Journal of Plant Biotechnology

The Korean Society of Plant Biotechnology (한국식물생명공학회)
권호 표지
DOI QR코드

DOI QR Code

In silico analysis of MeJA-induced comparative transcriptomes in Brassica oleraceae L. var. capitata

  • Lee, Ok Ran (Department of Plant Biotechnology, College of Agriculture and Life Science, Chonnam National University) ;
  • Kim, Dae-Soo (Rare Disease Research Center and Korea Research Institute of Bioscience and Biotechnology (KRIBB))
  • Received : 2016.05.23
  • Accepted : 2016.06.07
  • Published : 2016.06.30
Download PDF
⟨ Previous Next ⟩

Abstract

Brassica oleraceae var capitata is a member of the Brassicaceae family and is widely used as an horticultural crop. In the present study, transcriptome analysis of B. oleraceae L. var capitata was done for the first time using eight-week old seedlings treated with $50{\mu}m$ MeJA, versus mock-treated samples. The complete transcripts for both samples were obtained using the GS-FLX sequencer. Overall, we obtained 275,570 and 266,457 reads from seedlings treated with or without $50{\mu}m$ MeJA, respectively. All the obtained reads were annotated using biological databases and functionally classified using gene ontology (GO), the Kyoto Encyclopedia of Genes and Genomics (KEGG). By using GO analyses, putative transcripts were examined in terms of biotic and abiotic stresses, cellular component organization, biogenesis, and secondary metabolic processes. The KEGG pathways for most of the transcripts were involved in carbohydrate metabolism, energy metabolism, and secondary metabolite synthesis. In order to double the sequenced data, we randomly chose two putative genes involved in terpene biosynthetic pathways and studied their transcript patterns under MeJA treatment. This study will provide us a platform to further characterize the genes in B. oleracea var capitata.

