P (2004) Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc Natl Acad Sci USA 101:9891–9896PubMedCrossRefGoogle Scholar
  16. Ewing B, Hiller L, Wendl M, Green P (1998) Base-calling of automated sequence traces using phred. I. Accuracy assessment. Genome Res 8:175–185PubMedGoogle Scholar
  17. FAOSTAT (2005)
  18. Fei Z, Tang X, Alba RM, White JA, Ronning CM, Martin GB, Tanksley SD, Giovannoni JJ (2004) Comprehensive EST analysis of tomato and comparative genomics of fruit ripening. Plant J 40:47–59PubMedCrossRefGoogle Scholar
  19. Fernandes J, Brendel V, Gai X, Lal S, Chandler VL, Elumalai RP, Galbraith DW, Pierson EA, Walbot V (2002) Comparison of RNA expression profiles based on maize expressed sequence tag frequency analysis and micro-array hybridization. Plant Physiol 128:896–910PubMedCrossRefGoogle Scholar
  20. Folta KM, Staton M, Stewart PJ, Jung S, Bies DH, Jesdurai C, Main D (2005) Expressed sequence tags (ESTs) and simple sequence repeats (SSR) markers from octoploid strawberry (Fragaria x ananassa). BMC Plant Biol 5:12PubMedCrossRefGoogle Scholar
  21. Forment J, Gadea J, Huerta L, Abizanda L, Agusti J, Alamar S, Alos E, Andres F, Arribas R, Beltran JP, Berbel A, Blazquez MA, Brumos J, Canas LA, Cercos M, Colmenero-Flores JM, Conesa A, Estables B, Gandia M, Garcia-Martinez JL, Gimeno J, Gisbert A, Gomez G, Gonzalez-Candelas L, Granell A, Guerri J, Lafuente MT, Madueno F, Marcos JF, Marques MC, Martinez F, Martinez-Godoy MA, Miralles S, Moreno P, Navarro L, Pallas V, Perez-Amador MA, Perez-Valle J, Pons C, Rodrigo I, Rodriguez PL, Royo C, Serrano R, Soler G, Tadeo F, Talon M, Terol J, Trenor M, Vaello L, Vicente O, Vidal CH, Zacarias L, Conejero V (2005) Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies. Plant Mol Biol 57:375–391PubMedCrossRefGoogle Scholar
  22. Gang DR, Wang J, Dudareva N, Nam KH, Simon JE, Lewinsohn E, Pichersky E (2001) An investigation of the storage and biosynthesis of phenylpropenes in sweet basil. Plant Physiol 125:539–555PubMedCrossRefGoogle Scholar
  23. Gao LF, Tang JF, Li HW, Jia JZ (2003) Analysis of microsatellites in major crops assessed by computational and experimental approaches. Mol Breed 12:245–261CrossRefGoogle Scholar
  24. Goes da Silva F, Iandolino A, Al-Kayal F, Bohlmann MC, Cushman MA, Lim H, Ergul A, Figueroa R, Kabuloglu EK, Osborne C, Rowe J, Tattersall E, Leslie A, Xu J, Baek JM, Cramer GR, Cushman JC, Cook DR (2005) Characterizing the grape transcriptome. Analysis of expressed sequence tags from multiple Vitis species and development of a compendium of gene expression during berry development. Plant Physiol 139:574–597CrossRefGoogle Scholar
  25. Goulaoa LF, Santosb J, de Sousab I, Oliveira CM (2007) Patterns of enzymatic activity of cell wall-modifying enzymes during growth and ripening of apples. Postharv Biol Tech 43:307–318CrossRefGoogle Scholar
  26. Grimplet J, Romieu C, Audergon J-M, Marty I, Albagnac G, Lambert P, Bouchet J-P, Terrier N (2005) Transcriptomic study of apricot fruit (Prunus armeniaca) ripening among 13,006 expressed sequence tags. Physiol Plant 125:281–292CrossRefGoogle Scholar
  27. Horn R, Lecouls AC, Callahan A, Dandekar A, Garay L, McCord P, Howad W, Chan H, Verde I, Main D, Jung S, Georgi L, Forrest S, Mook J, Zhebentyayeva T, Yu Y, Kim HR, Jesudurai C, Sosinski B, Arus P, Baird V, Parfitt D, Reighard G, Scorza R, Tomkins J, Wing R, Abbott AG (2005) Candidate gene database and transcript map for peach, a model species for fruit trees. Theor Appl Genet 110:1419–1428PubMedCrossRefGoogle Scholar
  28. Hsiao Y-Y, Tasi W-C, Kuoh C-S, Huang T-H, Wang H-C, Wu T-S, Leu Y-L, Chen W-H, Chen H-H (2006) Comparison of transcripts in Phalaenopsis bellina and Phalaenopsis equestris (Orchidaceae) flowers to deduce monoterpene biosynthesis pathway. BMC Plant Biol 6:14PubMedCrossRefGoogle Scholar
  29. Huan X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Research 9:868–877CrossRefGoogle Scholar
