Transcriptomic analysis of Casuarina equisetifolia L. in responses to cold stress

Casuarina species are valued as pioneer trees for coastal shelter forest construction. However, low temperature stress limits its cultivation expansion, fast growth, and high yield. To investigate the molecular mechanism by which Casuarina trees cope with cold stress and to provide a comprehensive sequence resource for further molecular genetic research on Casuarina species, we employed RNA-Seq technology to study the genome-wide expression profiles during cold stress in Casuarina equisetifolia L. Four cDNA libraries constructed from mRNAs of control and cold-treated seedlings (at -5 degrees C for 5 h) were sequenced by using the Illumina sequencing platform. A total of 118,270 unigenes were obtained by de novo assembly, creating an initial reference transcriptome dataset of C. equisetifolia. Among these unigenes, 4639 were identified as early cold response genes including 2331 cold up-regulated and 2308 down-regulated. Furthermore, the expression changes of 18 genes under cold stress from RNA-Seq analysis were further validated by reverse transcription quantitative polymerase chain reaction (RT-qPCR). Functional network analysis indicate that modifications in the expression of genes involved in signal regulation by transcription factors, metabolic pathways including synthesis of carbohydrate, secondary metabolites, and antioxidant enzymes might play vital roles in responses to cold stress in C. equisetifolia. This study represents the first large-scale transcriptome annotation of C. equisetifolia and may be beneficial to elucidate the cold response mechanisms of Casuarina trees and will be useful in cold-tolerant Casuarina species breeding.