Table of Contents Author Guidelines Submit a Manuscript
BioMed Research International
Volume 2014, Article ID 404578, 9 pages
http://dx.doi.org/10.1155/2014/404578
Research Article

Gleditsia sinensis: Transcriptome Sequencing, Construction, and Application of Its Protein-Protein Interaction Network

1Institute of System Biology, Shanghai University, Shanghai 200444, China
2Yangzhou Breeding Biological Agriculture Technology Co. Ltd., Yangzhou 225200, China
3State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China

Received 11 March 2014; Accepted 21 April 2014; Published 27 May 2014

Academic Editor: Lei Chen

Copyright © 2014 Liucun Zhu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. X.-Y. Lian and Z. Zhang, “Quantitive analysis of gleditsia saponins in the fruits of Gleditsia sinensis Lam. by high performance liquid chromatography,” Journal of Pharmaceutical and Biomedical Analysis, vol. 75, pp. 41–46, 2013. View at Publisher · View at Google Scholar · View at Scopus
  2. H.-L. Jian, L.-W. Zhu, W.-M. Zhang, D.-F. Sun, and J.-X. Jiang, “Enzymatic production and characterization of manno-oligosaccharides from Gleditsia sinensis galactomannan gum,” International Journal of Biological Macromolecules, vol. 55, pp. 282–288, 2013. View at Publisher · View at Google Scholar · View at Scopus
  3. J.-M. Yi, J.-S. Park, S.-M. Oh et al., “Ethanol extract of Gleditsia sinensis thorn suppresses angiogenesis in vitro and in vivo,” BMC Complementary and Alternative Medicine, vol. 12, article 243, 2012. View at Publisher · View at Google Scholar · View at Scopus
  4. W. Wang, B. Vinocur, and A. Altman, “Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance,” Planta, vol. 218, no. 1, pp. 1–14, 2003. View at Publisher · View at Google Scholar · View at Scopus
  5. J. R. Witcombe, P. A. Hollington, C. J. Howarth, S. Reader, and K. A. Steele, “Breeding for abiotic stresses for sustainable agriculture,” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 363, no. 1492, pp. 703–716, 2008. View at Publisher · View at Google Scholar · View at Scopus
  6. S. Mahajan and N. Tuteja, “Cold, salinity and drought stresses: an overview,” Archives of Biochemistry and Biophysics, vol. 444, no. 2, pp. 139–158, 2005. View at Publisher · View at Google Scholar · View at Scopus
  7. J.-K. Zhu, “Cell signaling under salt, water and cold stresses,” Current Opinion in Plant Biology, vol. 4, no. 5, pp. 401–406, 2001. View at Publisher · View at Google Scholar · View at Scopus
  8. A. Matsui, J. Ishida, T. Morosawa et al., “Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array,” Plant and Cell Physiology, vol. 49, no. 8, pp. 1135–1149, 2008. View at Publisher · View at Google Scholar · View at Scopus
  9. G. Zeller, S. R. Henz, C. K. Widmer et al., “Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays,” Plant Journal, vol. 58, no. 6, pp. 1068–1082, 2009. View at Publisher · View at Google Scholar · View at Scopus
  10. X. Lin, J. Zhang, Y. Li et al., “Functional genomics of a living fossil tree, Ginkgo, based on next-generation sequencing technology,” Physiologia Plantarum, vol. 143, no. 3, pp. 207–218, 2011. View at Publisher · View at Google Scholar · View at Scopus
  11. K. Tanase, C. Nishitani, H. Hirakawa et al., “Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology,” BMC Genomics, vol. 13, no. 1, article 292, 2012. View at Publisher · View at Google Scholar · View at Scopus
  12. S. Alsford, D. J. Turner, S. O. Obado et al., “High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome,” Genome Research, vol. 21, no. 6, pp. 915–924, 2011. View at Publisher · View at Google Scholar · View at Scopus
  13. J. Halvardson, A. Zaghlool, and L. Feuk, “Exome RNA sequencing reveals rare and novel alternative transcripts,” Nucleic Acids Research, vol. 41, no. 1, article e6, 2013. View at Publisher · View at Google Scholar · View at Scopus
  14. L. Xiang, Y. Li, Y. Zhu et al., “Transcriptome analysis of the Ophiocordyceps sinensis fruiting body reveals putative genes involved in fruiting body development and cordycepin biosynthesis,” Genomics, vol. 103, no. 1, pp. 154–159, 2014. View at Google Scholar
  15. C.-Y. Shi, H. Yang, C.-L. Wei et al., “Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds,” BMC Genomics, vol. 12, article 131, 2011. View at Publisher · View at Google Scholar · View at Scopus
