Common and distinct organ and stress responsive transcriptomic patterns in Oryza sativa and Arabidopsis thaliana

Narsai, Reena; Castleden, Ian; Whelan, James
January 2010
BMC Plant Biology;2010, Vol. 10, p262
Academic Journal
Background: 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). 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. Results: 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 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. Conclusions: 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.


Related Articles

  • Conservation and Diversification of Meristem Maintenance Mechanism in Oryza sativa: Function of the FLORAL ORGAN NUMBER2 Gene. Suzaki, Takuya; Toriba, Taiyo; Fujimoto, Masaru; Tsutsumi, Nobuhiro; Kitano, Hidemi; Hirano, Hiro-Yuki // Plant & Cell Physiology;Dec2006, Vol. 47 Issue 12, p1591 

    To elucidate the genetic mechanism that regulates meristem maintenance in monocots, here we have examined the function of the gene FLORAL ORGAN NUMBER2 (FON2) in Oryza sativa (rice). Mutations in FON2 cause enlargement of the floral meristem, resulting in an increase in the number of floral...

  • The novel rice (Oryza sativa L.) gene OsSbf1 encodes a putative member of the Na+/bile acid symporter family. Rzewuski, Guillaume; Sauter, Margret // Journal of Experimental Botany;Sep2002, Vol. 53 Issue 376, p1991 

    PCR‐based differential screening was used to identify ethylene‐induced genes in deep‐water rice (Oryza sativa L.). One of the isolated cDNAs represented a novel protein, OsSBF1, with high homology to mammalian Na+/bile acid transporters and to sodium‐dependent...

  • Individual Leaf Development in Arabidopsis thaliana: a Stable Thermal‐time‐based Programme. GRANIER, CHRISTINE; MASSONNET, CATHERINE; TURC, OLIVIER; MULLER, BERTRAND; CHENU, KARINE; TARDIEU, FRANÇOIS // Annals of Botany;May2002, Vol. 89 Issue 5, p595 

    In crop species, the impact of temperature on plant development is classically modelled using thermal time. We examined whether this method could be used in a non‐crop species, Arabidopsis thaliana, to analyse the response to temperature of leaf initiation rate and of the development of...

  • Exploration of plant genomes in the FLAGdb++ environment. Dèrozier, Sandra; Samson, Franck; Tamby, Jean-Philippe; Guichard, Cécile; Brunaud, Véronique; Grevet, Philippe; Gagnot, Séverine; Label, Philippe; Leplé, Jean-Charles; Lecharny, Alain; Aubourg, Sébastien // Plant Methods;2011, Vol. 7 Issue 1, p8 

    Background: In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them...

  • Turning a Wild Plant into a Model -- A Déjà vu Story. PACURAR, Daniel Ioan // Notulae Botanicae Horti Agrobotanici Cluj-Napoca;2009, Vol. 37 Issue 1, p17 

    In the past two decades we have witnessed how a useless wild weed has been transformed from an anonymous into a model plant, probably the most widely "cultivated" plant species. The process has been rather slowly in the beginning, very laborious on the way, extremely expensive and time...

  • Disruption of a rice gene for a-glucan water dikinase, OsGWD1, leads to hyperaccumulation of starch in leaves but exhibits limited effects on growth. Hirose, Tatsuro; Aoki, Naohiro; Harada, Yusuke; Okamura, Masaki; Hashida, Yoichi; Ohsugi, Ryu; Miyao, Akio; Hirochika, Hirohiko; Terao, Tomio // Frontiers in Plant Science;May2013, Vol. 4, p1 

    To identify potential regulators of photoassimilate partitioning, we screened for rice mutant plants that accumulate high levels of starch in the leaf blades, and a mutant line leaf starch excess 1 (LSE1) was obtained and characterized. The starch content in the leaf blades of LSE1 was more than...

  • Cloning of a cDNA encoding an ETR2‐like protein (Os‐ERL1) from deep water rice (Oryza sativa L.) and increase in its mRNA level by submergence, ethylene, and gibberellin treatments. Watanabe, Hajime; Saigusa, Masahiko; Hase, Shu; Hayakawa, Toshihiko; Satoh, Shigeru // Journal of Experimental Botany;May2004, Vol. 55 Issue 399, p1145 

    A cDNA from deep water rice treated with ethylene, encoding an ethylene receptor homologous to Arabidopsis thaliana ETR2 and EIN4, was isolated using differential display and RACE techniques. The cDNA (2880 bp), corresponding to the Os‐ERL1 gene (Oryza sativa ETHYLENE RESPONSE 2 like 1;...

  • Microarray-based method for detection of unknown genetic modifications. Tengs, Torstein; Kristoffersen, Anja B.; Berdal, Knut G.; Thorstensen, Tage; Butenko, Melinka A.; Nesvold, Håvard; Holst-Jensen, Arne // BMC Biotechnology;2007, Vol. 7, p91 

    Background: Due to the increased use of genetic modifications in crop improvement, there is a need to develop effective methods for the detection of both known and unknown transgene constructs in plants. We have developed a strategy for detection and characterization of unknown genetic...

  • Characterization and Evolution of microRNA Genes Derived from Repetitive Elements and Duplication Events in Plants. Jie Sun; Meng Zhou; Zhitao Mao; Chuanxing Li // PLoS ONE;Apr2012, Vol. 7 Issue 4, p1 

    MicroRNAs (miRNAs) are a major class of small non-coding RNAs that act as negative regulators at the post-transcriptional level in animals and plants. In this study, all known miRNAs in four plant species (Arabidopsis thaliana, Populus trichocarpa, Oryza sativa and Sorghum bicolor) have been...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics