Comparative transcriptional profiling analysis of olive ripe-fruit pericarp and abscission zone tissues shows expression differences and distinct patterns of transcriptional regulation

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Parra, Ruben ^a   Paredes, Miguel A ^a   Sanchez Calle, Isabel M ^b   Gomez Jimenez, Maria C ^a  

^a UNIVERSITY OF EXTREMADURA   (Spain)

^b UNIVERSITY OF GRANADA   (Spain)

Author keywords

454 Pyrosequencing; Abscission; Gene expression; Olea europaea; Ripening; Transcriptomic comparative

Indexed keywords

ADENOSINE TRIPHOSPHATE; AROMATIC AMINO ACID; CONTIG; ISOPRENOID; LIGNIN; MESSENGER RNA; TRANSCRIPTION FACTOR; TRANSCRIPTOME;

ABSCISSION ZONE; AMINO ACID SYNTHESIS; AMINO ACID TRANSPORT; ARTICLE; CELL WALL; COMPARATIVE STUDY; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; FRUIT RIPENING; GENE EXPRESSION; GLYCOLYSIS; NONHUMAN; OLIVE; PERICARP; PHOTOSYNTHESIS; PLANT METABOLISM; PROTEIN DEPHOSPHORYLATION; PROTON TRANSPORT; RNA SEQUENCE; TRANSCRIPTION REGULATION;

OLEA EUROPAEA;

FRUIT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METABOLIC NETWORKS AND PATHWAYS; MOLECULAR SEQUENCE ANNOTATION; OLEA; ORGAN SPECIFICITY; PHENOTYPE; REPRODUCIBILITY OF RESULTS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EID: 84889795035     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-866     Document Type: Article

References (53)

