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Open Access Research article

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

Jinhuan Chen12, Qianqian Tian2, Tao Pang1, Libo Jiang3, Rongling Wu34, Xinli Xia12* and Weilun Yin12*

Author Affiliations

1 National Engineering Laboratory for Tree Breeding, Beijing 100083, China

2 College of Biological Sciences and technology, Beijing Forestry University, Beijing 100083, China

3 Center for Computational Biology, Beijing Forestry University, Beijing 100083, China

4 Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA 17033, USA

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BMC Genomics 2014, 15:326  doi:10.1186/1471-2164-15-326

Published: 1 May 2014

Abstract

Background

Compared 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.

Results

Using 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.

Conclusions

Our 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.

Keywords:
Illumina/Solexa; Low temperature; Populus euphratica; Transcriptome