title: A comparison of the low temperature transcriptomes of two tomato genotypes that differ in freezing tolerance: Solanum lycopersicum and Solanum habrochaites.
abstract: BACKGROUND
  Solanum lycopersicum and Solanum habrochaites are closely related plant species; however, their cold tolerance capacities are different. The wild species S. habrochaites is more cold tolerant than the cultivated species S. lycopersicum.
  
  
  RESULTS
  The transcriptomes of S. lycopersicum and S. habrochaites leaf tissues under cold stress were studied using Illumina high-throughput RNA sequencing. The results showed that more than 200 million reads could be mapped to identify genes, microRNAs (miRNAs), and alternative splicing (AS) events to confirm the transcript abundance under cold stress. The results indicated that 21% and 23% of genes were differentially expressed in the cultivated and wild tomato species, respectively, and a series of changes in S. lycopersicum and S. habrochaites transcriptomes occur when plants are moved from warm to cold conditions. Moreover, the gene expression patterns for S. lycopersicum and S. habrochaites were dissimilar; however, there were some overlapping genes that were regulated by low temperature in both tomato species. An AS analysis identified 75,885 novel splice junctions among 172,910 total splice junctions, which suggested that the relative abundance of alternative intron isoforms in S. lycopersicum and S. habrochaites shifted significantly under cold stress. In addition, we identified 89 miRNA sequences that may regulate relevant target genes. Our data indicated that some miRNAs (e.g., miR159, miR319, and miR6022) play roles in the response to cold stress.
  
  
  CONCLUSIONS
  Differences in gene expression, AS events, and miRNAs under cold stress may contribute to the observed differences in cold tolerance of these two tomato species.
authors.affiliation: Heilongjiang Provincial Key University Laboratory of Agricultural Functional Genes, College of Life Science, Northeast Agricultural University, Harbin, 150030, China. chy810501@163.com.
authors.forename: Hongyu
authors.initials: H
authors.lastname: Chen
authors.affiliation: College of Horticulture, Northeast Agricultural University, Harbin, 150030, China. xiuling.chen@ymail.com.
authors.forename: Xiuling
authors.initials: X
authors.lastname: Chen
authors.affiliation: ABLife, Inc, Wuhan, 430075, China. dongchen@ablife.cc.
authors.forename: Dong
authors.initials: D
authors.lastname: Chen
authors.affiliation: College of Horticulture, Northeast Agricultural University, Harbin, 150030, China. lijf_2005@126.com.
authors.forename: Jingfu
authors.initials: J
authors.lastname: Li
authors.affiliation: ABLife, Inc, Wuhan, 430075, China. yizhang@ablife.cc.
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Heilongjiang Provincial Key University Laboratory of Agricultural Functional Genes, College of Life Science, Northeast Agricultural University, Harbin, 150030, China. axwang@neau.edu.cn.|College of Horticulture, Northeast Agricultural University, Harbin, 150030, China. axwang@neau.edu.cn.
authors.forename: Aoxue
authors.initials: A
authors.lastname: Wang
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D017398:Alternative Splicing / Q000235:genetics; D016000:Cluster Analysis; D003080:Cold Temperature; D020224:Expressed Sequence Tags; D005615:Freezing; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D032322:Solanum / Q000235:genetics* / Q000502:physiology*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D035683:MicroRNAs