1. Loureiro J, Rodriguez E, Costa A, Santos C. Nuclear DNA content estimations in wild olive (Olea europaea L. ssp. europaea var. sylvestris Brot.) and Portuguese cultivars of O. europaea using flow cytometry. Genet Resour Crop Evol 2007, 54:21-25.
2. Alagna F, D'Agostino N, Torchia L, Servili M, Rao R, Pietrella M, Giuliano G, Chiusano ML, Baldoni L, Perrotta G. Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development. BMC Genomics 2009, 10:399. 10.1186/1471-2164-10-399, 2748093, 19709400.
3. Galla G, Barcaccia G, Ramina A, Collani S, Alagna F, Baldoni L, Cultrera NG, Martinelli F, Sebastiani L, Tonutti P. Computational annotation of genes differentially expressed along olive fruit development. BMC Plant Biol 2009, 9:128. 10.1186/1471-2229-9-128, 2774695, 19852839.
4. Bianco L, Alagna F, Baldoni L, Finnie C, Svensson B, Perrotta G. Proteome regulation during Olea europaea fruit development. PLoS ONE 2013, 10.1371/journal.pone.0053563.
5. Stiti N, Triki S, Hartmann MA. Formation of triterpenoids throughout Olea europaea fruit ontogeny. Lipids 2007, 42:55-67. 10.1007/s11745-006-3002-8, 17393211.
6. De la Rosa R, Angiolillo A, Guerrero M, Pellegrini M, Rallo L, Besnard G, Bervillé A, Martin A, Baldoni L. A first linkage map of olive (Olea europaea L.) cultivars using RAPD, AFLP, RFLP and SSR markers. Theor Appl Genet 2003, 106:1273-1282.
7. Wu S, Collins G, Sedgley M. A molecular linkage map of olive (Olea europaea L.) based on RAPD, microsatellite, and SCAR markers. Genome 2004, 47:26-35. 10.1139/g03-091, 15060599.
8. Mariotti R, Cultrera NGM, Munoz-Diez C, Baldoni L, Rubini A. Identification of new polymorphic regions and differentiation of cultivated olives (Olea europaea L.) through platome sequence comparison. BMC Plant Biol 2010, 10:211. 10.1186/1471-2229-10-211, 2956560, 20868482.
9. Gil-Amado JA, Gomez-Jimenez MC. Transcriptome analysis of mature fruit abscission control in olive. Plant Cell Physiol 2013, 54(2):244-269. 10.1093/pcp/pcs179, 23292600.
10. Muñoz-Mérida A, González-Plaza JJ, Cañada A, Blanco AM, Del García-López MC, Rodríguez JM, Pedrola L, Sicardo MD, Hernández ML, De la Rosa R, Belaj A, Gil-Borja M, Luque F, Martínez-Rivas JM, Pisano DG, Trelles O, Valpuesta V, Beuzón CR. De novo assembly and functional annotation of the olive (olea europaea) transcriptome. DNA Res 2013, 20(1):93-108. 10.1093/dnares/dss036, 3576661, 23297299.
11. Nath P, Sane AP, Trivedi PK, Sane VA, Asif MH. Role of transcription factors in regulating ripening, senescence and organ abscission in plants. Stewart Postharvest Rev 2007, 3:1-14.
12. Conde C, Delrot S, Gerós H. Physiological, biochemical and molecular changes occurring during olive development and ripening. J Plant Physiol 2008, 165(15):1545-1562. 10.1016/j.jplph.2008.04.018, 18571766.
13. Gomez-Jimenez MC, Paredes MA, Gallardo M, Fernandez-Garcia N, Olmos E, Sanchez-Calle IM. Tissue-specific expression of olive S-adenosyl methionine decarboxylase and spermidine synthase genes and polyamine metabolism during flower opening and early fruit development. Planta 2010, 232(3):629-647. 10.1007/s00425-010-1198-6, 20532909.
14. Gomez-Jimenez MC, Paredes MA, Gallardo M, Sanchez-Calle IM. Mature fruit abscission is associated with up-regulation of polyamine metabolism in the olive abscission zone. J Plant Physiol 2010, 167(17):1432-1441. 10.1016/j.jplph.2010.05.020, 20643493.
15. Parra-Lobato MC, Gomez-Jimenez MC. Polyamine-induced modulation of genes involved in ethylene biosynthesis and signalling pathways and nitric oxide production during olive mature fruit abscission. J Exp Bot 2011, 62(13):4447-4465. 10.1093/jxb/err124, 3170544, 21633085.
16. Yu K, Xu Q, Da X, Guo F, Ding Y, Deng X. Transcriptome changes during fruit development and ripening of sweet orange (Citrus sinensis). BMC Genomics 2012, 13:10. 10.1186/1471-2164-13-10, 3267696, 22230690.
17. Xiao S, Dai L, Liu F, Wang Z, Peng W, Xie D. COS1: an Arabidopsis coronatine insensitive1 suppressor essential for regulation of jasmonate-mediated plant defense and senescence. Plant Cell 2004, 16:1132-1142. 10.1105/tpc.020370, 423205, 15075400.
