Research On The Drought-responsive Transcriptome Of Populus Using RNA-Seq

Drought is a major limitation to the growth and productivity of trees in genus populus. P. simonii is one of the most popular planted forest species in China and it is a drought-tolerant and low temperature-tolerant species, so it could be an ideal material to study the mechanism of drought resistance. P. deltoides is also wildly planted, but it is not a kind of drought-tolerant species. In order to explore the mechanism of poplar in response to drought, the transcriptomes of P. deltoides and P. simonii grown under drought and normal conditions were sequenced in this study. We performed several procedures for RNA-Seq data analysis, including sequence quality controlling, mapping, detection of different expression genes, functional annotation, identification of new transcripts and new splice variants.After quality controlling, a total of 17.33 Gbp data was obtained. We mapped the clean data of each sample to the reference genome and the reference genes. Then different expression genes(DEGs) were detected by comparing the gene expression level between different-treatment samples. Functional categorization and KEGG Pathway analysis revealed the main biological functions of differentially expressed genes and the biological process they involved in. Between the P. deltoides normal group and P. deltoides drought-treatment group, a total of 791 DEGs played an important role in response to stress. Between the P. simonii normal group and P. simonii drought-treatment group, there were 639 DEGs playing an important role in response to stress. We found 7 up-regulated genes annotated with ABF-like genes, 8 up-regulated genes annotated with ERF-like genes, 17 up-regulated genes annotated with MYC-like genes in both Populus species. We also found that there were 3 more up-regulated genes annotated with ABF-like genes, 3 more up-regulated genes annotated with ERF-like genes, and 8 more up-regulated genes annotated with MYC-like genes in P. simonii, which had no significant changes in P. deltoides. In addition, by comparing our assembled transcriptomes with available gene information, we detected 300 novel transcripts from the sample of normal P. deltoides, 333 novel transcripts from the sample of drought-treated P. deltoides, 235 novel transcripts from the sample of normal P. simonii, and 235 novel transcripts from the sample of drought-treated P. simonii. Finally, we studied 4 kinds of alternative splicing events: Alternative 5’splice site(A5SS), Alternative 3’splice site(A3SS), Exon skipping(ES) and Intron retention(IR). The result showed that the frequency of occurrence of IR was much higher than the other 3 kinds of alternative splicing types.