The transcriptomes of columnar and standard type apple trees (Malus x domestica) - A comparative study

Gene

Volumn 498, Issue 2, 2012, Pages 223-230

  Krost, Clemens ^a   Petersen, Romina ^a   Schmidt, Erwin R ^a  

^a JOHANNES GUTENBERG UNIVERSITY   (Germany)

Author keywords

454; Co gene; De novo assembly; Illumina; MAPMAN; NGS

Indexed keywords

CO PROTEIN; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ALLELE; APICAL MERISTEM; APPLE; ARTICLE; CELL GROWTH; CELL STRUCTURE; CELL WALL; CHROMOSOME 10; COMPARATIVE STUDY; CONTROLLED STUDY; GENE EXPRESSION; GENE SEQUENCE; GENE STRUCTURE; NEXT GENERATION SEQUENCING; NONHUMAN; PHENOTYPE; PLANT GENE; PRIORITY JOURNAL; TREE;

CELL MEMBRANE; CELL WALL; GENE EXPRESSION REGULATION, PLANT; MALUS; MERISTEM; PHENOTYPE; SEQUENCE ANALYSIS, DNA; TRANSCRIPTOME;

MALUS X DOMESTICA;

EID: 84858746853     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.01.078     Document Type: Article

References (44)

1. Alagna F., D'Agostino N., Torchia L., Servili M., Rao R., Pietrella M., Giuliano G., Chiusano M.L., Baldoni L., Perrotta G. Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development. BMC Genomics 2009, 10:399.
2. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
3. Birol I., Jackman S.D., Nielsen C.B., Qian J.Q., Varhol R., Stazyk G., Morin R.D., Zhao Y., Hirst M., Schein J.E., Horsman D.E., Connors J.M., Gascoyne R.D., Marra M.A., Jones S.J.D. novo transcriptome assembly with ABySS. Bioinformatics 2009, 25:2872-2877.
4. Blažek J. Segregation and general evaluation of spur type or compact growth habits in apples. Acta Hortic. 1992, 317:71-79.
5. Cheng N.H., Pittman J.K., Shigaki T., Lachmansingh J., LeClere S., Lahner B., Salt D.E., Hirschi K.D. Functional association of Arabidopsis CAX1 and CAX3 is required for normal growth and ion homeostasis. Plant Physiol. 2005, 138:2048-2060.
6. Fisher D.V. Spur-type strains of McIntosh for high density plantings. Br. Columbia Fruit Growers' Association Quarterly Report 1969, 14:3-10.
7. Flachowsky H., Hattasch C., Hofer M., Peil A., Hanke M.V. Overexpression of LEAFY in apple leads to a columnar phenotype with shorter internodes. Planta 2009, 231:251-263.
8. Galinha C., Bilsborough G., Tsiantis M. Hormonal input in plant meristems: a balancing act. Semin. Cell Dev. Biol. 2009, 20:1149-1156.
9. Hartig K., Beck E. Crosstalk between auxin, cytokinins, and sugars in the plant cell cycle. Plant Biol. (Stuttg.) 2006, 8:389-396.
10. Huber D.P., Philippe R.N., Madilao L.L., Sturrock R.N., Bohlmann J. Changes in anatomy and terpene chemistry in roots of Douglas-fir seedlings following treatment with methyl jasmonate. Tree Physiol. 2005, 25:1075-1083.
11. Hyodo H., Yamakawa S., Takeda Y., Tsuduki M., Yokota A., Nishitani K., Kohchi T. Active gene expression of a xyloglucan endotransglucosylase/hydrolase gene, XTH9, in inflorescence apices is related to cell elongation in Arabidopsis thaliana. Plant Mol. Biol. 2003, 52:473-482.
12. Kuppusamy K.T., Walcher C.L., Nemhauser J.L. Cross-regulatory mechanisms in hormone signaling. Plant Mol. Biol. 2009, 69:375-381.
13. Lapins K.O. Segregation of compact growth types in certain apple seedling progenies. Can. J. Plant Sci. 1969, 49:765-768.
14. Lapins K.O., Watkins R. Genetics of compact growth habit. Report of East Malling Research Station for 1972 1973, 136.
15. Liu Y., Liu D., Zhang H., Gao H., Guo X., Wang D., Zhang X., Zhang A. The alpha- and beta-expansin and xyloglucan endotransglucosylase/hydrolase gene families of wheat: molecular cloning, gene expression, and EST data mining. Genomics 2007, 90:516-529.
