Transcriptome analyses of early cucumber fruit growth identifies distinct gene modules associated with phases of development

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Ando, Kaori ^a,b   Carr, Kevin M ^a   Grumet, Rebecca ^a  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

Cucumis sativus; Exponential fruit growth; Fruit maturation; Fruit set; Fruit surface; Gene expression

Indexed keywords

CYCLINE; HISTONE; TRANSCRIPTOME;

ARTICLE; CELL DIVISION; CELL WALL; CONTIG MAPPING; CONTROLLED STUDY; CUCUMBER; CYTOSKELETON; EXPRESSED SEQUENCE TAG; FRUIT DEVELOPMENT; FRUIT GROWTH; FRUIT MORPHOLOGY; GENE EXPRESSION; LIPID METABOLISM; NONHUMAN; PHLOEM; PHOTOSYNTHESIS; PLANT GENETICS; PLANT STRESS; PLASTID; POLLINATION; PRINCIPAL COMPONENT ANALYSIS; PYROSEQUENCING;

CUCUMIS SATIVUS; FRUIT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT;

CUCUMIS SATIVUS;

EID: 84866792774     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-518     Document Type: Article

References (46)

1. Gillaspy G, Ben-David H, Gruissem W. Fruits: A developmental perspective. Plant Cell 1993, 5:1439-1451. 160374, 12271039.
2. Boonkorkaew P, Hikosaka S, Sugiyama N. Effect of pollination on cell division, cell enlargement, and endogenous hormones in fruit development in a gynoecious cucumber. Scientia Hortic 2008, 116:1-7.
3. Fu FQ, Mao WH, Shi K, Zhou YH, Asami T, Yu JQ. A role of brassinosteroids in early fruit development in cucumber. J Exp Bot 2008, 9:2299-2308.
4. Marcelis LFM, Hofman-Eijer LRB. Cell division and expansion in the cucumber fruit. J Hortic Sci 1993, 68:665-671.
5. Robinson RW, Decker-Walters DS. Cucurbits 1997, CAB International, New York, NY.
6. Ando K, Grumet R. Transcriptional profiling of rapidly growing cucumber fruit by 454-pyrosequencing analysis. J Amer Soc Hortic Sci 2010, 135:291-302.
7. Colle M, Shaaban M, Grumet R. Characterization of component factors associated with differences in cucumber fruit size and shape. HortSci 2011, 46:S281.
8. Ando K, Hammar S, Grumet R. Age-related resistance of diverse cucurbit fruits to infection by Phytophthora capsici. J Amer Soc Hortic Sci 2009, 134:176-182.
9. Gevens AJ, Ando K, Lamour KH, Grumet R, Hausbeck MK. Development of a detached cucumber fruit assay to screen for resistance and effect of fruit age on susceptibility to infection by Phytophthora capsici. Plant Dis 2006, 90:1276-1282.
10. Lemaire-Chamley M, Petit J, Garcia V, Just D, Baldet P, Germain V, Fagard F, Mouassite M, Cheniclet C, Rothan C. Changes in transcriptional profiles are associated with early fruit tissue specialization in tomato. Plant Physiol 2005, 139:750-769. 10.1104/pp.105.063719, 1255993, 16183847.
11. Pascual L, Blanca JM, Canizares J, Nuez F. Analysis of gene expression during the fruit set of tomato: a comparative approach. Plant Sci 2007, 173:609-620.
12. Wang H, Schauer N, Usadel B, Frasse P, Zouine M, Hernould M, Latche A, Pech J-C, Fernie AR, Bouzayen M. Regulatory features underlying pollination-dependent and -independent tomato fruit set revealed by transcript and primary metabolite profiling. Plant Cell 2009, 21:1428-1452. 10.1105/tpc.108.060830, 2700536, 19435935.
13. Amemiya T, Kanayama Y, Yamaki S, Yamada K, Shiratake K. Fruit-specific V-ATPase suppression in antisense-transgenic tomato reduces fruit growth and seed formation. Planta 2006, 223:1272-1280. 10.1007/s00425-005-0176-x, 16322982.
14. Janssen BJ, Thodey K, Schaffer RJ, Alba R, Balakrishnan L, Bishop R, Bowen JH, Crowhurst RN, Gleave AP, Ledger S, McArtney S, Pichler FB, Snowden KC, Ward S. Global gene expression of apple fruit development from the floral bud to ripe fruit. BMC Plant Biol 2008, 8:16. 10.1186/1471-2229-8-16, 2287172, 18279528.
15. Lee YP, Yu GH, Seo YS, Han SE, Choi YO, Kim D, Mok IG, Kim WT, Sung SK. Microarray analysis of apple gene expression engaged in early fruit development. Plant Cell Rep 2007, 26:917-926. 10.1007/s00299-007-0308-9, 17294193.
