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Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes
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 typ...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4690246/ https://www.ncbi.nlm.nih.gov/pubmed/26699716 http://dx.doi.org/10.1186/s12864-015-2319-1 |
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author | Horiuchi, Youko Harushima, Yoshiaki Fujisawa, Hironori Mochizuki, Takako Fujita, Masahiro Ohyanagi, Hajime Kurata, Nori |
author_facet | Horiuchi, Youko Harushima, Yoshiaki Fujisawa, Hironori Mochizuki, Takako Fujita, Masahiro Ohyanagi, Hajime Kurata, Nori |
author_sort | Horiuchi, Youko |
collection | PubMed |
description | 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2319-1) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4690246 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-46902462015-12-25 Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes Horiuchi, Youko Harushima, Yoshiaki Fujisawa, Hironori Mochizuki, Takako Fujita, Masahiro Ohyanagi, Hajime Kurata, Nori BMC Genomics Research Article 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2319-1) contains supplementary material, which is available to authorized users. BioMed Central 2015-12-23 /pmc/articles/PMC4690246/ /pubmed/26699716 http://dx.doi.org/10.1186/s12864-015-2319-1 Text en © Horiuchi et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Horiuchi, Youko Harushima, Yoshiaki Fujisawa, Hironori Mochizuki, Takako Fujita, Masahiro Ohyanagi, Hajime Kurata, Nori Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes |
title | Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes |
title_full | Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes |
title_fullStr | Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes |
title_full_unstemmed | Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes |
title_short | Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes |
title_sort | global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4690246/ https://www.ncbi.nlm.nih.gov/pubmed/26699716 http://dx.doi.org/10.1186/s12864-015-2319-1 |
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