16. Liu Y.B., Lu S.M., Zhang J.F., Liu S., Lu Y.T. A xyloglucan endotransglucosylase/hydrolase involves in growth of primary root and alters the deposition of cellulose in Arabidopsis. Planta 2007, 226:1547-1560.
17. Looney N.E., Lane W.D. Spur-type growth mutants of McIntosh apple: a review of their genetics, physiology and field performance. Acta Hortic. 1984, 146:31-46.
18. Looney N.E., Taylor J.S., Pharis R.P. Relationship of endogenous gibberellin and cytokinin levels in shoot tips to apical form in four strains of 'McIntosh' apple. J. Am. Soc. Hortic. Sci. 1988, 113:395-398.
19. Morozova O., Hirst M., Marra M.A. Applications of new sequencing technologies for transcriptome analysis. Annu. Rev. Genomics Hum. Genet. 2009, 10:135-151.
20. Morris J., Tian H., Park S., Sreevidya C.S., Ward J.M., Hirschi K.D. AtCCX3 is an Arabidopsis endomembrane H+-dependent K+ transporter. Plant Physiol. 2008, 148:1474-1486.
21. Munne-Bosch S., Falk J. New insights into the function of tocopherols in plants. Planta 2004, 218:323-326.
22. Munne-Bosch S., Weiler E.W., Alegre L., Muller M., Duchting P., Falk J. Alpha-tocopherol may influence cellular signaling by modulating jasmonic acid levels in plants. Planta 2007, 225:681-691.
23. Ohlrogge J., Browse J. Lipid biosynthesis. Plant Cell 1995, 7:957-970.
24. Pauwels L., Morreel K., De Witte E., Lammertyn F., Van Montagu M., Boerjan W., Inze D., Goossens A. Mapping methyl jasmonate-mediated transcriptional reprogramming of metabolism and cell cycle progression in cultured Arabidopsis cells. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:1380-1385.
25. Simpson J.T., Wong K., Jackman S.D., Schein J.E., Jones S.J., Birol I. ABySS: a parallel assembler for short read sequence data. Genome Res. 2009, 19:1117-1123.
26. Stekel D.J., Git Y., Falciani F. The comparison of gene expression from multiple cDNA libraries. Genome Res. 2000, 10:2055-2061.
27. Sun C., Li Y., Wu Q., Luo H., Sun Y., Song J., Lui E.M., Chen S.D. novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis. BMC Genomics 2010, 11:262.
28. Surget-Groba Y., Montoya-Burgos J.I. Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res. 2010, 20:1432-1440.
29. Thimm O., Blasing O., Gibon Y., Nagel A., Meyer S., Kruger P., Selbig J., Muller L.A., Rhee S.Y., Stitt M. MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 2004, 37:914-939.
30. Tian Y.K., Wang C.H., Dai H.Y., Zhang J.S. Screening of a RAPD marker tightly linked to Co gene in apple and the SCAR marker conversion. Yi Chuan Xue Bao 2004, 31:919-925.
31. Tian Y.K., Wang C.H., Zhang J.S., James C., Dai H.Y. Mapping Co, a gene controlling the columnar phenotype of apple, with molecular markers. Euphytica 2005, 145:181-188.
32. Tobutt K.R. Breeding columnar apples at east malling. Acta Hortic. 1985, 159:63-68.
33. Tromas A., Perrot-Rechenmann C. Recent progress in auxin biology. C. R. Biol. 2010, 333:297-306.
