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Osmoprotectants in the Sugarcane (Saccharum spp.) Transcriptome Revealed by in Silico Evaluation

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Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2010)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 6685))

Abstract

Environmental stresses such as drought and salinity limit crop productivity in worldwide level. These stresses often lead to the accumulation of osmoprotectants in most organisms, including plants. In the present work, a search of known osmoprotectants (P5CS, P5CR, INPS1, BADH, CMO, TPS, TPP, OASTL and SAT) was carried out in the sugarcane transcriptome (237,954 expressed sequence tags) using in silico procedures. Alignments revealed that sugarcane presents a high number of osmoprotectant candidate genes, with 56 clusters found. In silico expression revealed higher expression in stressed callus tissues and those infected by Herbaspirilum rubrisubalbicans (HR), confirming the multi-function character of the osmoprotectants. As expected, the phylogenetic analysis revealed distinct groups among angiosperms, algae, animals, fungi and bacteria, in almost all dendrograms, with high degree of sequence conservation among angiosperms. As observed in comparative analysis between the ORFs of sugarcane and other organisms, the genic structure of these plants was relatively conserved suggesting that the accumulation of compatible solutes is an ancient metabolic adaptation.

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Authors and Affiliations

  1. Department of Genetics, Laboratory of Plant Genetics and Biotechnology, Universidade Federal de Pernambuco, Center of Biological Sciences, R. Prof. Moraes Rêgo 1235, CEP 50670-420, Recife, PE, Brazil

    Petra Barros dos Santos, Nina da Mota Soares-Cavalcanti, Gabriela S. Vieira-de-Melo & Ana Maria Benko-Iseppon

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  1. Petra Barros dos Santos
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  2. Nina da Mota Soares-Cavalcanti
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  3. Gabriela S. Vieira-de-Melo
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  4. Ana Maria Benko-Iseppon
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  1. ICAR-CNR, Consiglio Nazionale delle Ricerche, 90128, Palermo, Italy

    Riccardo Rizzo

  2. School of Computing and Mathematical Sciences, Liverpool John Moores University, L3 3AF, Liverpool, UK

    Paulo J. G. Lisboa

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Barros dos Santos, P., da Mota Soares-Cavalcanti, N., Vieira-de-Melo, G.S., Benko-Iseppon, A.M. (2011). Osmoprotectants in the Sugarcane (Saccharum spp.) Transcriptome Revealed by in Silico Evaluation. In: Rizzo, R., Lisboa, P.J.G. (eds) Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2010. Lecture Notes in Computer Science(), vol 6685. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21946-7_4

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  • DOI: https://doi.org/10.1007/978-3-642-21946-7_4

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