Eukaryotic transcriptomics in silico: Optimizing cDNA-AFLP efficiency

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Stölting, Kai N ^a   Gort, Gerrit ^b   Wüst, Christian ^a   Wilson, Anthony B ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; RESTRICTION ENDONUCLEASE; TRANSCRIPTOME;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; COMPUTER MODEL; COMPUTER SIMULATION; CONTROLLED STUDY; DNA BASE COMPOSITION; EUKARYOTE; GENE EXPRESSION PROFILING; POLYMERASE CHAIN REACTION; PROCESS OPTIMIZATION; SEQUENCE ANALYSIS; TRANSCRIPTOMICS; BIOLOGY; CHEMISTRY; CLASSIFICATION; GENETICS; MOLECULAR EVOLUTION;

EUKARYOTA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; COMPUTATIONAL BIOLOGY; DNA, COMPLEMENTARY; EUKARYOTA; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING;

EID: 73449089757     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-565     Document Type: Article

References (38)

1. Liang P, Pardee AB. Differential display of eukaryotic messenger-RNA by means of the polymerase chain-reaction. Science 1992, 257:967-971. 10.1126/science.1354393, 1354393.
2. Breyne P, Dreesen R, Cannoot B, Rombaut D, Vandepoele K, Rombauts S, Vanderhaeghen R, Inze D, Zabeau M. Quantitative cDNA-AFLP analysis for genome-wide expression studies. Mol Genet Genomics 2003, 269:173-179.
3. Vos P, Hogers R, Bleeker M, Reijans M, Vandelee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M. AFLP - A new technique for DNA-fingerprinting. Nucleic Acids Res 1995, 23:4407-4414. 10.1093/nar/23.21.4407, 307397, 7501463.
4. Meudt HM, Clarke AC. Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends Plant Sci 2007, 12:106-117. 10.1016/j.tplants.2007.02.001, 17303467.
5. Koopman WJM, Gort G. Significance tests and weighted values for AFLP similarities, based on Arabidopsis in silico AFLP fragment length distributions. Genetics 2004, 167:1915-1928. 10.1534/genetics.103.015693, 1471014, 15342529.
6. Kivioja T, Arvas M, Saloheimo M, Penttila M, Ukkonen E. Optimization of cDNA-AFLP experiments using genomic sequence data. Bioinformatics 2005, 21:2573-2579. 10.1093/bioinformatics/bti393, 15774551.
7. Weiberg A, Pöhler D, Morris J, Karlovsky P. Improved coverage of cDNA-AFLP by sequential digestion of immobilized cDNA. BMC Genomics 2008, 9:480. 10.1186/1471-2164-9-480, 2577664, 18851732.
8. Gort G, Koopman WJM, Stein A. Fragment length distributions and collision probabilities for AFLP markers. Biometrics 2006, 62:1107-1115. 10.1111/j.1541-0420.2006.00613.x, 17156285.
9. Gunnarsson GH, Thormar HG, Gudmundsson B, Akesson L, Jonsson JJ. Two-dimensional conformation-dependent electrophoresis (2D-CDE) to separate DNA fragments containing unmatched bulge from complex DNA samples. Nucleic Acids Res 2004, 32:e23. 10.1093/nar/gnh018, 373374, 14762200.
10. Subramanian S. Nearly neutrality and the evolution of codon usage bias in eukaryotic genomes. Genetics 2008, 178:2429-2432. 10.1534/genetics.107.086405, 2323827, 18430960.
11. Bachem CWB, Hoeven RS, de Bruijn SM, Vreugdenhil D, Zabeau M, Visser RGF. Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: Analysis of gene expression during potato tuber development. Plant J 1996, 9:745-753. 10.1046/j.1365-313X.1996.9050745.x, 8653120.