16. Mascarell-Creus A, Canizares J, Vilarrasa-Blasi J, Mora-Garcia S, Blanca J, Gonzalez-Ibeas D, Saladie M, Roig C, Deleu W, Pico-Silvent B, Lopez-Bigas N, Aranda MA, Garcia-Mas J, Nuez F, Puigdomenech P, Cano-Delgado AI. An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.). BMC Genomics 2009, 10:467. 10.1186/1471-2164-10-467, 2767371, 19821986.
17. Schlosser J, Olsson N, Weis M, Reid K, Peng F, Lund S, Bowen P. Cellular expansion and gene expression in the developing grape (Vitis vinifera L.). Protoplasma 2008, 232:255-265. 10.1007/s00709-008-0280-9, 18421552.
18. Wechter WP, Levi A, Harris KR, Davis AR, Fei Z, Katzir N, Giovannoni JJ, Salman-Minkov A, Hernandez A, Thimmapuram J, Tadmor Y, Portnoy V, Trebitsh T. Gene expression in developing watermelon fruit. BMC Genomics 2008, 9:275. 10.1186/1471-2164-9-275, 2440768, 18534026.
19. Guo SG, Liu JG, Zheng Y, Huang MY, Zhang HY, Gong GY, He HJ, Ren Y, Zhong SL, Fei ZJ, Xu Y. Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles. BMC Genomics 2011, 12:454. 10.1186/1471-2164-12-454, 3197533, 21936920.
20. Manganaris GA, Rasori A, Bassi D, Geuna F, Ramina A, Tonutti P, Bonghi C. Comparative transcript profiling of apricot (Prunus armeniaca L. fruit development and on-tree ripening. Tree Genet Genom 2011, 7:609-616.
21. Portnoy V, Diber A, Pollock S, Karchi H, Lev S, Tzuri G, Harel-Beja R, Forer R, Portnoy VH, Lewinsohn E, Tadmor Y, Burger J, Schaffer A, Katzir N. Use of non-normalized, non-amplified cDNA for 454-based RNA sequencing of fleshy melon fruit. Plant Genome 2011, 4:36-46.
22. Zenoni S, Ferrarani A, Giancomelli E, Xumerle L, Fasoli M, Malerba G, Bellin D, Pezzotti M, Delledonne M. Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq. Plant Physiol 2010, 152:1787-1795. 10.1104/pp.109.149716, 2850006, 20118272.
23. Mitani N, Yamaji N, Ago Y, Iwasaki K, Ma JF. Isolation and functional characterization of an influx silicon transporter in two pumpkin cultivars contrasting in silicon accumulation. Plant J 2011, 66:231-240. 10.1111/j.1365-313X.2011.04483.x, 21205032.
24. Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P, Ren Y, Zhu H, Li J, Lin K, Jin W, Fei Z, Li G, Staub J, Kilian A, van der Vossen EAG, Wu Y, Guo J, He J, Jia J, Ren Y, Tan G, Lu Y, Ruan J, Qian W, Wang M, Huang Q, Li B, Xuan Z, Cao J, San A, Wu Z, Ahang J, Cai Q, Bai Y, Zho B, Han Y, Li Y, Li X, Wang S, Shi Q, Liu S, Cho WK, Kim JY, Xu Y, Heller-Uszynska K, Miao H, Cheng Z, Zhang S, Wu J, Yang Y, Kang H, Li M, Liang H, Ren X, Shi A, Wen M, Jian M, Yang H, Zhang G, Yang Z, Chen R, Liu S, Li J, Ma L, Liu H, Zhou Y, Zhao J, Fang X, Li G, Fang L, Li Y, Liu D, Zheng H, Zhang Y, Qin N, Li Z, Yang G, Yang S, Bolund L, Kristiansen K, Zheng H, Li S, Zhang X, Yang H, Wang J, Sun R, Zhang B, Jiang S, Wang J, Du Y, Li S. The genome of the cucumber, Cucumis sativus L. Nature Genet 2009, 41:1275-1281. 10.1038/ng.475, 19881527.
25. Provart N, Zhu T. A browser-based functional classification SuperViewer for Arabidopsis genomics. Curr Compu Molec Biol 2003, 2003:271-272.
26. Van Leene J, Hollunder J, Eeckhout D, Persiau G, Van De Slijke E, Stals H, Van Isterdal G, Verkest A, Neirynck S, Buffel Y, De Bodt S, Maere S, Laukens K, Pharazyn A, Ferreira PCG, Eloy N, Renne C, Meyer C, Faure JD, Steinbrenner J, Beynon J, Larkin JC, Van de Peer Y, Hilson P, Kuiper M, De Veylder L, Van Onckelen H, Inze D, Witters E, De Jaeger G. Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Molec Sys Biol 2010, 6:37. Article 397.
27. Malladi A, Johnson LK. Expression profiling of cell cycle genes reveals key facilitators of cell production during carpel development, fruit set, and fruit growth in apple (Malus x domestica Borkh.). J Exp Bot 2011, 62:205-219. 10.1093/jxb/erq258, 2993910, 20732881.
28. Clark AM, Jacobsen KR, Bostwick DE, Dannenhoffer JM, Skaggs MI, Thompson GA. Molecular characterization of a phloem specific- gene encoding the filament protein, phloem protein 1 (PP1), from Cucurbita maxima. Plant J 1997, 12:49-61. 10.1046/j.1365-313X.1997.12010049.x, 9263452.