34. Tuskan G.A., Difazio S., Jansson S., Bohlmann J., Grigoriev I., Hellsten U., Putnam N., Ralph S., Rombauts S., Salamov A., Schein J., Sterck L., Aerts A., Bhalerao R.R., Bhalerao R.P., Blaudez D., Boerjan W., Brun A., Brunner A., Busov V., Campbell M., Carlson J., Chalot M., Chapman J., Chen G.L., Cooper D., Coutinho P.M., Couturier J., Covert S., Cronk Q., Cunningham R., Davis J., Degroeve S., Dejardin A., Depamphilis C., Detter J., Dirks B., Dubchak I., Duplessis S., Ehlting J., Ellis B., Gendler K., Goodstein D., Gribskov M., Grimwood J., Groover A., Gunter L., Hamberger B., Heinze B., Helariutta Y., Henrissat B., Holligan D., Holt R., Huang W., Islam-Faridi N., Jones S., Jones-Rhoades M., Jorgensen R., Joshi C., Kangasjarvi J., Karlsson J., Kelleher C., Kirkpatrick R., Kirst M., Kohler A., Kalluri U., Larimer F., Leebens-Mack J., Leple J.C., Locascio P., Lou Y., Lucas S., Martin F., Montanini B., Napoli C., Nelson D.R., Nelson C., Nieminen K., Nilsson O., Pereda V., Peter G., Philippe R., Pilate G., Poliakov A., Razumovskaya J., Richardson P., Rinaldi C., Ritland K., Rouze P., Ryaboy D., Schmutz J., Schrader J., Segerman B., Shin H., Siddiqui A., Sterky F., Terry A., Tsai C.J., Uberbacher E., Unneberg P., et al. The genome of black cottonwood, Populus trichocarpa (Torr & Gray). Science 2006, 313:1596-1604.
35. UniProt-Consortium The universal protein resource (UniProt) in 2010. Nucleic Acids Res. 2010, 38:D142-D148.
36. van Schie C.C., Haring M.A., Schuurink R.C. Tomato linalool synthase is induced in trichomes by jasmonic acid. Plant Mol. Biol. 2007, 64:251-263.
37. Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., Kalyanaraman A., Fontana P., Bhatnagar S.K., Troggio M., Pruss D., Salvi S., Pindo M., Baldi P., Castelletti S., Cavaiuolo M., Coppola G., Costa F., Cova V., Dal Ri A., Goremykin V., Komjanc M., Longhi S., Magnago P., Malacarne G., Malnoy M., Micheletti D., Moretto M., Perazzolli M., Si-Ammour A., Vezzulli S., Zini E., Eldredge G., Fitzgerald L.M., Gutin N., Lanchbury J., Macalma T., Mitchell J.T., Reid J., Wardell B., Kodira C., Chen Z., Desany B., Niazi F., Palmer M., Koepke T., Jiwan D., Schaeffer S., Krishnan V., Wu C., Chu V.T., King S.T., Vick J., Tao Q., Mraz A., Stormo A., Stormo K., Bogden R., Ederle D., Stella A., Vecchietti A., Kater M.M., Masiero S., Lasserre P., Lespinasse Y., Allan A.C., Bus V., Chagne D., Crowhurst R.N., Gleave A.P., Lavezzo E., Fawcett J.A., Proost S., Rouze P., Sterck L., Toppo S., Lazzari B., Hellens R.P., Durel C.E., Gutin A., Bumgarner R.E., Gardiner S.E., Skolnick M., Egholm M., Van de Peer Y., Salamini F., Viola R. The genome of the domesticated apple (Malus x domestica Borkh). Nat. Genet. 2010, 42:833-839.
38. Wall P.K., Leebens-Mack J., Chanderbali A.S., Barakat A., Wolcott E., Liang H., Landherr L., Tomsho L.P., Hu Y., Carlson J.E., Ma H., Schuster S.C., Soltis D.E., Soltis P.S., Altman N., dePamphilis C.W. Comparison of next generationsequencing technologies for transcriptome characterization. BMC Genomics 2009, 10:347.
39. Wang W., Wang Y., Zhang Q., Qi Y., Guo D. Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing. BMC Genomics 2009, 10:465.
40. Wang Z., Fang B., Chen J., Zhang X., Luo Z., Huang L., Chen X., Li Y.D. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genomics 2010, 11:726.
41. Wasternack C. Jasmonates: an update on biosynthesis, signal transduction and action in plant stress response, growth and development. Ann. Bot. 2007, 100:681-697.
42. Watanabe M., Suzuki A., Komori S., Bessho H. Comparison of endogenous IAA and cytokinins in shoots of columnar and normal type apple trees. J. Jpn. Soc. Hortic. Sci. 2004, 73:19-24.
43. Watanabe M., Bessho H., Suzuki A., Komori S. Seasonal changes of IAAand cytokinin in shoots of columnar type apple trees. Acta Hortic. 2008, 774:75-80.
44. Wu G.Z., Xue H.W. Arabidopsis {beta}-ketoacyl-[acyl carrier protein] synthase I is crucial for fatty acid synthesis and plays a role in chloroplast division and embryo development. Plant Cell 2010, 22:3726-3744.