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Abstract
BackgroundTrifoliate orange (Poncirus trifoliata (L.) Raf.) is extremely cold hardy after a full acclimation; however the underlying molecular mechanisms underlying this economically valuable trait remain poorly understood. In this study, global transcriptome profiles of trifoliate orange under cold conditions (4 °C) over a time course were generated by high-throughput sequencing.ResultsMore than 68 million high-quality reads were produced and assembled into a non-redundant data of 77,292 unigenes with an average length of 1112 bp (N50 = 1778 bp). Of these, 23,846 had significant sequence similarity to known genes and these were assigned to 61 gene ontology (GO) categories and 25 clusters of orthologous groups (COG) involved in 128 KEGG pathways. Sequences derived from cold-treated and control plants were mapped to the assembled transcriptome, resulting in the identification of 5549 differentially expressed genes (DEGs). These comprised 600 (462 up-regulated, 138 down-regulated), 2346 (1631 up-regulated, 715 down-regulated), and 5177 (2702 up-regulated, 2475 down-regulated) genes from the cold-treated samples at 6, 24 and 72 h, respectively. The accuracy of the RNA-seq derived transcript expression data was validated by analyzing the expression patterns of 17 DEGs by qPCR. Plant hormone signal transduction, plant-pathogen interaction, and secondary metabolism were the most significantly enriched GO categories amongst in the DEGs. A total of 60 transcription factors were shown to be cold responsive. In addition, a number of genes involved in the catabolism and signaling of hormones, such as abscisic acid, ethylene and gibberellin, were affected by the cold stress. Meanwhile, levels of putrescine progressively increased under cold, which was consistent with up-regulation of an arginine decarboxylase gene.ConclusionsThis dataset provides valuable information regarding the trifoliate orange transcriptome changes in response to cold stress and may help guide future identification and functional analysis of genes that are importnatn for enhancing cold hardiness.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1629-7) contains supplementary material, which is available to authorized users.
Highlights
Trifoliate orange (Poncirus trifoliata (L.) Raf.) is extremely cold hardy after a full acclimation; the underlying molecular mechanisms underlying this economically valuable trait remain poorly understood
Transcriptome sequencing and de novo assembly A cDNA library was constructed using equal amounts of RNA extracted from P. trifoliata seedlings that had been exposed to various stresses, including cold temperatures (4 °C), high salinity and drought
Further analysis showed that sequencing depth of the unigenes ranged from 0.0175 to 93,708, with an average of 49.57, while the number of reads uniquely mapped to a unigene ranged from 1 to 1,675,941
Summary
Trifoliate orange (Poncirus trifoliata (L.) Raf.) is extremely cold hardy after a full acclimation; the underlying molecular mechanisms underlying this economically valuable trait remain poorly understood. Global transcriptome profiles of trifoliate orange under cold conditions (4 °C) over a time course were generated by high-throughput sequencing. Wang et al BMC Genomics (2015) 16:555 roles in mediating cold stress response by regulating a spectrum of cold-regulated (COR) genes, collectively called the CBF regulon, through binding to the cis-acting element (CRT/DRE) within their promoters [4, 5]. Regulation of COR genes by CBFs constitutes the predominant cold signaling pathway in plants. Characterization of either positive or negative regulators of CBF genes, including ICE1 (Inducer of CBF Expression 1), HOS1 (High Expression of Osmotically Responsive Gene 1), and MYB15 has provided a more complete understanding of the complexity of CBF-mediated cold signaling [6,7,8]
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