18. Castellarin S, Di Gaspero G. Transcriptional control of anthocyanin biosynthetic genes in extreme phenotypes for berry pigmentation of naturally occurring grapevines. BMC Plant Biol 2007, 7(1):46. 10.1186/1471-2229-7-46, 2147006, 17760970.
19. Espley RV, Hellens RP, Putterill J, Stevenson DE, Kutty-Amma S, Allan AC. Red colouration in apple fruit is due to the activity of the MYB transcription factor, MdMYB10. Plant J 2007, 49(3):414-427. 10.1111/j.1365-313X.2006.02964.x, 1865000, 17181777.
20. Wei YZ, Hu FC, Hu GB, Li XJ, Huang XM, Wang HC. Differential expression of anthocyanin biosynthetic genes in relation to anthocyanin accumulation in the pericarp of Litchi Chinensis Sonn. PLoS One 2011, 6(4):e19455. 10.1371/journal.pone.0019455, 3084873, 21559331.
21. Niu SS, Xu CJ, Zhang WS, Zhang B, Li X, Lin-Wang K, Ferguson IB, Allan AC, Chen KS. Coordinated regulation of anthocyanin biosynthesis in Chinese bayberry (Myrica rubra) fruit by a R2R3 MYB transcription factor. Planta 2010, 231(4):887-899. 10.1007/s00425-009-1095-z, 20183921.
22. Barrat D, Clark J. Proteins arising during the late stages of embryogenesis in Pisum sativum L. Planta 1991, 184:14-23.
23. Suarez-Rodriguez MC, Edsga D, Hussain SS, Alquezar D, Rasmussen M, Gilbert T, Nielsen BH, Bartels D, Mundy J. Transcriptomes of the desiccation-tolerant resurrection plant Craterostigma plantagineum. Plant J 2010, 63:212-228. 10.1111/j.1365-313X.2010.04243.x, 20444235.
24. Wang L, Li Z, Qian W, Guo W, Gao X, Huang L, Wang H, Zhu H, Wu JW, Wang D, Liu D. The Arabidopsis purple acid phosphatase AtPAP10 is predominantly associated with the root surface and plays an important role in plant tolerance to phosphate limitation. Plant Physiol 2011, 157(3):1283-1299. 10.1104/pp.111.183723, 3252131, 21941000.
25. Barford D, Das AK, Egloff MP. The structure and mechanism of protein phosphatases: insights into catalysis and regulation. Annu Rev Biophys Biomol Struct 1998, 27:133-164. 10.1146/annurev.biophys.27.1.133, 9646865.
26. Brugiere N, Dubois F, Limami AM, Lelandais M, Roux Y, Sangwan RS, Hirel B. Glutamine synthetase in the phloem plays a major role in controlling proline production. Plant Cell 1999, 11(10):1995-2012. 144111, 10521528.
27. Wu CT, Bradford KJ. Class I chitinase and beta-1,3-glucanase are differentially regulated by wounding, methyl jasmonate, ethylene, and gibberellin in tomato seeds and leaves. Plant Physiol 2003, 133(1):263-273. 10.1104/pp.103.024687, 196603, 12970492.
28. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 1999, 27:29-34. 10.1093/nar/27.1.29, 148090, 9847135.
29. Fabi JP, Seymour GB, Graham NS, Broadley MR, May ST, Lajolo FM, Cordenunsi BR, Oliveira do Nascimento JR. Analysis of ripening-related gene expression in papaya using an Arabidopsis-based microarray. BMC Plant Biol 2012, 12:242. 10.1186/1471-2229-12-242, 3562526, 23256600.
30. Klee HJ, Giovannoni JJ. Genetics and control of tomato fruit ripening and quality attributes. Annu Rev Genet 2011, 45:41-59. 10.1146/annurev-genet-110410-132507, 22060040.
31. Scharf KD, Berberich T, Ebersberger I, Nover L. The plant heat stress transcription factor (Hsf) family: structure, function and evolution. Biochim Biophys Acta 1819, 2012:104-119.
32. Pajerowska-Mukhtar KM, Wang W, Tada Y, Oka N, Tucker CL, Fonseca JP, Dong X. The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transition. Curr Biol 2012, 22:103-112. 10.1016/j.cub.2011.12.015, 3298764, 22244999.
33. Mayrose M, Ekengren SK, Melech-Bonfil S, Martin GB, Sessa G. A novel link between tomato GRAS genes, plant disease resistance and mechanical stress response. Mol Plant Pathol 2006, 7(6):593-604. 10.1111/j.1364-3703.2006.00364.x, 20507472.
34. Xu G, Livingston DM, Krek W. Multiple members of the E2F transcription factor family are the products of oncogenes. Proc Natl Acad Sci U S A 1995, 92:1357-1361. 10.1073/pnas.92.5.1357, 42518, 7877982.
