Abstract
Advances in transcriptome sequencing provide fast, cost-effective and reliable approach to generate large expression datasets especially suitable for non-model species to identify putative genes, key pathway and regulatory mechanism. Citronella (Cymbopogon winterianus) is an aromatic medicinal grass used for anti-tumoral, antibacterial, anti-fungal, antiviral, detoxifying and natural insect repellent properties. Despite of having number of utilities, the genes involved in terpenes biosynthetic pathway is not yet clearly elucidated. The present study is a pioneering attempt to generate an exhaustive molecular information of secondary metabolite pathway and to increase genomic resources in Citronella. Using high-throughput RNA-Seq technology, root and leaf transcriptome was analysed at an unprecedented depth (11.7 Gb). Targeted searches identified majority of the genes associated with metabolic pathway and other natural product pathway viz. antibiotics synthesis along with many novel genes. Terpenoid biosynthesis genes comparative expression results were validated for 15 unigenes by RT-PCR and qRT-PCR. Thus the coverage of these transcriptome is comprehensive enough to discover all known genes of major metabolic pathways. This transcriptome dataset can serve as important public information for gene expression, genomics and function genomics studies in Citronella and shall act as a benchmark for future improvement of the crop.
Highlights
Advances in sequencing technology and bioinformatics tools for annotation of the transcriptome provides a rapid, cost-effective route to develop sequence resources for organisms in which the assembly of a complete genome sequence remains out of reach
The paired end (PE) library of leaf and root tissue with an average size of 518 bp and 959 bp respectively were subjected to whole transcriptome sequencing
High GC content is found to be associated with other genomic characteristics i.e., higher gene density[33], higher recombination[34], expression level[35] and replication timing[36]
Summary
Advances in sequencing technology and bioinformatics tools for annotation of the transcriptome provides a rapid, cost-effective route to develop sequence resources for organisms in which the assembly of a complete genome sequence remains out of reach. A pioneering attempt was made to sequence whole transcriptome of leaf and root tissue of C. winterianus so as to gain information on terpenoid synthesis gene with comparative DEG analysis. On the basis of Nr annotation, the Blast2GO program[42] could annotate a total 27,876 unigenes (16,155 of leaf and 11,721 of root transcriptome) with BLAST matches to known proteins were assigned to gene ontology classes with 56,622 functional terms.
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call