tritici on gene expression of the biocontrol bacterium Pseudomonas fluorescens Pf29Arp. BMC Genomics 15:378.).Ĭhanges in gene expression or transcriptomes were first studied by microarray experiments focusing on only one of the interacting organisms ( Barret et al., 2009 Barret M, Frey-Klett P, Guillerm-Erckelboudt AY, Boutin M, Guernec G and Sarniguet A (2009) Effect of wheat roots infected with the pathogenic fungus Gaeumannomyces graminis var. (2014) Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals up-regulation of nutrient acquisition and cell cycle genes. Sci Rep 4:6261., Camilios-Neto et al., 2014 Camilios-Neto D, Bonato P, Wassem R, Tadra-Sfeir MZ, Brusamarello-Santos LCC, Valdameri G, Donatti L, Faoro H, Weiss VA, Chubatsu LS et al. Environ Microbiol 18:2343-2356., Bruto et al., 2014 Bruto M, Prigent-Combaret C, Muller D and Moënne-Loccoz Y (2014) Analysis of genes contributing to plant-beneficial functions in plant growth-promoting rhizobacteria and related proteobacteria. Besides that, another successful molecular interaction being widely studied is the relationship between plants and beneficial plant growth promoting bacteria (PGPB), which finds application in the understanding of agricultural inoculants ( Balsanelli et al., 2016 Balsanelli E, Tadra-Sfeir MZ, Faoro H, Pankievicz VCS, de Baura VA, Pedrosa FO, Souza EM, Dixon R and Monteiro RA (2016) Molecular adaptations of Herbaspirillum seropedicae during colonization of the maize rhizosphere. In: Arluison V and Valverde C (eds) Bacterial Regulatory RNA - Methods in Molecular Biology. There is a myriad of eukaryotic-prokaryotic interaction systems being studied, mainly focusing on pathogens and host gene expression responses, and pathogen-associated molecular patterns (PAMPs) ( Westermann et al., 2012 Westermann AJ and Vogel J (2018) Host-Pathogen Transcriptomics by Dual RNA-Seq. Organisms modulate their gene expression in order to establish many interactions, from pathogenic to beneficial relationships ( Wolf et al., 2018 Wolf T, Philipp K, Brunke S and Linde J (2018) Two’s company: studying interspecies relationships with dual RNA-seq. Since most studies first map the RNA-Seq libraries to the eukaryotic genome, much prokaryotic information has probably been lost.ĭual RNA-Seq sequential analysis combined analysis mapping strategies Our results highlight the necessity of combining the reference genomes to sort reads previously to the counting step to avoid losing information in Dual RNA-Seq experiments. More importantly, the combined analysis resulted in lower numbers of cross-mapped reads. The sequential analysis consistently attributed more reads to the first reference genome used in the analysis (due to cross-mapping) than the combined approach. Libraries from real Dual RNA-Seq experiments were also used. Two RNA-Seq libraries available in public databases consisting of a eukaryotic ( Zea mays) and a prokaryotic ( Herbaspirillum seropediceae) organisms were mixed to simulate a Dual RNA-Seq experiment. A comparison of this method with the sequential analysis was performed. Here we present a combined approach in which the libraries were aligned to a concatenated genome to sort the reads before mapping them to the respective annotated genomes. There are two main mapping methods used: sequential and combined. One alternative is separating the reads during in silico data analysis. In Dual RNA-Seq experiments the simultaneous extraction of RNA and analysis of gene expression data from both interacting organisms could be a challenge.
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