12. Xu L, Chen H, Hu XH, Zhang RM, Zhang Z, Luo ZW. Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between the two kingdoms. Mol Biol Evol 2006, 23:1107-1108. 10.1093/molbev/msk019, 16611645.
13. Vuylsteke M, Daele H, Vercauteren A, Zabeau M, Kuiper M. Genetic dissection of transcriptional regulation by cDNA-AFLP. Plant J 2006, 45:439-446. 10.1111/j.1365-313X.2005.02630.x, 16412088.
14. Reijans M, Lascaris R, Groeneger AO, Wittenberg A, Wesselink E, van Oeveren J, de Wit E, Boorsma A, Voetdijk B, Spek H, Grivell LA, Simons G. Quantitative comparison of cDNA-AFLP, microarrays, and GeneChip expression data in Saccharomyces cerevisiae. Genomics 2003, 82:606-618. 10.1016/S0888-7543(03)00179-4, 14611802.
15. Ogihara Y, Mochida K, Kawaura K, Murai K, Seki M, Kamiya A, Shinozaki K, Carninci P, Hayashizaki Y, Shin I, Kohara Y, Yamazaki Y. Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags. Genes Genet Syst 2004, 79:227-232. 10.1266/ggs.79.227, 15514442.
16. Alexandrov NN, Troukhan ME, Brover VV, Tatarinova T, Flavell RB, Feldmann KA. Features of Arabidopsis genes and genome discovered using full-length cDNAs. Plant Mol Biol 2006, 60:69-85. 10.1007/s11103-005-2564-9, 16463100.
17. Umezawa T, Sakurai T, Totoki Y, Toyoda A, Seki M, Ishiwata A, Akiyama K, Kurotani A, Yoshida T, Mochida K, Kasuga M, Todaka D, Maruyama K, Nakashima K, Enju A, Mizukado S, Ahmed S, Yoshiwara K, Harada K, Tsubokura Y, Hayashi M, Sato S, Anai T, Ishimoto M, Funatsuki H, Teraishi M, Osaki M, Shinano T, Akashi R, Sakaki Y. Sequencing and analysis of approximately 40 000 soybean cDNA clones from a full-length-enriched cDNA library. DNA Res 2008, 15:333-346. 10.1093/dnares/dsn024, 2608845, 18927222.
18. Sato K, Shin I, Seki M, Shinozaki K, Yoshida T, Takeda K, Conte M, Kohara Y. Development of 5006 full-length cDNAs in barley: a tool for accessing cereal genomics resources. DNA Res 2009, 16:81-89. 10.1093/dnares/dsn034, 2671202, 19150987.
19. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schonbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 2002, 420:563-573. 10.1038/nature01266, 12466851.
20. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS. The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC). Genome Res 2004, 14:2121-2127. 10.1101/gr.2596504, 528928, 15489334.
21. Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H, Nagai K, Kimura K, Makita H, Sekine M, Obayashi M, Nishi T, Shibahara T, Tanaka T, Ishii S, Yamamoto J, Saito K, Kawai Y, Isono Y, Nakamura Y, Nagahari K, Murakami K, Yasuda T, Iwayanagi T, Wagatsuma M, Shiratori A, Sudo H. Complete sequencing and characterization of 21,243 full-length human cDNAs. Nature Genet 2004, 36:40-45. 10.1038/ng1285, 14702039.
22. Harhay GP, Sonstegard TS, Keele JW, Heaton MP, Clawson ML, Snelling WM, Wiedmann RT, Van Tassell CP, Smith TP. Characterization of 954 bovine full-CDS cDNA sequences. BMC Genomics 2005, 6:166. 10.1186/1471-2164-6-166, 1314900, 16305752.
23. Sakate R, Suto Y, Imanishi T, Tanoue T, Hida M, Hayasaka I, Kusuda J, Gojobori T, Hashimoto K, Hirai M. Mapping of chimpanzee full-length cDNAs onto the human genome unveils large potential divergence of the transcriptome. Gene 2007, 399:1-10. 10.1016/j.gene.2007.04.013, 17574350.
