Transcriptome profiling of Populus tomentosa under cold stress.

• A transcriptome of Populus tomentosa during cold stress has been analyzed. • This work identified numerous cold-related genes involved in sugar metabolisms, antioxidant defense system, hormone signal transduction and photosynthesis. • Our study provides valuable information for further studies on cold response mechanisms and genetic improvement of cold tolerance in Populus tomentosa. Low temperature affects the growth, development, and even survival in plants. Populus tomentosa is a major industrial tree species used for timber and pulp manufacturing in northern China. Low temperature is an important stress factor for this species, and restricts its extensive cultivation and distribution. To face this problem, an understanding of the molecular mechanism underlying responses to cold stress in this species is necessary for molecular breeding. In this study, Illumina RNA-sequencing was employed to comprehensively investigate the gene expression profiles of P. tomentosa in response to cold stress. Two cDNA libraries from cold-treated and control samples were constructed and sequenced, generating a total of 94,226 unigenes. Of these, 1978 were differentially expressed, with 1468 upregulated and 510 downregulated. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses identified the relevant biological functions and metabolic pathways of these differentially expressed genes. Based on enrichment results, a diverse range of cold response candidate genes were obtained and mainly involved in sugar metabolism, antioxidant defense system, hormone signal transduction, and photosynthesis, such as genes encoding sucrose synthase, superoxide dismutase, brassinosteroid-signaling kinase, and ferredoxin. Various transcription factors with divergent expression patterns were identified. Finally, RNA-seq data were validated using real-time quantitative polymerase chain reaction analyses. This study provides valuable information for further studies on cold response mechanisms and genetic improvement of cold tolerance in P. tomentosa. [ABSTRACT FROM AUTHOR]