Transcriptome sequencing and differential gene expression analysis in Viola yedoensis Makino (Fam. Violaceae) responsive to cadmium (Cd) pollution.
Viola yedoensis Makino is an important Chinese traditional medicine plant adapted to cadmium (Cd) pollution regions. Illumina sequencing technology was used to sequence the transcriptome of V. yedoensis Makino. We sequenced Cd-treated (VIYCd) and untreated (VIYCK) samples of V. yedoensis, and obtained 100,410,834 and 83,587,676 high quality reads, respectively. After de novo assembly and quantitative assessment, 109,800 unigenes were finally generated with an average length of 661 bp. We then obtained functional annotations by aligning unigenes with public protein databases including NR, NT, SwissProt, KEGG and COG. In addition, 892 differentially expressed genes (DEGs) were investigated between the two libraries of untreated (VIYCK) and Cd-treated (VIYCd) plants. Moreover, 15 randomly selected DEGs were further validated with qRT-PCR and the results were highly accordant with the Solexa analysis. This study firstly generated a successful global analysis of the V. yedoensis transcriptome and it will provide for further studies on gene expression, genomics, and functional genomics in Violaceae.
Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, China.
Jian
J
Gao
Drug Discovery Research Center of Luzhou Medical College, Luzhou, Sichuan, China.
Mao
M
Luo
Department of Pharmacy of Luzhou Medical College, Luzhou, Sichuan, China.
Ye
Y
Zhu
Department of Pharmacy of Luzhou Medical College, Luzhou, Sichuan, China.
Ying
Y
He
Department of Pharmacy of Luzhou Medical College, Luzhou, Sichuan, China.
Qin
Q
Wang
Department of Pharmacy of Luzhou Medical College, Luzhou, Sichuan, China. Electronic address: zc83good@126.com.
Chun
C
Zhang
D002104:Cadmium / Q000633:toxicity*; D004785:Environmental Pollutants / Q000633:toxicity; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D059467:Transcriptome; D032413:Viola / Q000187:drug effects* / Q000235:genetics*
D004785:Environmental Pollutants; D002104:Cadmium
Differential expression genes (DEGs); Functional annotation; Transcriptome assembly; Viola yedoensis