Analysis of Transcriptome and Alternative Splicing Landscape in Pineapple

  • Ching Man Wai
  • Brian Powell
  • Ray Ming
  • Xiang Jia MinEmail author
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 22)


Gene expression profiling and alternative splicing (AS) landscapes were analyzed in pineapple. Among 27,024 protein-coding genes, based on the transcripts to gene models mapping data, a total of 17,308 predicted genes are supported by expressed transcripts. Between leaf and root tissue, 795 genes were upregulated in leaf tissue relative to root tissue, and 1391 genes were upregulated in root tissue relative to leaf tissue. Between young fruit tissue and ripening fruit tissue, 931 genes were upregulated, and 189 genes were downregulated in ripening fruit tissue relative to young fruit tissue. Genes involved in crassulacean acid metabolism (CAM) pathway and in ethylene biosynthesis and responses were identified and further analyzed in details. A total of 10,348 AS events involving 13,449 unique transcripts which were generated from a total of 5146 genes were identified. The identification of differentially expressed genes, assembled transcripts, along with the identified AS isoforms and events, provides a solid foundation for further examination of the gene functions in pineapple metabolism, growth, development, and fruit ripening. The data are available at Plant Alternative Splicing Database (


Alternative splicing Expressed sequence tags Gene expression mRNA Transcriptome Pineapple 



Alternative splicing


Crassulacean acid metabolism


Expressed sequence tags


Fragments per kilobase of exon model per million mapped reads


Pineapple unique transcript



The work was supported by the University of Illinois at Urbana-Champaign to RM and the Youngstown State University Research Professorship award to XJM.


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Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • Ching Man Wai
    • 1
  • Brian Powell
    • 2
  • Ray Ming
    • 1
  • Xiang Jia Min
    • 3
    Email author
  1. 1.Department of Plant BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  2. 2.Department of Computer Science and Information SystemsYoungstown State UniversityYoungstownUSA
  3. 3.Center for Applied Chemical Biology, Department of Biological SciencesYoungstown State UniversityYoungstownUSA

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