Keywords

References

  1. Brandle JE, Richman A, Swanson AK, Chapman BP (2000) Leaf ESTs from Stevia rebaudiana: a resource for gene discovery in diterpene synthesis. Plant Mol Biol 50:613-622
  2. Conesa A, Gotz S (2008) Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics 2008:619832
  3. Dixon RA, Lamb CJ (1990) Molecular communication in interactions between plants and microbial pathogens. Annu Rev Plant Physiol Plant Mol Biol 41:339-367 https://doi.org/10.1146/annurev.pp.41.060190.002011
  4. Falgueras J, Antonio JL, Noe FP, Francisco RC, Guillermo PT, Claros MG (2010) SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read. BMC Bioinformatics 1471-2105
  5. Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talon M, Dopazo J, Conesa A (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36:3420-3435 https://doi.org/10.1093/nar/gkn176
  6. Hayashi H, Huang P, Inoue K (2003) Up-regulation of soyasaponin biosynthesis by methyl jasmonate in cultured cells of Glycyrrhiza glabra. Plant Cell Physiol 44:401-411
  7. Horan K, Jang C, Bailey-Serres J, Mittler R, Shelton C, Harper JF, Zhu JK, Cushman JC, Gollery M, Girke T (2008) Annotating genes of known and unknown function by large-scale coexpression analysis. Plant Physiol 147:41-57 https://doi.org/10.1104/pp.108.117366
  8. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32(Database issue):D277-D280 https://doi.org/10.1093/nar/gkh063
  9. Kim SI, Kim JY, Kim EA, Kwon KH, Kim KW, Cho K, Lee JH, Nam MH, Yang DC, Yoo JS, Park YM (2003) Proteome analysis of hairy root from Panax ginseng C.A. Meyer using peptide finger printing, internal sequencing and expressed sequence tag data. Proteomics 3:2379-2392 https://doi.org/10.1002/pmic.200300619
  10. Korkina L.G (2007) Phenylpropanoids as naturally occurring antioxidants: from plant defense to human health. Cell Mol Biol 53:15-25
  11. La Camera S, Gouzerh G, Dhondt S, Hoffmann L, Fritig B, Legrand M, Heitz T (2004) Metabolic reprogramming in plant innate immunity: the contributions of phenylpropanoid and oxylipin pathways. Immunol Rev. 198:267-284 https://doi.org/10.1111/j.0105-2896.2004.0129.x
  12. Mao X, Cai T, Olyarchuk JG, Wei L (2005). Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21:3787-3793 https://doi.org/10.1093/bioinformatics/bti430
  13. Mikkelsen MD, Petersen BL, Glawisching E, Jensen AB, Andreasson E, Halkier BA (2003) Modulation of CYP79 genes and glucosinolate profiles in Arabidopsis by defense signaling pathways. Plant Physiology 131:298-308 https://doi.org/10.1104/pp.011015
  14. Nagaraj SH, Gasser RB, Ranganathan S (2007) Ahitchhiker's guide to expressed sequence tag (EST) analysis. Brief Bioinform 8:6-21
  15. Ohlrogge J, Benning C (2000) Unraveling plant metabolism by EST analysis. Curr Opin Plant Biol. 3:224-228 https://doi.org/10.1016/S1369-5266(00)00068-6
  16. Pal D (2006) On gene ontology and function annotation. Bioinformation 1:97-98 https://doi.org/10.6026/97320630001097
  17. Pozo MJ, Van Der Ent S, Van Loon C, Pieterse CMJ (2008) Transcription factor MYC2 is involved in priming for enhanced defense during rhizobacteria-induced systemic resistance in Arabidopsis thaliana. New Phytologist 180(2):511-523 https://doi.org/10.1111/j.1469-8137.2008.02578.x
  18. Ramakrishna A, Ravishankar GA (2011) Influence of abiotic stress signals on secondary metabolites in plants. Plant Signal Behav. 6(11):1720-1731 https://doi.org/10.4161/psb.6.11.17613
  19. Ren A, Li MJ, Shi L, Mu DS, Jiang AL, Han Q, Zhao MW (2013) Profiling and quantifying differential gene transcription provide insights into ganoderic acid biosynthesis in Ganoderma lucidum in response to methyl jasmonate. PloS One 8:e65027 https://doi.org/10.1371/journal.pone.0065027
  20. Sarikami SG, Balkaya A, Yanmaz R (2009) Glucosinolates within a collection of white head cabbages (Brassica oleracea var. capitata sub. var. alba) from Turkey. African Journal of Biotechnology. 8(19):5046-5052
  21. Shim JS, Lee OR, Kim YJ, Lee JH, Jung DY, In JK, Lee BS, Yang DC (2010). Increased production of ginsenosides by overexpressing PgSQS1 affects on ginseng growth rate. J. Ginseng Res 34(2):98-103 https://doi.org/10.5142/jgr.2010.34.2.098
  22. The Gene Ontology Consortium 2010. The Gene Ontology in 2010: extensions and refinements. Nucl Acids Res 38(suppl 1): D331-D335 https://doi.org/10.1093/nar/gkp1018
  23. War AR, Paulraj MG, Ahmad T, Buhroo AA, Hussain B, Ignacimuthu S, Sharma HC (2012) Mechanisms of plant defense against insect herbivores. Plant Signal Behav. 7(10): 1306-1320 https://doi.org/10.4161/psb.21663
  24. Wasternack C, Parthier B (1997) Jasmonate-singalled plant gene expresseion. Trends in Plant Science 2:302-307 https://doi.org/10.1016/S1360-1385(97)89952-9
  25. Aoyagi H, Kobayashi Y, Yamada K, Yokoyama M, Kusakari K, Tanaka H (2001) Efficient production of saikosaponins in Bupleurum falcatum root fragments combined with signal transducers. Applied Microbiology and Biotechnology. 57(4): 482-488 https://doi.org/10.1007/s002530100819
  26. Yukimine Y, Tabata H, Higashi Y, Hara Y (1996) Methyl jasmonateinduced overproduction of paclitaxel and baccatin III in Taxus cell suspension cultures. Nat Biotechnol. 14: 1129-1132 https://doi.org/10.1038/nbt0996-1129