Common and distinct organ and stress responsive transcriptomic patterns in <it>Oryza sativa </it>and <it>Arabidopsis thaliana</it>

<p>Abstract</p> <p>Background</p> <p><it>Arabidopsis thaliana </it>is clearly established as the model plant species. Given the ever-growing demand for food, there is a need to translate the knowledge learned in Arabidopsis to agronomically important species...

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Main Authors: Castleden Ian, Narsai Reena, Whelan James
Format: Article
Language:English
Published: BMC 2010-11-01
Series:BMC Plant Biology
Online Access:http://www.biomedcentral.com/1471-2229/10/262
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spelling doaj-e7d816d91f0a4ac99c5af141bf03b6ae2020-11-24T23:02:01ZengBMCBMC Plant Biology1471-22292010-11-0110126210.1186/1471-2229-10-262Common and distinct organ and stress responsive transcriptomic patterns in <it>Oryza sativa </it>and <it>Arabidopsis thaliana</it>Castleden IanNarsai ReenaWhelan James<p>Abstract</p> <p>Background</p> <p><it>Arabidopsis thaliana </it>is clearly established as the model plant species. Given the ever-growing demand for food, there is a need to translate the knowledge learned in Arabidopsis to agronomically important species, such as rice (<it>Oryza sativa</it>). To gain a comparative insight into the similarities and differences into how organs are built and how plants respond to stress, the transcriptomes of Arabidopsis and rice were compared at the level of gene orthology and functional categorisation.</p> <p>Results</p> <p>Organ specific transcripts in rice and Arabidopsis display less overlap in terms of gene orthology compared to the orthology observed between both genomes. Although greater overlap in terms of functional classification was observed between root specific transcripts in rice and Arabidopsis, this did not extend to flower, leaf or seed specific transcripts. In contrast, the overall abiotic stress response transcriptome displayed a significantly greater overlap in terms of gene orthology compared to the orthology observed between both genomes. However, ~50% or less of these orthologues responded in a similar manner in both species. In fact, under cold and heat treatments as many or more orthologous genes responded in an opposite manner or were unchanged in one species compared to the other. Examples of transcripts that responded oppositely include several genes encoding proteins involved in stress and redox responses and non-symbiotic hemoglobins that play central roles in stress signalling pathways. The differences observed in the abiotic transcriptomes were mirrored in the presence of <it>cis</it>-acting regulatory elements in the promoter regions of stress responsive genes and the transcription factors that potentially bind these regulatory elements. Thus, both the abiotic transcriptome and its regulation differ between rice and Arabidopsis.</p> <p>Conclusions</p> <p>These results reveal significant divergence between Arabidopsis and rice, in terms of the abiotic stress response and its regulation. Both plants are shown to employ unique combinations of genes to achieve growth and stress responses. Comparison of these networks provides a more rational approach to translational studies that is based on the response observed in these two diverse plant models.</p> http://www.biomedcentral.com/1471-2229/10/262
collection DOAJ
language English
format Article
sources DOAJ
author Castleden Ian
Narsai Reena
Whelan James
spellingShingle Castleden Ian
Narsai Reena
Whelan James
Common and distinct organ and stress responsive transcriptomic patterns in <it>Oryza sativa </it>and <it>Arabidopsis thaliana</it>
BMC Plant Biology
author_facet Castleden Ian
Narsai Reena
Whelan James
author_sort Castleden Ian
title Common and distinct organ and stress responsive transcriptomic patterns in <it>Oryza sativa </it>and <it>Arabidopsis thaliana</it>
title_short Common and distinct organ and stress responsive transcriptomic patterns in <it>Oryza sativa </it>and <it>Arabidopsis thaliana</it>
title_full Common and distinct organ and stress responsive transcriptomic patterns in <it>Oryza sativa </it>and <it>Arabidopsis thaliana</it>
title_fullStr Common and distinct organ and stress responsive transcriptomic patterns in <it>Oryza sativa </it>and <it>Arabidopsis thaliana</it>
title_full_unstemmed Common and distinct organ and stress responsive transcriptomic patterns in <it>Oryza sativa </it>and <it>Arabidopsis thaliana</it>
title_sort common and distinct organ and stress responsive transcriptomic patterns in <it>oryza sativa </it>and <it>arabidopsis thaliana</it>
publisher BMC
series BMC Plant Biology
issn 1471-2229
publishDate 2010-11-01
description <p>Abstract</p> <p>Background</p> <p><it>Arabidopsis thaliana </it>is clearly established as the model plant species. Given the ever-growing demand for food, there is a need to translate the knowledge learned in Arabidopsis to agronomically important species, such as rice (<it>Oryza sativa</it>). To gain a comparative insight into the similarities and differences into how organs are built and how plants respond to stress, the transcriptomes of Arabidopsis and rice were compared at the level of gene orthology and functional categorisation.</p> <p>Results</p> <p>Organ specific transcripts in rice and Arabidopsis display less overlap in terms of gene orthology compared to the orthology observed between both genomes. Although greater overlap in terms of functional classification was observed between root specific transcripts in rice and Arabidopsis, this did not extend to flower, leaf or seed specific transcripts. In contrast, the overall abiotic stress response transcriptome displayed a significantly greater overlap in terms of gene orthology compared to the orthology observed between both genomes. However, ~50% or less of these orthologues responded in a similar manner in both species. In fact, under cold and heat treatments as many or more orthologous genes responded in an opposite manner or were unchanged in one species compared to the other. Examples of transcripts that responded oppositely include several genes encoding proteins involved in stress and redox responses and non-symbiotic hemoglobins that play central roles in stress signalling pathways. The differences observed in the abiotic transcriptomes were mirrored in the presence of <it>cis</it>-acting regulatory elements in the promoter regions of stress responsive genes and the transcription factors that potentially bind these regulatory elements. Thus, both the abiotic transcriptome and its regulation differ between rice and Arabidopsis.</p> <p>Conclusions</p> <p>These results reveal significant divergence between Arabidopsis and rice, in terms of the abiotic stress response and its regulation. Both plants are shown to employ unique combinations of genes to achieve growth and stress responses. Comparison of these networks provides a more rational approach to translational studies that is based on the response observed in these two diverse plant models.</p>
url http://www.biomedcentral.com/1471-2229/10/262
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