Abstract

BackgroundArabidopsis thaliana 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 (Oryza sativa). 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.ResultsOrgan 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 cis-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.ConclusionsThese 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.

Highlights

  • Arabidopsis thaliana is clearly established as the model plant species

  • Global analysis of transcriptome datasets a variety of array platforms are used for transcriptome analysis in rice [24,25,26], the broadest collection of datasets is available on the Affymetrix platform

  • This is advantageous as it is the same platform as used for the Arabidopsis AtGenExpress project, so all parameters for parallel array comparisons could be identical with respect to statistical analysis

Read more

Summary

Introduction

Arabidopsis thaliana 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 (Oryza sativa). A major challenge in plant biology research is to translate the knowledge learned in Arabidopsis to agronomically important species in an attempt to address the growing demand for food to feed the 9 billion people by 2050, requiring an increase of 70% in food production [3,4]. Similar outcomes or traits can be achieved using different approaches, a good example of this is the evolution of C4 photosynthesis in plants, that has arisen independently many times in angiosperm plants [11]. Comparative systems biology scale approaches reveal that changes in phenotype are often a result of small changes in the way components interact or that similar biological outcomes can be achieved by networks of different components [13]

Methods
Results
Discussion
Conclusion
Full Text
Published version (Free)

Talk to us

Join us for a 30 min session where you can share your feedback and ask us any queries you have

Schedule a call