Building an mRNA transcriptome from the shoots of Betula platyphylla by using Solexa technology

Tree Genetics and Genomes

Volumn 8, Issue 5, 2012, Pages 1031-1040

  Wang, Yucheng ^a   Gao, Caiqiu ^a   Zheng, Lei ^a   Liu, Guifeng ^a   Jiang, Jing ^a   Yang, Chuanping ^a  

^a NORTHEAST FORESTRY UNIVERSITY   (China)

Author keywords

Birch; Gene expression; Next generation sequencing technique; Shoot development

Indexed keywords

BETULA PLATYPHYLLA;

EID: 84866734563     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-012-0483-x     Document Type: Article

References (34)

1. Baroja-Fernández E, Muñoz FJ, Montero M, Etxeberria E, Sesma MT, Ovecka M et al (2009) Enhancing sucrose synthase activity in transgenic potato (Solanum tuberosum L.) tubers results in increased levels of starch, ADPglucose and UDPglucose and total yield. Plant Cell Physiol 50: 1651-1662.
2. Cazalis R, Pulido P, Aussenac T, Pérez-Ruiz JM, Cejudo FJ (2006) Cloning and characterization of three thioredoxin h isoforms from wheat showing differential expression in seeds. J Exp Bot 57: 2165-2172.
3. Chen L, Zhao LP, Gao QK (2005) Generation and analysis of expressed sequence tags from the tender shoots cDNA library of tea plant (Camellia sinensis). Plant Sci 168: 359-363.
4. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
5. Cuddapah S, Barski A, Cui K, Schones DE, Wang Z, Wei G et al (2009) Native chromatin preparation and Illumina/Solexa library construction. Cold Spring Harb Protoc. doi: 10. 1101/pdb. prot5237.
6. Heather DC, Yan J, Mansfield SD (2009) Sucrose synthase affects carbon partitioning to increase cellulose production and altered cell wall ultrastructure. Proc Natl Acad Sci USA 106: 13118-13123.
7. Hegedus Z, Zakrzewska A, Agoston VC, Ordas A, Rácz P, Mink M et al (2009) Deep sequencing of the zebrafish transcriptome response to mycobacterium infection. Mol Immunol 46: 2918-2930.
8. Ihalainen JA, Croce R, Morosinotto T, van Stokkum IH, Bassi R, Dekker JP et al (2005) Excitation decay pathways of Lhca proteins: a time-resolved fluorescence study. J Phys Chem B 109: 21150-21158.
9. Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC et al (2005) Multiple laboratory comparison of microarray platforms. Nat Methods 2: 345-350.
10. Karsi A, Cao D, Li P, Patterson A, Kocabas A, Feng J et al (2002) Transcriptome analysis of channel catfish (Ictalurus punctatus): initial analysis of gene expression and microsatellite-containing cDNAs in the skin. Gene 285: 157-168.
11. Koning AJ, Rose R, Comai L (1992) Developmental expression of tomato heat-shock cognate protein 80. Plant Physiol 100: 801-811.
12. Li R, Li Y, Zheng H, Luo R, Zhu H, Li Q et al (2009) Building the sequence map of the human pan-genome. Nat Biotech 28: 57-63.
13. Libault M, Farmer A, Joshi T, Takahashi K, Langley RJ, Franklin LD et al (2010) An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J 63: 86-99.
14. Marx C, Wong JH, Buchanan BB (2003) Thioredoxin and germinating barley: targets and protein redox changes. Planta 216: 454-460.
15. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628.
16. Pedotti P, 't Hoen PA, Vreugdenhil E, Schenk GJ, Vossen RH, Ariyurek Y et al (2008) Can subtle changes in gene expression be consistently detected with different microarray platforms? BMC Genomics 9: 124.
17. Pegg AE (2009) S-Adenosylmethionine decarboxylase. Essays Biochem 46: 25-45.
18. Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19: 651-652.
19. Qin L, Smant G, Stokkermans J, Bakker J, Schots A, Helder J (1998) Cloning of a trans-spliced glyceraldehyde-3-phosphate-dehydrogenase gene from the potato cyst nematode Globodera rostochiensis and expression of its putative promoter region in Caenorhabditis elegans. Mol Biochem Parasitol 96: 59-67.
20. Schürmann P, Jacquot JP (2000) Plant thioredoxin systems revisited. Annu Rev Plant Physiol Plant Mol Biol 51: 371-400.
21. Serrato AJ, Cejudo FJ (2003) Type-h thioredoxins accumulate in the nucleus of developing wheat seed tissues suffering oxidative stress. Planta 217: 392-399.
22. Shan X, Wang J, Chua L, Jiang D, Peng W, Xie D (2011) The role of Arabidopsis Rubisco activase in jasmonate-induced leaf senescence. Plant Physiol 155: 751-764.
23. Sirover MA (1997) Role of the glycolytic protein, glyceraldehyde-3-phosphate dehydrogenase, in normal cell function and in cell pathology. J Cell Biol 66: 133-140.
24. Sulieman S, Fischinger SA, Gresshoff PM, Schulze J (2010) Asparagine as a major factor in the N-feedback regulation of N fixation in Medicago truncatula. Physiol Plant 140: 21-31.
25. Wada M, Shirahata A (2010) Identification of the primary structure and post-translational modification of rat S-adenosylmethionine decarboxylase. Biol Pharm Bull 33: 891-894.
26. Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, Liang H et al (2009) Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics 1(10).
27. Wang W, Vinocur B, Shoseyov O, Altman A (2004) Role of plant-heat-shock proteins and molecular chaperones in the abiotic stress response. Trends Plant Sci 9: 244-252.
28. Wilhelm BT, Landry JR (2009) RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Methods 48: 249-257.
29. Wong CE, Prem LB, Harald O, Mohan BS (2008) Transcriptional profiling of the pea shoot apical meristem reveals processes underlying its function and maintenance. BMC Plant Bio 8: 73.
30. Wu T, Qin Z, Zhou X, Feng Z, Du Y (2010) Transcriptome profile analysis of floral sex determination in cucumber. J Plant Physiol 167: 905-913.
31. Wyatt RE, Nagao RT, Key JL (1992) Patterns of soybean proline-rich protein gene expression. Plant Cell 4: 99-110.
32. Yano H, Wong JH, Cho MJ, Buchanan BB (2001) A strategy for the identification of proteins targeted by thioredoxin. Proc Natl Acad Sci USA 98: 4794-4799.
33. Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J. (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34 Web Server: W293-297.
34. Zhou X, Su Z, Sammons RD, Peng Y, Tranel PJ, Stewart CN Jr et al (2009) Novel software package for cross-platform transcriptome analysis (CPTRA). BMC Bioinforma 10(Suppl 11): S16.