24. Carter MG, Sharov AA, VanBuren V, Dudekula DB, Carmack CE, Nelson C, Ko MS. Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray. Genome Biol 2005, 6:R61. 10.1186/gb-2005-6-7-r61, 1175992, 15998450.
25. Stothard P. The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 2000, 28:1102.
26. Fields Development Team Fields: Tools for spatial data. 2006, National Center for Atmospheric Research, Boulder, CO., http://www.image.ucar.edu/GSP/Software/Fields/
27. Edwards LJ, Muller KE, Wolfinger RD, Qaqish BF, Schabenberger O. An R2 statistic for fixed effects in the linear mixed model. Statistics in Medicine 2008, 27:6137-6157. 10.1002/sim.3429, 18816511.
28. Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000, 28:10-14. 10.1093/nar/28.1.10, 102437, 10592169.
29. Aquea F, Arce-Johnson P. Identification of genes expressed during early somatic embryogenesis in Pinus radiata. Plant Physiol Bioch 2008, 46:559-568.
30. Muller LA, Craciun AR, Ruytinx J, Lambaerts M, Verbruggen N, Vangronsveld J, Colpaert JV. Gene expression profiling of a Zn-tolerant and a Zn-sensitive Suillus luteus isolate exposed to increased external zinc concentrations. Mycorrhiza 2007, 17:571-580. 10.1007/s00572-007-0134-5, 17530303.
31. Pellny TK, Van Aken O, Dutilleul C, Wolff T, Groten K, Bor M, De Paepe R, Reyss A, Van Breusegem F, Noctor G, Foyer CH. Mitochondrial respiratory pathways modulate nitrate sensing and nitrogen-dependent regulation of plant architecture in Nicotiana sylvestris. Plant J 2008, 54:976-992. 10.1111/j.1365-313X.2008.03472.x, 2440565, 18318685.
32. Polesani M, Desario F, Ferrarini A, Zamboni A, Pezzotti M, Kortekamp A, Polverari A. CDNA-AFLP analysis of plant and pathogen genes expressed in grapevine infected with Plasmopara viticola. BMC Genomics 2008, 9:142. 10.1186/1471-2164-9-142, 2292706, 18366764.
33. Huang YC, Chang YL, Hsu JJ, Chuang HW. Transcriptome analysis of auxin-regulated genes of Arabidopsis thaliana. Gene 2008, 420:118-124. 10.1016/j.gene.2008.05.017, 18577427.
34. Miao L, Shou S, Zhu Z, Jiang F, Zai W, Yang Y. Isolation of a novel tomato caffeoyl CoA 3-O-methyltransferase gene following infection with the bacterium Ralstonia solanacearum. J Phytopathol 2008, 156:588-596.
35. Hsu TW, Tsai WC, Wang DP, Lin S, Hsiao YY, Chen WH, Chen HH. Differential gene expression analysis by cDNA-AFLP between flower buds of Phalaenopsis Hsiang Fei cv. H. F. and its somaclonal variant. Plant Sci 2008, 175:415-422.
36. Wee CW, Lee SF, Robin C, Heckel DG. Identification of candidate genes for fenvalerate resistance in Helicoverpa armigera using cDNA-AFLP. Insect Mol Biol 2008, 17:351-360. 10.1111/j.1365-2583.2008.00809.x, 18651917.
37. Neveu C, Charvet C, Fauvin A, Cortet J, Castagnone-Sereno P, Cabaret J. Identification of levamisole resistance markers in the parasitic nematode Haemonchus contortus using a cDNA-AFLP approach. Parasitology 2007, 134:1105-1110. 10.1017/S0031182007000030, 17608970.
38. Pathan AAK, Devi KU, Vogel H, Reineke A. Analysis of differential gene expression in the generalist entomopatho genic fungus Beauveria bassiana (Bals.) Vuillemin grown on different insect cuticular extracts and synthetic medium through cDNA-AFLPs. Fungal Genet Biol 2007, 44:1231-1241. 10.1016/j.fgb.2007.07.002, 17723310.