title: Comparative transcriptome analysis of tomato (Solanum lycopersicum) in response to exogenous abscisic acid.
abstract: BACKGROUND
  Abscisic acid (ABA) can regulate the expressions of many stress-responsive genes in plants. However, in defense responses to pathogens, mounting evidence suggests that ABA plays variable roles. Little information exists about genome-wide gene expression in ABA responses in tomato (Solanum lycopersicum L.), a model fruit crop plant.
  
  
  RESULTS
  Global transcriptome profiles of tomato leaf responses to exogenous ABA were generated using Illumina RNA-sequencing. More than 173 million base pair reads were mapped onto the tomato reference genome and the expression pattern differences between treated and control leaves were assessed. In total, 50,616 transcripts were generated. Among them, 42,583 were functionally annotated in the NCBI non-redundant database and 47,877 in the tomato genome reference. Additionally, 31,107 transcripts were categorized into 57 functional groups based on Gene Ontology terms, and 14,371 were assigned to 310 Kyoto Encyclopedia of Genes and Genomes pathways. In both the ABA treatment and control samples, 39,671 transcripts were available to analyze their expressions, of which 21,712 (54.73%) responded to exogenous ABA. Of these transcripts, 2,787 were significantly differently expressed genes (DEGs). Many known and novel ABA-induced and -repressed genes were found. Exogenous ABA can influence the ABA signaling pathway with PYR/PYL/RCARs-PP2Cs-SnRK2s as the center. Eighteen PYL genes were detected. A large number of genes related to various transcription factors, heat shock proteins, pathogen resistance, and the salicylic acid, jasmonic acid, and ethylene signaling pathways were up-regulated by exogenous ABA.
  
  
  CONCLUSIONS
  The results indicated that ABA has the potential to improve pathogen-resistance and abiotic stress tolerance in tomato. This study presents the global expression analysis of ABA-regulated transcripts in tomato and provides a robust database for investigating the functions of genes induced by ABA.
authors.affiliation: Chengdu Institute of Biology, Chinese Academy of Sciences, No 9, Section 4, Renmin South Road, Chengdu 610041, China. maxr@cib.ac.cn.
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.forename: Xiang
authors.initials: X
authors.lastname: Tao
authors.forename: Xiao-Mei
authors.initials: XM
authors.lastname: Tang
authors.forename: Liang
authors.initials: L
authors.lastname: Xiao
authors.forename: Jiao-Long
authors.initials: JL
authors.lastname: Sun
authors.forename: Xue-Feng
authors.initials: XF
authors.lastname: Yan
authors.forename: Dan
authors.initials: D
authors.lastname: Li
authors.forename: Hong-Yuan
authors.initials: HY
authors.lastname: Deng
authors.forename: Xin-Rong
authors.initials: XR
authors.lastname: Ma
mesh_terms: D000040:Abscisic Acid / Q000494:pharmacology* / Q000502:physiology; D030541:Databases, Genetic; D060467:Disease Resistance / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant; D006360:Heat-Shock Proteins / Q000235:genetics / Q000378:metabolism; D018551:Solanum lycopersicum / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D010937:Plant Growth Regulators / Q000494:pharmacology* / Q000502:physiology; D018515:Plant Leaves / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D006360:Heat-Shock Proteins; D010937:Plant Growth Regulators; D010940:Plant Proteins; D014157:Transcription Factors; D000040:Abscisic Acid