29. Turgeon R, Wolf S. Phloem transport: Cellular pathways and molecular trafficking. Annu Rev Plant Biol 2009, 60:207-221. 10.1146/annurev.arplant.043008.092045, 19025382.
30. Zhang B, Tolstikov V, Turnbull C, Hicks LM, Fiehn O. Divergent metabolome and proteome suggest functional independence of dual phloem transport systems in cucurbits. Proc Nat Acad Sci USA 2010, 107:13532-13537. 10.1073/pnas.0910558107, 2922161, 20566864.
31. Dinant S, Clark AM, Zhu YM, Vilaine F, Palauque JC, Kusiak C, Thompson GA. Diversity of the superfamily of phloem lectins (phloem protein 2) in angiosperms. Plant Physiol 2003, 131:114-128. 10.1104/pp.013086, 166792, 12529520.
32. Dannenhoffer JM, Schulz A, Skaggs MI, Bostwick DE, Thompson GA. Expression of the phloem lectin is developmentally linked to vascular differentiation in cucurbits. Planta 1997, 201:405-414.
33. Yeats TH, Howe K, Matas AJ, Buda GJ, Thannhauser TW, Rose JKC. Mining the surface proteome of tomato (Solanum lycopersicum) fruit for proteins associated with cuticle biogenesis. J Exp Bot 2010, 61:3759-3771. 10.1093/jxb/erq194, 2921210, 20571035.
34. Mintz-Oron S, Mandel T, Rogachev I, Feldber L, Lotan O, Yativ M, Wang Z, Jetter R, Venger I, Adato A, Aharoni A. Gene expression and metabolism in tomato fruit surface tissues. Plant Physiol 2008, 147:823-851. 10.1104/pp.108.116004, 2409049, 18441227.
35. Samuels L, Kunst L, Jetter R. Sealing plant surfaces: cuticular wax formation by epidermal cells. Annu Rev Plant Biol 2008, 59:683-707. 10.1146/annurev.arplant.59.103006.093219, 18251711.
36. Suh MC, Samuels AL, Jetter R, Kunst L, Pollard M, Ohlrogge J, Beisson F. Cuticular lipid composition, surface structure, and gene expression in Arabidopsis stem epidermis. Plant Physiol 2005, 139:1649-1665. 10.1104/pp.105.070805, 1310549, 16299169.
37. Aharoni A, Dixit S, Jetter R, Thoenes E, van Arkel G, Pereira A. The SHINE clade of AP2 domain transcription factors activates wax biosynthesis, alters cuticle properties and confers drought tolerance when overexpressed in Arabidopsis. Plant Cell 2004, 16:2463-2480. 10.1105/tpc.104.022897, 520946, 15319479.
38. Li-Beisson Y, Pollard M, Sauveplane V, Pinot F, Ohlrogge J, Beisson F. Nanoridges that characterize the surface morphology of flowers require the synthesis of cutin polyester. Proc Nat Acad Sci USA 2009, 51:22008-22013.
39. Wang ZH, Guhling O, Yao RN, Li FL, Yeats TH, Rose JKC, Jetter R. Two oxidosqualene cyclases responsible for biosynthesis of tomato fruit cuticular triterpenoids. Plant Physiol 2011, 155:540-552. 10.1104/pp.110.162883, 3075788, 21059824.
40. Inskeep WP, Bloom PR. Extinction coefficients of chlorophyll a and b in N, N-dimethylformanide and 80% acetone. Plant Physiol 1985, 77:483-485. 10.1104/pp.77.2.483, 1064541, 16664080.
41. Buda GJ, Isaacson T, Matas AJ, Paolillo DJ, Rose JK. Three-dimensional imaging of plant cuticle architecture using confocal scanning laser microscopy. Plant J 2009, 60:378-385. 10.1111/j.1365-313X.2009.03960.x, 19563439.
42. Schilmiller AL, Schauvinhold I, Larson M, Xu M, Charbonneaua AL, Schmidt A, Wilkerson C, Last RL, Pichersky E. Monoterpenes in the glandular trichomes of tomato are synthesized from a neryl diphosphate precursor rather than geranyl diphosphate. Proc Nat Acad Sci USA 2009, 106:0865-10870.
43. The Institute for Genomic Research (TIGR). http://compbio.dfci.harvard.edu/tgi/software.
44. Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J. TIGR gene indices clustering tools (TIGCL): a software system for fast clustering of large EST databases. Bioinformatics 2003, 19:651-652. 10.1093/bioinformatics/btg034, 12651724.
45. Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome Res 1999, 9:868-877. 10.1101/gr.9.9.868, 310812, 10508846.
46. DeHoon MJL, Imoto S, Nolan J, Miyano S. Open source clustering software. Bioinformatics 2004, 20:1453-1454. LINK http://bioinformatics.oupjournals.org, 10.1093/bioinformatics/bth078, 14871861.