  16. “Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1. 21) [Software],” https://github.com/najoshi/sickle.
  17. M. G. Grabherr, B. J. Haas, M. Yassour et al., “Full-length transcriptome assembly from RNA-Seq data without a reference genome,” Nature Biotechnology, vol. 29, no. 7, pp. 644–652, 2011. View at Publisher · View at Google Scholar · View at Scopus
  18. B. J. Haas, A. Papanicolaou, M. Yassour et al., “De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis,” Nature Protocols, vol. 8, no. 8, pp. 1494–1512, 2013. View at Publisher · View at Google Scholar · View at Scopus
  19. B. Li and C. N. Dewey, “RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome,” BMC Bioinformatics, vol. 12, article 323, 2011. View at Publisher · View at Google Scholar · View at Scopus
  20. A. Conesa, S. Götz, J. M. García-Gómez, J. Terol, M. Talón, and M. Robles, “Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research,” Bioinformatics, vol. 21, no. 18, pp. 3674–3676, 2005. View at Publisher · View at Google Scholar · View at Scopus
  21. R. L. Tatusov, D. A. Natale, I. V. Garkavtsev et al., “The COG database: new developments in phylogenetic classification of proteins from complete genomes,” Nucleic Acids Research, vol. 29, no. 1, pp. 22–28, 2001. View at Google Scholar · View at Scopus
  22. M. Kanehisa, S. Goto, S. Kawashima, Y. Okuno, and M. Hattori, “The KEGG resource for deciphering the genome,” Nucleic Acids Research, vol. 32, pp. D277–D280, 2004. View at Google Scholar · View at Scopus
  23. Y. Moriya, M. Itoh, S. Okuda, A. C. Yoshizawa, and M. Kanehisa, “KAAS: an automatic genome annotation and pathway reconstruction server,” Nucleic Acids Research, vol. 35, no. 2, pp. W182–W185, 2007. View at Publisher · View at Google Scholar · View at Scopus
  24. D. Szklarczyk, A. Franceschini, M. Kuhn et al., “The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored,” Nucleic Acids Research, vol. 39, no. 1, pp. D561–D568, 2011. View at Publisher · View at Google Scholar · View at Scopus
  25. R. M. Ferreira, J. L. Rybarczyk-Filho, R. J. S. Dalmolin et al., “Preferential duplication of intermodular hub genes: an evolutionary signature in eukaryotes genome networks,” PLoS ONE, vol. 8, no. 2, Article ID e56579, 2013. View at Publisher · View at Google Scholar · View at Scopus
  26. M. Naika, K. Shameer, O. K. Mathew, R. Gowda, and R. Sowdhamini, “STIFDB2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in arabidopsis and rice,” Plant and Cell Physiology, vol. 54, no. 2, article e8, 2013. View at Publisher · View at Google Scholar · View at Scopus
  27. R. Sowdhamini, K. Shameer, S. Ambika, S. M. Varghese, N. Karaba, and M. Udayakumar, “STIFDB Arabidopsis stress responsive transcription factor dataBase,” International Journal of Plant Genomics, vol. 2009, Article ID 583429, 8 pages, 2009. View at Publisher · View at Google Scholar · View at Scopus
  28. A. S. Sundar, S. M. Varghese, K. Shameer, N. Karaba, M. Udayakumar, and R. Sowdhamini, “STIF: identification of stress-upregulated transcription factor binding sites in Arabidopsis thaliana,” Bioinformation, vol. 2, no. 10, pp. 431–437, 2008. View at Google Scholar
  29. Y. Peng, X. Gao, R. Li, and G. Cao, “Transcriptome sequencing and De Novo analysis of Youngia japonica using the illumina platform,” PLoS ONE, vol. 9, no. 3, Article ID e90636, 2014. View at Google Scholar
  30. N. K. Izzah, J. Lee, M. Jayakodi et al., “Transcriptome sequencing of two parental lines of cabbage (Brassica oleracea L. var. capitata L.) and construction of an EST-based genetic map,” BMC Genomics, vol. 15, article 149, 2014. View at Google Scholar
  31. J. Reese, M. K. Christenson, N. Leng et al., “Characterization of the Asian citrus psyllid transcriptome,” Journal of Genomics, vol. 2, pp. 54–58, 2014. View at Google Scholar
  32. R. A. George, J. Y. Liu, L. L. Feng, R. J. Bryson-Richardson, D. Fatkin, and M. A. Wouters, “Analysis of protein sequence and interaction data for candidate disease gene prediction,” Nucleic Acids Research, vol. 34, no. 19, article e130, 2006. View at Publisher · View at Google Scholar · View at Scopus
  33. J. Xu and Y. Li, “Discovering disease-genes by topological features in human protein-protein interaction network,” Bioinformatics, vol. 22, no. 22, pp. 2800–2805, 2006. View at Publisher · View at Google Scholar · View at Scopus