Deep-sequencing transcriptome analysis of low temperature perception in a desert tree, Populus euphratica

Abstract

BackgroundCompared with other Populus species, Populus euphratica Oliv. exhibits better tolerance to abiotic stress, especially those involving extreme temperatures. However, little is known about gene regulation and signaling pathways involved in low temperature stress responses in this species. Recent development of Illumina/Solexa-based deep-sequencing technologies has accelerated the study of global transcription profiling under specific conditions. To understand the gene network controlling low temperature perception in P. euphratica, we performed transcriptome sequencing using Solexa sequence analysis to generate a leaf transcriptome at a depth of 10 gigabases for each sample.ResultsUsing the Trinity method, 52,081,238 high-quality trimmed reads were assembled into a non-redundant set and 108,502 unigenes with an average length of 1,047 bp were generated. After performing functional annotations by aligning all-unigenes with public protein databases, 85,584 unigenes were annotated. Differentially expressed genes were investigated using the FPKM method by applying the Benjamini and Hochberg corrections. Overall, 2,858 transcripts were identified as differentially expressed unigenes in at least two samples and 131 were assigned as unigenes expressed differently in all three samples. In 4°C-treated sample and -4°C-treated sample, 1,661 and 866 differently expressed unigenes were detected at an estimated absolute log2-fold change of > 1, respectively. Among them, the respective number of up-regulated unigenes in C4 and F4 sample was 1,113 and 630, while the respective number of down-regulated ungenes is 548 and 236. To increase our understanding of these differentially expressed genes, we performed gene ontology enrichment and metabolic pathway enrichment analyses. A large number of early cold (below or above freezing temperature)-responsive genes were identified, suggesting that a multitude of transcriptional cascades function in cold perception. Analyses of multiple cold-responsive genes, transcription factors, and some key transduction components involved in ABA and calcium signaling revealed their potential function in low temperature responses in P. euphratica.ConclusionsOur results provide a global transcriptome picture of P. euphratica under low temperature stress. The potential cold stress related transcripts identified in this study provide valuable information for further understanding the molecular mechanisms of low temperature perception in P. euphratica.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-326) contains supplementary material, which is available to authorized users.

Physiological characterization, transcriptomic profiling, and microsatellite marker mining of Lycium ruthenicum

“…The functions of the Primer ALS U20 KEL U21 GZ U25 YJ U26 NMH U31 BC U31 AKS U36 SY U20+U21+U25+U26+U31+U36+D1 GEM U20+U21+U25+U26+U31+U36+D1+U25 unigenes were classified by COG and GO, and the metabolic pathways were assigned using the KEGG database. The GO classification analysis showed that the predominant terms of metabolic and cellular processes in biological process were similar to those of numerous other plants, such as Populus euphratica, Boehmeria nivea, and Ipomoea batatas (Wang et al, 2010;Liu et al, 2013;Chen et al, 2014). The predominant term of "single-organism process" is similar to Halogeton glomeratus, another salt-tolerant plant species distributed in arid regions .…”

“…The cutoff P-value after correction was 0.05 on a rigorous Bonferroni correction method (Chen et al, 2014). GO terms that meet this standard were defined as significantly enriched GO terms.…”

“…By using paired-end information, the contigs were then joined with assembled unigenes (Chen et al, 2014). A total of 68 063 unigenes were obtained with an average length of 877 bp and N50 (the shortest sequence length at 50% of the genome) of 1411 bp ( Table 2), suggesting that this non-model organism has been effectively and accurately assembled.…”

“…The 2 −∆∆C T method was used to calculate the relative quantification value. The reactions were prepared and performed as described previously (Chen et al, 2014). The gene-specific primers used in the qPCR analysis are listed in Table S1.…”

“…RNA-sequencing, which can generate massive ESTs in a short time, has been widely used in plants. Furthermore, the sequencing results could be used to explore studies of global expression patterns and networks of genes that respond to diverse stresses, such as cold, drought, and salinity in a variety of plants (Chen et al, 2014). The transcriptome dataset is a valuable resource not only for the construction of expression profiles but also for novel gene discovery as well as for a large number of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers, which are highly useful for variety identification, population structure analysis, and linkage map development, and will contribute to the acceleration of breeding programs.…”