Sequencing and characterization of leaf transcriptomes of six diploid Nicotiana species.
BACKGROUND
Nicotiana belongs to the Solanaceae family that includes important crops such as tomato, potato, eggplant, and pepper. Nicotiana species are of worldwide economic importance and are important model plants for scientific research. Here we present the comparative analysis of the transcriptomes of six wild diploid Nicotiana species. Wild relatives provide an excellent study system for the analysis of the genetic basis for various traits, especially disease resistance.


RESULTS
Whole transcriptome sequencing (RNA-seq) was performed for leaves of six diploid Nicotiana species, i.e. Nicotiana glauca, Nicotiana noctiflora, Nicotiana cordifolia, Nicotiana knightiana, Nicotiana setchellii and Nicotiana tomentosiformis. For each species, 9.0-22.3 Gb high-quality clean data were generated, and 67,073-182,046 transcripts were assembled with lengths greater than 100 bp. Over 90 % of the ORFs in each species had significant similarity with proteins in the NCBI non-redundant protein sequence (NR) database. A total of 2491 homologs were identified and used to construct a phylogenetic tree from the respective transcriptomes in Nicotiana. Bioinformatic analysis identified resistance gene analogs, major transcription factor families, and alkaloid transporter genes linked to plant defense.


CONCLUSIONS
This is the first report on the leaf transcriptomes of six wild Nicotiana species by Illumina paired-end sequencing and de novo assembly without a reference genome. These sequence resources hopefully will provide an opportunity for identifying genes involved in plant defense and several important quality traits in wild Nicotiana and will accelerate functional genomic studies and genetic improvement efforts of Nicotiana or other important Solanaceae crops in the future.
Faculty of Life Science and Technology, Kunming University of Science and Technology, South Jingming Road No.727, Kunming, 650500 Yunnan China.
Ni
N
Long
Guizhou Tobacco Research Institute, North Yuntan Road, Jinyang District, Guiyang, 550003 Guizhou China.
Xueliang
X
Ren
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming, 650223 Yunnan China.
Zhidan
Z
Xiang
Faculty of Life Science and Technology, Kunming University of Science and Technology, South Jingming Road No.727, Kunming, 650500 Yunnan China.
Wenting
W
Wan
Faculty of Life Science and Technology, Kunming University of Science and Technology, South Jingming Road No.727, Kunming, 650500 Yunnan China ; Biological Big Data College, Yunnan Agricultural University, Kunming, 650201 Yunnan China.
Yang
Y
Dong
De novo assembly; Nicotiana; Nicotiana cordifolia; Nicotiana glauca; Nicotiana knightiana; Nicotiana noctiflora; Nicotiana setchellii; Nicotiana tomentosiformis; Phylogenetic relationship; Transcriptome