title: Comparison of the transcriptomes of ginger (Zingiber officinale Rosc.) and mango ginger (Curcuma amada Roxb.) in response to the bacterial wilt infection.
abstract: Bacterial wilt in ginger (Zingiber officinale Rosc.) caused by Ralstonia solanacearum is one of the most important production constraints in tropical, sub-tropical and warm temperature regions of the world. Lack of resistant genotype adds constraints to the crop management. However, mango ginger (Curcuma amada Roxb.), which is resistant to R. solanacearum, is a potential donor, if the exact mechanism of resistance is understood. To identify genes involved in resistance to R. solanacearum, we have sequenced the transcriptome from wilt-sensitive ginger and wilt-resistant mango ginger using Illumina sequencing technology. A total of 26387032 and 22268804 paired-end reads were obtained after quality filtering for C. amada and Z. officinale, respectively. A total of 36359 and 32312 assembled transcript sequences were obtained from both the species. The functions of the unigenes cover a diverse set of molecular functions and biological processes, among which we identified a large number of genes associated with resistance to stresses and response to biotic stimuli. Large scale expression profiling showed that many of the disease resistance related genes were expressed more in C. amada. Comparative analysis also identified genes belonging to different pathways of plant defense against biotic stresses that are differentially expressed in either ginger or mango ginger. The identification of many defense related genes differentially expressed provides many insights to the resistance mechanism to R. solanacearum and for studying potential pathways involved in responses to pathogen. Also, several candidate genes that may underline the difference in resistance to R. solanacearum between ginger and mango ginger were identified. Finally, we have developed a web resource, ginger transcriptome database, which provides public access to the data. Our study is among the first to demonstrate the use of Illumina short read sequencing for de novo transcriptome assembly and comparison in non-model species of Zingiberaceae.
authors.affiliation: Indian Institute of Spices Research, Kozhikode (Calicut), Kerala, India.
authors.forename: Duraisamy
authors.initials: D
authors.lastname: Prasath
authors.affiliation: Indian Institute of Spices Research, Kozhikode (Calicut), Kerala, India.
authors.forename: Raveendran
authors.initials: R
authors.lastname: Karthika
authors.affiliation: Indian Institute of Spices Research, Kozhikode (Calicut), Kerala, India.
authors.forename: Naduva Thadath
authors.initials: NT
authors.lastname: Habeeba
authors.affiliation: Indian Institute of Spices Research, Kozhikode (Calicut), Kerala, India.
authors.forename: Erinjery Jose
authors.initials: EJ
authors.lastname: Suraby
authors.affiliation: Indian Institute of Spices Research, Kozhikode (Calicut), Kerala, India.
authors.forename: Ottakandathil Babu
authors.initials: OB
authors.lastname: Rosana
authors.affiliation: Indian Institute of Spices Research, Kozhikode (Calicut), Kerala, India.
authors.forename: Avaroth
authors.initials: A
authors.lastname: Shaji
authors.affiliation: Indian Institute of Spices Research, Kozhikode (Calicut), Kerala, India.
authors.forename: Santhosh Joseph
authors.initials: SJ
authors.lastname: Eapen
authors.affiliation: Labindia-GPOD Research and Training Division, Thane, Maharashtra, India.
authors.forename: Uday
authors.initials: U
authors.lastname: Deshpande
authors.affiliation: Indian Institute of Spices Research, Kozhikode (Calicut), Kerala, India.
authors.forename: Muthuswamy
authors.initials: M
authors.lastname: Anandaraj
mesh_terms: D020451:Contig Mapping; D030024:Curcuma / Q000235:genetics* / Q000382:microbiology*; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant; D020939:Zingiber officinale / Q000235:genetics* / Q000382:microbiology*; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D058977:Molecular Sequence Annotation; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D043368:Ralstonia solanacearum / Q000502:physiology*; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics*; D015854:Up-Regulation / Q000235:genetics
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D014157:Transcription Factors