  30. Ibdah M, Azulay Y, Portnoy V, Wasserman B, Bar E, Meir A, Burger Y, Hirschberg J, Schaffer AA, Katzir N, Tadmor Y, Lewinsohn E (2006) Functional characterization of CmCCD1, a carotenoid cleavage dioxygenase from melon. Phytochemistry 67:1579–1589PubMedCrossRefGoogle Scholar
  31. Inaba A, Liu X, Yokotami N, Yamane M, Liu W-J, Nakano R, Kubo Y (2006) Differential feedback regulation of ethylene biosynthesis in pulp and peel tissues of banana fruit. J Exp Bot Adv 58(5):1047–1057. doi:10.1093/jxb/erl265 CrossRefGoogle Scholar
  32. Jansen RK, Kaittanis C, Lee SB, Saski C, Tomkins J, Alverson AJ, Daniell H (2006) Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol Biol 6:32PubMedCrossRefGoogle Scholar
  33. Jung S, Jesudurai C, Staton M, Du Z, Ficklin S, Cho I, Abbott A, Tomkins J, Main D (2004) GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomic and genetic research. BMC Bioinformatics 5:130PubMedCrossRefGoogle Scholar
  34. Jung S, Abbott A, Jesudurai C, Tomkins J, Main D (2005) Frequency, type, distribution and annotation of simple sequence repeats in Rosaceae ESTs. Funct Integr Genomics 5:136–143PubMedCrossRefGoogle Scholar
  35. Lazzari B, Caprera A, Vecchietti A, Stella A, Milanesi L, Pozzi C (2005) ESTree db: a tool for peach functional genomics. BMC Bioinformatics 6(Suppl 4):S16PubMedCrossRefGoogle Scholar
  36. Lazzari B, Caprera A, Vecchietti A, Merelli I, Barale F, Milanesi L, Stella A, Pozzi C (2008) Version VI of the ESTree db: an improved tool for peach transcriptome analysis. BMC Bioinformatics 9(Suppl 2):S9PubMedCrossRefGoogle Scholar
  37. Li D, Xu Y, Xu G, Gu L, Li D, Shu H (2006) Molecular cloning and expression of a gene encoding alcohol acyltransferase (MdAAT2) from apple (cv. Golden Delicious). Phytochemistry 67:658–667PubMedCrossRefGoogle Scholar
  38. Liebhard R, Kellerhals M, Pfammatter W, Jermini M, Gessler C (2003) Mapping quantitative physiological traits in apple (Malus x domestica Borkh.). Plant Mol Biol 52:511–526PubMedCrossRefGoogle Scholar
  39. Manriquez D, El-Sharkawy I, Flores FB, El-Yahyaoui F, Regad F, Bouzayen M, Latche A, Pech JC (2006) Two highly divergent alcohol dehydrogenases of melon exhibit fruit ripening-specific expression and distinct biochemical characteristics. Plant Mol Biol 61:675–685PubMedCrossRefGoogle Scholar
  40. Martsinkovskaya AI, Poghosyan ZP, Haralampidis K, Murphy DJ, Hatzopoulos P (1999) Temporal and spatial gene expression of cytochrome B5 during flower and fruit development in olives. Plant Mol Biol 40:79–90PubMedCrossRefGoogle Scholar
  41. Marty I, Bureau S, Sarkissian G, Gouble B, Audergon JM, Albagnac G (2005) Ethylene regulation of carotenoid accumulation and carotenogenic gene expression in colour-contrasted apricot varieties (Prunus armeniaca). J Exp Bot 56:1877–1886PubMedCrossRefGoogle Scholar
  42. Matarasso N, Schuster S, Avni A (2005) A novel plant cysteine protease has a dual function as a regulator of 1-aminocyclopropane-1-carboxylic acid synthase gene expression. Plant Cell 17:1205–1216PubMedCrossRefGoogle Scholar
  43. Mita S, Nagai Y, Asai T (2006) Isolation of cDNA clones corresponding to genes differentially expressed in pericarp of mume (Prunus mume) in response to ripening, ethylene, and wounding signals. Physiol Plant 128:531–545CrossRefGoogle Scholar
  44. Moser C, Segala C, Fontana P, Salakhudtinov I, Gatto P, Pindo M, Zyprian E, Toepfer R, Grando MS, Velasco R (2005) Comparative analysis of expressed sequence tags from different organs of Vitis vinifera L. Funct Integr Genomics 5:208–217PubMedCrossRefGoogle Scholar
  45. Park S, Sugimoto N, Larson MD, Beaudry R, van Nocker S (2006) Identification of genes with potential roles in apple fruit development and biochemistry through large-scale statistical analysis of expressed sequence tags. Plant Physiol 141:811–824PubMedCrossRefGoogle Scholar
