Global Analysis of Gene Expression and Identification of Modules in Echinacea purpurea Using Systems Biology Approach

Document Type : Research Articles

Authors

• Ahmad Tahmasebi ¹
• Farzaneh Aram ¹
• Hassan Pakniyat ¹
• Ali Niazi ¹
• Elahe Tavakol ¹
• Esmaeil Ebrahimie ²

¹ Shiraz University

² The University of Adelaide; Shiraz University; University of South Australia; Flinders University

https://doi.org/10.22067/jcmr.v10i1.67357

Abstract

Co-expression analysis is a useful tool to analysis data and detection of genes that act in the same pathway or biological process. Echinacea purpurea is one of the most important medicinal plant of the Asteraceae family that is known as antioxidative and antiviral agent. Despite medicinal importance of E. purpurea, very few reports are available for metabolic mechanisms in this plant. With the aim to elucidate the gene expression profiling and identification of modules in E. purpurea, we performed a systems biology analysis on publicly available transcriptome data. Gene ontology and KEGG pathway enrichment analysis revealed that the unigenes were highly related to the cellular process, primary metabolic process, carbon metabolism and biosynthesis of antibiotics. The co-expression networks divided genes into multiple modules. Of these, module M2 associated with secondary metabolic process. Moreover, a total of 47 transcription factor families such as bHLH, bZIP, C2H2, MYB and WRKY in modules were identified. These findings can provide an overall picture for better understanding the gene expression patterns and common transcriptional mechanisms in E. purpurea.

Keywords

• Co-expression analysis
• Echinacea purpurea
• Transcriptomics data

20.1001.1.20089147.2018.10.1.5.7

References

Abbasi BH., Stiles AR., Saxena PK. and Liu C-Z. (2012) Gibberellic acid increases secondary metabolite production in Echinacea purpurea hairy roots. Applied biochemistry and biotechnology 168: 2057-2066.

Ali MB. and McNear DH. (2014) Induced transcriptional profiling of phenylpropanoid pathway genes increased flavonoid and lignin content in Arabidopsis leaves in response to microbial products. BMC plant biology 14: 84.

Deluc L., Barrieu F., Marchive C., Lauvergeat V., Decendit A., Richard T., Carde J-P., Merillon J-M. and Hamdi S. (2006) Characterization of a grapevine R2R3-MYB transcription factor that regulates the phenylpropanoid pathway. Plant physiology 140: 499-511.

Dennis G., Sherman BT., Hosack DA., Yang J., Gao W., Lane HC. and Lempicki RA. (2003) DAVID: database for annotation, visualization, and integrated discovery. Genome biology 4: R60.

Du Z., Zhou X., Ling Y., Zhang Z. and Su Z. (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic acids research 38: W64-W70.

Fraser CM. and Chapple C. (2011) The phenylpropanoid pathway in Arabidopsis. The Arabidopsis Book, e0152.

Gongora-Castillo E., Childs KL., Fedewa G., Hamilton JP., Liscombe DK., Magallanes-Lundback M., Mandadi KK., Nims E., Runguphan W. and Vaillancourt B. (2012) Development of transcriptomic resources for interrogating the biosynthesis of monoterpene indole alkaloids in medicinal plant species. PloS one 7: e52506.

Graham IA., Besser K., Blumer S., Branigan CA., Czechowski T., Elias L., Guterman I., Harvey D., Isaac PG. and Khan AM. (2010) The genetic map of Artemisia annua L. identifies loci affecting yield of the antimalarial drug artemisinin. science 327: 328-331.

Guo K., Zou W., Feng Y., Zhang M., Zhang J., Tu F., Xie G., Wang L., Wang Y. and Klie S. (2014) An integrated genomic and metabolomic framework for cell wall biology in rice. BMC genomics 15: 596.

Hirsch S. and Oldroyd GE. (2009) GRAS-domain transcription factors that regulate plant development. Plant signaling & behavior 4: 698-700.

Hur M., Campbell AA., Almeida-de-Macedo M., Li L., Ransom N., Jose A., Crispin M., Nikolau BJ. and Wurtele ES. (2013) A global approach to analysis and interpretation of metabolic data for plant natural product discovery. Natural product reports 30: 565-583.

Langfelder P. and Horvath S. (2008) WGCNA: an R package for weighted correlation network analysis. BMC bioinformatics 9: 559.

Lee I., Ambaru B., Thakkar P., Marcotte EM. and Rhee SY. (2010) Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nature biotechnology 28: 149-156.

Lee J. and Scagel CF. (2010) Chicoric acid levels in commercial basil (Ocimum basilicum) and Echinacea purpurea products. Journal of functional foods 2: 77-84.

Liu Q., Wang Z., Xu X., Zhang H. and Li C. (2015) Genome-wide analysis of C2H2 zinc-finger family transcription factors and their responses to abiotic stresses in poplar (Populus trichocarpa). PloS one 10: e0134753.

Mitsuda N. and Ohme-Takagi M. (2009) Functional analysis of transcription factors in Arabidopsis. Plant and Cell Physiology 50: 1232-1248.

Patra B., Schluttenhofer C., Wu Y., Pattanaik S. and Yuan L. (2013) Transcriptional regulation of secondary metabolite biosynthesis in plants. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1829: 1236-1247.

Pellati F., Benvenuti S., Magro L., Melegari M. and Soragni F. (2004) Analysis of phenolic compounds and radical scavenging activity of Echinacea spp. Journal of Pharmaceutical and Biomedical Analysis 35: 289-301.

Ramamoorthy V., Dhingra S., Kincaid A., Shantappa S., Feng X. and Calvo AM. (2013) The putative C2H2 transcription factor MtfA is a novel regulator of secondary metabolism and morphogenesis in Aspergillus nidulans. PLoS One 8: e74122.

Tsai Y-L., Chiu C-C., Chen JY-F., Chan K-C. and Lin S-D. (2012) Cytotoxic effects of Echinacea purpurea flower extracts and cichoric acid on human colon cancer cells through induction of apoptosis. Journal of ethnopharmacology 143: 914-919.

Vogt T. (2010) Phenylpropanoid biosynthesis. Molecular plant 3: 2-20.

Wu C., You C., Li C., Long T., Chen G., Byrne ME. and Zhang Q. (2008) RID1, encoding a Cys2/His2-type zinc finger transcription factor, acts as a master switch from vegetative to floral development in rice. Proceedings of the National Academy of Sciences 105: 12915-12920.

Xiao M., Zhang Y., Chen X., Lee E-J., Barber CJ., Chakrabarty R., Desgagne-Penix I., Haslam TM., Kim Y-B. and Liu E. (2013) Transcriptome analysis based on next-generation sequencing of non-model plants producing specialized metabolites of biotechnological interest. Journal of biotechnology 166: 122-134.

Yang CQ., Fang X., Wu XM., Mao YB., Wang LJ. and Chen XY. (2012) Transcriptional regulation of plant secondary metabolism. Journal of integrative plant biology 54: 703-712.