Abstract
Salix matsudana Koidz. is a deciduous, rapidly growing, and drought resistant tree and is one of the most widely distributed and commonly cultivated willow species in China. Currently little transcriptomic and small RNAomic data are available to reveal the genes involve in the stress resistant in S. matsudana. Here, we report the RNA-seq analysis results of both transcriptome and small RNAome data using Illumina deep sequencing of shoot tips from two willow variants(Salix. matsudana and Salix matsudana Koidz. cultivar ‘Tortuosa’). De novo gene assembly was used to generate the consensus transcriptome and small RNAome, which contained 106,403 unique transcripts with an average length of 944 bp and a total length of 100.45 MB, and 166 known miRNAs representing 35 miRNA families. Comparison of transcriptomes and small RNAomes combined with quantitative real-time PCR from the two Salix libraries revealed a total of 292 different expressed genes(DEGs) and 36 different expressed miRNAs (DEMs). Among the DEGs and DEMs, 196 genes and 24 miRNAs were up regulated, 96 genes and 12 miRNA were down regulated in S. matsudana. Functional analysis of DEGs and miRNA targets showed that many genes were involved in stress resistance in S. matsudana. Our global gene expression profiling presents a comprehensive view of the transcriptome and small RNAome which provide valuable information and sequence resources for uncovering the stress response genes in S. matsudana. Moreover the transcriptome and small RNAome data provide a basis for future study of genetic resistance in Salix.
Highlights
The increasing concern about climate change and energy security has resulted in the focusing on the economic importance of Salix species, given their utility for bioenergy production
Overview of the deep sequencing datasets many studies have reported the transcriptome analysis of willow, here have been no studies on mRNA and miRNA expression profiles in S. matsudana
This work demonstrates that RNA-seq is a useful and effective tool for de novo transcriptome and small RNA assembly. It facilitates the identification of differentially expressed miRNAs and their target genes between the two willow cultivars, even in the absence of a genomic database
Summary
The increasing concern about climate change and energy security has resulted in the focusing on the economic importance of Salix species, given their utility for bioenergy production. Plants have to tolerate many abiotic and biotic stresses, which are serious threats to agriculture and forestry These common environmental stresses include salinity, extreme temperatures, drought, chemical toxicity, oxidative stress, pests, and pathogen infection. Cultivar ‘Tortuosa’ using deep sequencing technology to discover the differentially expressed genes and miRNAs in stem shoots of the two varieties of Salix. Our results showed that 196 transcripts, which are mainly related to plant abiotic and biotic stress responses, are commonly up-regulated in S. matsudana. These up-regulated genes in S. matsudana included a set of biotic and abiotic stress response genes, such as pathogen defense, insect resistance, antibiotics tolerance, antioxidant, and hormone related genes.
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