De novo transcriptome sequence assembly and analysis of RNA silencing genes of Nicotiana benthamiana.

ABSTRACT:

Background

Nicotiana benthamiana has been widely used for transient gene expression assays and as a model plant in the study of plant-microbe interactions, lipid engineering and RNA silencing pathways. Assembling the sequence of its transcriptome provides information that, in conjunction with the genome sequence, will facilitate gaining insight into the plant's capacity for high-level transient transgene expression, generation of mobile gene silencing signals, and hyper-susceptibility to viral infection.

Methodology/results

RNA-seq libraries from 9 different tissues were deep sequenced and assembled, de novo, into a representation of the transcriptome. The assembly, of 16GB of sequence, yielded 237,340 contigs, clustering into 119,014 transcripts (unigenes). Between 80 and 8

SUBMITTER: Nakasugi K 

PROVIDER: S-EPMC3610648 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature