Huaizhi Mu, Yuting Gao, Fushan Cheng, Lin Lin, Gerong Wang, Fucai Xia
Transcriptomic analysis of different tissues in Korean arborvitae
Dendrobiology 2019, vol. 81: 31-39
Korean arborvitae (Thuja koraiensis) is an evergreen shrub or small tree native to Korea and the extreme Changbai Mountain of China threatened by habitat loss. Due to the limited genomic sources of Korean arborvitae, it is important to explore transcriptome to understand this economically important plant. We used RNA-seq technology to characterize the transcriptome of root, stem and leaf in Korean arborvitae, respectively. Based on the bioinformatics analysis of assembled transcriptome data, transcriptional pathways and differentially expressed genes (DEGs) were identified.
There were 152.26 million reads generated, and 446,568 unigenes with a mean size of 423.51 nt obtained via de novo assembly. Of these, 204,091 unigenes (45.70%) were further annotated by comparison to public protein databases. A total of 63,495 unigenes (14.22%) were associated into 130 pathways by searching against the KEGG database. DEGs analysis identified 11,890, 5,900 and 10,136 DEGs from the comparison of root vs. stem, root vs. leaf and stem vs. leaf, respectively. Besides, photosynthesis, plant hormone signal transduction and metabolism and biosynthesis of sugar and amino acids were changed in different tissues. We obtained 446,568 unigenes in Korean arborvitae and 11,890, 5,900 and 10,136 DEGs from the comparison of root vs. stem, root vs. leaf and stem vs. leaf, respectively. These results will aid in understanding and carrying out future studies on the molecular basis of Korean arborvitae and contribute to future artificial production and applications.
Keywords: Thuja koraiensis, transcriptome, tissue specific