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Effects of low temperature on mRNA and small RNA transcriptomes in Solanum lycopersicoides leaf revealed by RNA-Seq
- Chen, Hongyu, Chen, Xiuling, Chai, Xinfeng, Qiu, Youwen, Gong, Chao, Zhang, Zhenzhu, Wang, Tingting, Zhang, Yue, Li, Jingfu, Wang, Aoxue
- Biochemical and biophysical research communications 2015 v.464 pp. 768-773
- Arabidopsis, Chinese cabbage, Chorispora, Solanum commersonii, Solanum lycopersicoides, Solanum tuberosum, cold stress, cold tolerance, cold treatment, gene expression regulation, high-throughput nucleotide sequencing, leaves, messenger RNA, microRNA, quantitative polymerase chain reaction, temperature, tomatoes, transcription (genetics), transcriptome, unigenes
- The plant low temperature tolerance mechanisms have been studied in the Arabidopsis, tomato, Solanum commersonii, Solanum tuberosum, Chorispora bungeana, and Chinese cabbage at the transcriptional level. Some genome-wide works to identify cold-regulated genes, but no comprehensive research of the Solanum lycopersicoides transcriptome under low temperature stress have been performed. S. lycopersicoides is more freeze-tolerant than the cultivated tomato. We analyzed the low temperature transcriptomes and small RNA fractions of S. lycopersicoides leaf tissue using an Illumina platform for high-throughput RNA sequencing (RNA-seq). There were 59,286 unigenes obtained using de novo assembly, and 2052 down-regulated and 2409 up-regulated unigenes were identified in response to chilling. The expression of six cold-regulated genes was confirmed by qPCR. Some biological processes were showed, by gene ontology term enrichment analysis of the cold-regulated genes, including ‘response to stimulus’, ‘signaling’, and ‘cell killing’ in the response of S. lycopersicoides to chilling. In addition, we identified a total of 952 novel miRNA candidates that may regulate relevant target genes. Our data indicated that certain miRNAs (e.g., sly-miR156a, sly-miR397, and unconservative_SL2.50ch00_21686) play roles in response to low temperature stress. Sequencing of mRNAs and miRNAs revealed new genes and allowed us to have new assumptions for a low temperature tolerance mechanism.