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Open Access Research article

Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals up-regulation of nutrient acquisition and cell cycle genes

Doumit Camilios-Neto14, Paloma Bonato1, Roseli Wassem2, Michelle Z Tadra-Sfeir1, Liziane CC Brusamarello-Santos1, Glaucio Valdameri1, Lucélia Donatti3, Helisson Faoro1, Vinicius A Weiss1, Leda S Chubatsu1, Fábio O Pedrosa1 and Emanuel M Souza1*

Author Affiliations

1 Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR 81531-990, Brazil

2 Department of Genetics, Universidade Federal do Paraná, Curitiba, PR, Brazil

3 Department of Cellular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil

4 Departament of Biochemistry and Biotechnology, Universidade Estadual de Londrina, Londrina, PR, Brazil

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BMC Genomics 2014, 15:378  doi:10.1186/1471-2164-15-378

Published: 16 May 2014



The rapid growth of the world’s population demands an increase in food production that no longer can be reached by increasing amounts of nitrogenous fertilizers. Plant growth promoting bacteria (PGPB) might be an alternative to increase nitrogenous use efficiency (NUE) in important crops such wheat. Azospirillum brasilense is one of the most promising PGPB and wheat roots colonized by A. brasilense is a good model to investigate the molecular basis of plant-PGPB interaction including improvement in plant-NUE promoted by PGPB.


We performed a dual RNA-Seq transcriptional profiling of wheat roots colonized by A. brasilense strain FP2. cDNA libraries from biological replicates of colonized and non-inoculated wheat roots were sequenced and mapped to wheat and A. brasilense reference sequences. The unmapped reads were assembled de novo. Overall, we identified 23,215 wheat expressed ESTs and 702 A. brasilense expressed transcripts. Bacterial colonization caused changes in the expression of 776 wheat ESTs belonging to various functional categories, ranging from transport activity to biological regulation as well as defense mechanism, production of phytohormones and phytochemicals. In addition, genes encoding proteins related to bacterial chemotaxi, biofilm formation and nitrogen fixation were highly expressed in the sub-set of A. brasilense expressed genes.


PGPB colonization enhanced the expression of plant genes related to nutrient up-take, nitrogen assimilation, DNA replication and regulation of cell division, which is consistent with a higher proportion of colonized root cells in the S-phase. Our data support the use of PGPB as an alternative to improve nutrient acquisition in important crops such as wheat, enhancing plant productivity and sustainability.

RNA-seq; Transcriptional analysis; Wheat; Triticum aestivum; Azospirilum brasilense; PGPB; Cell cycle and nitrogen fixation