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    Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

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    Type
    Article
    Authors
    Horiuchi, Youko
    Harushima, Yoshiaki
    Fujisawa, Hironori
    Mochizuki, Takako
    Fujita, Masahiro
    Ohyanagi, Hajime
    Kurata, Nori
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Computational Bioscience Research Center (CBRC)
    Date
    2015-12-23
    Online Publication Date
    2015-12-23
    Print Publication Date
    2015-12
    Permanent link to this record
    http://hdl.handle.net/10754/592602
    
    Metadata
    Show full item record
    Abstract
    Background Since the development of transcriptome analysis systems, many expression evolution studies characterized evolutionary forces acting on gene expression, without explicit discrimination between global expression differences and tissue specific expression differences. However, different types of gene expression alteration should have different effects on an organism, the evolutionary forces that act on them might be different, and different types of genes might show different types of differential expression between species. To confirm this, we studied differentially expressed (DE) genes among closely related groups that have extensive gene expression atlases, and clarified characteristics of different types of DE genes including the identification of regulating loci for differential expression using expression quantitative loci (eQTL) analysis data. Results We detected differentially expressed (DE) genes between rice subspecies in five homologous tissues that were verified using japonica and indica transcriptome atlases in public databases. Using the transcriptome atlases, we classified DE genes into two types, global DE genes and changed-tissues DE genes. Global type DE genes were not expressed in any tissues in the atlas of one subspecies, however changed-tissues type DE genes were expressed in both subspecies with different tissue specificity. For the five tissues in the two japonica-indica combinations, 4.6 ± 0.8 and 5.9 ± 1.5 % of highly expressed genes were global and changed-tissues DE genes, respectively. Changed-tissues DE genes varied in number between tissues, increasing linearly with the abundance of tissue specifically expressed genes in the tissue. Molecular evolution of global DE genes was rapid, unlike that of changed-tissues DE genes. Based on gene ontology, global and changed-tissues DE genes were different, having no common GO terms. Expression differences of most global DE genes were regulated by cis-eQTLs. Expression evolution of changed-tissues DE genes was rapid in tissue specifically expressed genes and those rapidly evolved changed-tissues DE genes were regulated not by cis-eQTLs, but by complicated trans-eQTLs. Conclusions Global DE genes and changed-tissues DE genes had contrasting characteristics. The two contrasting types of DE genes provide possible explanations for the previous controversial conclusions about the relationships between molecular evolution and expression evolution of genes in different species, and the relationship between expression breadth and expression conservation in evolution.
    Citation
    Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes 2015, 16 (1) BMC Genomics
    Publisher
    Springer Nature
    Journal
    BMC Genomics
    DOI
    10.1186/s12864-015-2319-1
    PubMed ID
    26699716
    Additional Links
    http://www.biomedcentral.com/1471-2164/16/1099
    Relations
    Is Supplemented By:
    • [Dataset]
      Horiuchi, Y., Harushima, Y., Fujisawa, H., Mochizuki, T., Fujita, M., Ohyanagi, H., & Kurata, N. (2015). Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes. Figshare. https://doi.org/10.6084/m9.figshare.c.3643793. DOI: 10.6084/m9.figshare.c.3643793 HANDLE: 10754/624141
    ae974a485f413a2113503eed53cd6c53
    10.1186/s12864-015-2319-1
    Scopus Count
    Collections
    Articles; Biological and Environmental Sciences and Engineering (BESE) Division; Computational Bioscience Research Center (CBRC)

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