De Novo Transcriptome and Small RNA Analysis of Two Chinese Willow Cultivars Reveals Stress Response Genes in Salix matsudana

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.

De novo transcriptome assembly, development of EST-SSR markers and population genetic analyses for the desert biomass willow, Salix psammophila

“…The full genome sequences of S. suchowensis (http://115.29.234.170/willow/)37 and S. purpurea (http://phytozome.jgi.doe.gov/pz/portal.html#) have been released in public databases. In addition, transcriptome analyses of S. matsudana and S. viminalis have been performed to reveal their stress response mechanisms4849. However, no genomic or transcriptomic data have been reported for S. psammophila .…”

The identification and characteristics of salinity-related microRNAs in gills of Portunus trituberculatus

“…Measurement of miRNA expression levels and elucidation of the regulatory relationship between miRNA and its corresponding mRNA target are important to clarify pathways and biological processes including biotic and abiotic stress responses (Rao et al 2014). Transcriptome analyses of P. trituberculatus growth (Lv et al 2015) and responses to salinity challenged (Lv et al 2013) by high-throughput nextgeneration sequencing technology have been reported; however, the study or experimental identification of miRNAs has been no performed.…”

Origin and evolution of MIR1444 genes in Salicaceae

“…They regulate copper homeostasis and stress responses through cleaving the transcripts of PPO genes in P. trichocarpa 1789. Previously, MIR1444 genes were reported only in P. trichocarpa , although the mature sequences of miR1444 had been identified from S. matsudana and various Populus species17111214151617. In this study, we found two MIR1444 genes in various Populus species and one in Salix .…”

“…Although its genome has not been sequenced, there are 228.7 million of RNA-seq reads from five illumina runs available (Table S1)1237. Blast analysis of MIR1444 sequences against RNA-seq data of S. matsudana showed the existence of an expressed MIR1444 gene, termed sma-MIR1444 , in S. matsudana (Fig.…”

“…MIR1444 genes were reported only in P. trichocarpa 111. Mature miR1444 sequences were isolated only from Salix matsudana 12 and various Populus species, such as P. trichocarpa 111, P. euphratica 13, P. tomentosa 1415, P. beijingensis 16, and P. szechuanica 17. Both Populus and Salix are members of the family Salicaceae.…”