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
ArticleAuthors
Horiuchi, YoukoHarushima, Yoshiaki
Fujisawa, Hironori
Mochizuki, Takako
Fujita, Masahiro
Ohyanagi, Hajime
Kurata, Nori
KAUST Department
Biological and Environmental Sciences and Engineering (BESE) DivisionComputational Bioscience Research Center (CBRC)
Date
2015-12-23Online Publication Date
2015-12-23Print Publication Date
2015-12Permanent link to this record
http://hdl.handle.net/10754/592602
Metadata
Show full item recordAbstract
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 GenomicsPublisher
Springer NatureJournal
BMC GenomicsPubMed ID
26699716Additional Links
http://www.biomedcentral.com/1471-2164/16/1099Relations
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
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