  46. Pechous SW, Whitaker BD (2004) Cloning and functional expression of an (E,E)-α-farnesene synthase cDNA from peel tissue of apple fruit. Planta 219:84–94PubMedCrossRefGoogle Scholar
  47. Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J (2001) The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res 29:159–164PubMedCrossRefGoogle Scholar
  48. Quilot B, Kervella J, Genard M, Lescourret F (2005) Analysing the genetic control of peach fruit quality through an ecophysiological model combined with a QTL approach. J Exp Bot 56:3083–3092PubMedCrossRefGoogle Scholar
  49. Raab T, Lopez-Raez JA, Klein D, Caballero JL, Moyano E, Schwab W, Munoz-Blanco J (2006) FaQR, required for the biosynthesis of the strawberry flavor compound 4-hydroxy-2,5-dimethyl-3(2H)-furanone, encodes an enone oxidoreductase. Plant Cell 18:1023–1037PubMedCrossRefGoogle Scholar
  50. Schottler M, Boland W (1996) Biosynthesis of dodecano-4-lactone in ripening fruits: crucial role of an epoxide-hydrolase in enantioselective generation of aroma components of the nectarine (Prunus persica var. nucipersica) and the strawberry (Fragaria ananassa). Helvetica Chimica Acta 79:1488–1496CrossRefGoogle Scholar
  51. Sharon-Asa L, Shalit M, Frydman A, Bar E, Holland D, Or E, Lavi U, Lewinsohn E, Eyal Y (2003) Citrus fruit flavor and aroma biosynthesis: isolation, functional characterization, and developmental regulation of Cstps1, a key gene in the production of the sesquiterpene aroma compound valencene. Plant J 36:664–674PubMedCrossRefGoogle Scholar
  52. Stein N (2007) Triticeae genomics: advances in sequence analysis of large genome cereal crops. Chromosome Res 15:21–31PubMedCrossRefGoogle Scholar
  53. Terrier N, Ageorges A, Abbal P, Romieu C (2001) Generation of ESTs from grape berry at various developmental stages. J Plant Physiol 158:1575–1583CrossRefGoogle Scholar
  54. Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422PubMedGoogle Scholar
  55. Trainotti L, Zanin D, Casadoro G (2003) A cell-wall oriented genomic approach reveals a new and unexpected complexity of the softening in peaches. J Exp Bot 54:1821–1832PubMedCrossRefGoogle Scholar
  56. Trainotti L, Ravanello A, Casadoro G (2004) Differential expression of genes in apical and basal tissues of expanding tobacco leaves. Plant Sci 167:679–686CrossRefGoogle Scholar
  57. Trainotti L, Bonghi C, Ziliotto F, Zanin D, Rasori A, Casadoro G, Ramina A, Tonutti P (2006) The use of microarray μPEACH1.0 to investigate transcriptome changes during transition from pre-climacteric to climacteric phase in peach fruit. Plant Sci 170:606–613CrossRefGoogle Scholar
  58. van der Rest B, Danoun S, Boudet A-M, Rochange SF (2006) Down-regulation of cinnamoyl-CoA reductase in tomato (Solanum lycopersicum L.) induces dramatic changes in soluble phenolic pools. J Exp Bot 6:1399–1411CrossRefGoogle Scholar
  59. Yahayaoui FE, Wongs-Aree C, Latche A, Hackett R, Grierson D, Pech JC (2002) Molecular and biochemical characteristics of a gene encoding an alcohol-acyl-transferase involved in the generation of aroma volatile esters during melon ripening. Eur J Biochem 269:2359–2366CrossRefGoogle Scholar
  60. Zhang B, Chen K, Bowen J, Allan A, Espley R, Karunairetnam S, Ferguson I (2006) Differential expression within the LOX gene family in ripening kiwi fruit. J Exp Bot 57:3825–3836PubMedCrossRefGoogle Scholar
  61. Zhou L, Ke D, Kader AA, Zhou LL, Ke DY (1995) Mode of controlled atmosphere action on ester biosynthesis of strawberries. Acta Agric Univ Pekinensis 21:180–186Google Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • A. Vecchietti
    • 1
  • B. Lazzari
    • 1
  • C. Ortugno
    • 2
  • F. Bianchi
    • 2
  • R. Malinverni
    • 1
  • A. Caprera
    • 1
  • I. Mignani
    • 2
  • C. Pozzi
    • 1
  1. 1.Fondazione Parco Tecnologico PadanoLodiItaly
  2. 2.Dipartimento di Produzione VegetaleUniversità degli Studi di MilanoMilanItaly

Personalised recommendations