35. Rushton PJ, Somssich IE, Ringler P, Shen QJ. WRKY transcription factors. Trends Plant Sci 2010, 15(5):247-258. 10.1016/j.tplants.2010.02.006, 20304701.
36. Meir S, Philosoph-Hadas S, Sundaresan S, Selvaraj KSV, Burd S, Ophir R, Kochanek B, Reid MS, Jiang CZ, Lers A. Microarray analysis of the abscission-related transcriptome in the tomato flower abscission zone in response to auxin depletion. Plant Physiol 2010, 154:1929-1956. 10.1104/pp.110.160697, 2996037, 20947671.
37. Cai S, Lashbrook CC. Stamen abscission zone transcriptome profiling reveals new candidates for abscission control: enhanced retention of floral organs in transgenic plants overexpressing Arabidopsis ZINC FINGER PROTEIN2. Plant Physiol 2008, 146:1305-1321. 10.1104/pp.107.110908, 2259061, 18192438.
38. Feller A, Machemer K, Braun EL, Grotewold E. Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. Plant J 2011, 66(1):94-116. 10.1111/j.1365-313X.2010.04459.x, 21443626.
39. Wolberger C. Multiprotein-DNA complexes in transcriptional regulation. Annu Rev Biophys Biomol Struct 1999, 28:29-56. 10.1146/annurev.biophys.28.1.29, 10410794.
40. Zimmermann IM, Heim MA, Weisshaar B, Uhrig JF. Comprehensive identification of Arabidopsis thaliana MYB transcription factors interacting with R/B-like BHLH proteins. Plant J 2004, 40:22-34. 10.1111/j.1365-313X.2004.02183.x, 15361138.
41. Nijhawan A, Jain M, Tyagi AK, Khurana JP. Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice. Plant Physiol 2008, 146:333-350. 2245831, 18065552.
42. Corbacho J, Romojaro F, Pech JC, Latché A, Gomez-Jimenez MC. Transcriptomic events involved in melon mature-fruit abscission comprise the sequential induction of cell-wall degrading genes coupled to a stimulation of endo and exocytosis. PLoS ONE 2013, 8(3):e58363. 10.1371/journal.pone.0058363, 3590154, 23484021.
43. Osterlund MT, Hardtke CS, Wei N, Deng XW. Targeted destabilization of HY5 during light-regulated development of Arabidopsis. Nature 2000, 405(6785):462-466. 10.1038/35013076, 10839542.
44. Liu Y, Dai S, Beachy RN. Role of the C-terminal domains of rice (Oryza sativa L.) bZIP proteins RF2a and RF2b in regulating transcription. Biochem J 2007, 405(2):243-249. 10.1042/BJ20061375, 1904516, 17371296.
45. Tucker ML, Whitelaw CA, Lyssenko NN, Nath P. Functional analysis of regulatory elements in the gene promoter for an abscission-specific cellulase from bean and isolation, expression, and binding affinity of three TGA-type basic leucine zipper transcription factors. Plant Physiol 2002, 130:1487-1496. 10.1104/pp.007971, 166667, 12428013.
46. Botton A, Eccher G, Forcato C, Ferrarini A, Begheldo M, Zermiani M, Moscatello S, Battistelli A, Velasco R, Ruperti B, Ramina A. Signaling pathways mediating the induction of apple fruitlet abscission. Plant Physiol 2011, 155:185-208. 10.1104/pp.110.165779, 3075760, 21037112.
47. Olsen AN, Ernst HA, Leggio LL, Skriver K. NAC transcription factors: structurally distinct, functionally diverse. Trends Plant Sci 2005, 10:79-87. 10.1016/j.tplants.2004.12.010, 15708345.
48. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621-628. 10.1038/nmeth.1226, 18516045.
49. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26(1):139-140. 10.1093/bioinformatics/btp616, 2796818, 19910308.
50. Garber M, Grabherr MG, Guttman M, Trapnell C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods 2011, 8(6):469-477. 10.1038/nmeth.1613, 21623353.
51. Vijay N, Poelstra JW, Künstner A, Wolf JB. Challenges and strategies in transcriptome assembly and differential gene expression quantification: a comprehensive in silico assessment of RNA-seq experiments. Mol Ecol 2013, 22(3):620-634. 10.1111/mec.12014, 22998089.
52. Gene ontology consortium: The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res 2010, 38(Database issue):D331-D335. 2808930, 19920128.
53. Gil-Amado JA, Gomez-Jimenez MC. Regulation of polyamine metabolism and biosynthetic gene expression during olive mature-fruit abscission. Planta 2012, 235(6):1221-1237. 10.1007/s00425-011-1570-1, 22167259.