title: Effects of low temperature on mRNA and small RNA transcriptomes in Solanum lycopersicoides leaf revealed by RNA-Seq.
abstract: 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.
authors.affiliation: Heilongjiang Provincial Key University Laboratory of Agricultural Functional Genes, College of Life Science, Northeast Agricultural University, Harbin 150030, China.
authors.forename: Hongyu
authors.initials: H
authors.lastname: Chen
authors.affiliation: College of Horticulture, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin 150030, China.
authors.forename: Xiuling
authors.initials: X
authors.lastname: Chen
authors.affiliation: Heilongjiang Provincial Key University Laboratory of Agricultural Functional Genes, College of Life Science, Northeast Agricultural University, Harbin 150030, China.
authors.forename: Xinfeng
authors.initials: X
authors.lastname: Chai
authors.affiliation: Heilongjiang Provincial Key University Laboratory of Agricultural Functional Genes, College of Life Science, Northeast Agricultural University, Harbin 150030, China.
authors.forename: Youwen
authors.initials: Y
authors.lastname: Qiu
authors.affiliation: Heilongjiang Provincial Key University Laboratory of Agricultural Functional Genes, College of Life Science, Northeast Agricultural University, Harbin 150030, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Gong
authors.affiliation: College of Life Sciences and Agriculture & Forestry, Qiqihar University, Qiqihar 161006, China.
authors.forename: Zhenzhu
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: College of Horticulture, Northeast Agricultural University, Harbin 150030, China.
authors.forename: Tingting
authors.initials: T
authors.lastname: Wang
authors.affiliation: College of Horticulture, Northeast Agricultural University, Harbin 150030, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: College of Horticulture, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin 150030, China.
authors.forename: Jingfu
authors.initials: J
authors.lastname: Li
authors.affiliation: Heilongjiang Provincial Key University Laboratory of Agricultural Functional Genes, College of Life Science, Northeast Agricultural University, Harbin 150030, China; College of Horticulture, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin 150030, China. Electronic address: axwang@neau.edu.cn.
authors.forename: Aoxue
authors.initials: A
authors.lastname: Wang
mesh_terms: D000064:Acclimatization / Q000235:genetics / Q000502:physiology; D003081:Cold Climate; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D035683:MicroRNAs / Q000235:genetics; D018515:Plant Leaves / Q000235:genetics / Q000502:physiology; D012333:RNA, Messenger / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*; D017423:Sequence Analysis, RNA; D032322:Solanum / Q000235:genetics* / Q000502:physiology*; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D018749:RNA, Plant
keywords: Cold; RNA sequencing; Solanum lycopersicoides; Transcriptome; microRNA