title: Large-scale bioinformatic analysis of the regulation of the disease resistance NBS gene family by microRNAs in Poaceae.
abstract: In the present study, we have screened 71, 713, 525, 119 and 241 mature miRNA variants from Hordeum vulgare, Oryza sativa, Brachypodium distachyon, Triticum aestivum, and Sorghum bicolor, respectively, and classified them with respect to their conservation status and expression levels. These Poaceae non-redundant miRNA species (1,669) were distributed over a total of 625 MIR families, among which only 54 were conserved across two or more plant species, confirming the relatively recent evolutionary differentiation of miRNAs in grasses. On the other hand, we have used 257 H. vulgare, 286T. aestivum, 119 B. distachyon, 269 O. sativa, and 139 S. bicolor NBS domains, which were either mined directly from the annotated proteomes, or predicted from whole genome sequence assemblies. The hybridization potential between miRNAs and their putative NBS genes targets was analyzed, revealing that at least 454 NBS genes from all five Poaceae were potentially regulated by 265 distinct miRNA species, most of them expressed in leaves and predominantly co-expressed in additional tissues. Based on gene ontology, we could assign these probable miRNA target genes to 16 functional groups, among which three conferring resistance to bacteria (Rpm1, Xa1 and Rps2), and 13 groups of resistance to fungi (Rpp8,13, Rp3, Tsn1, Lr10, Rps1-k-1, Pm3, Rpg5, and MLA1,6,10,12,13). The results of the present analysis provide a large-scale platform for a better understanding of biological control strategies of disease resistance genes in Poaceae, and will serve as an important starting point for enhancing crop disease resistance improvement by means of transgenic lines with artificial miRNAs.
authors.affiliation: Unité de recherche UR11ES10, Génomique des insectes ravageurs des cultures d'intérêt agronomique (GIRC), faculté des sciences de Tunis, université de Tunis El Manar, 2092 El Manar, Tunis, Tunisia.
authors.forename: Yosra
authors.initials: Y
authors.lastname: Habachi-Houimli
authors.affiliation: Unité de recherche UR11ES10, Génomique des insectes ravageurs des cultures d'intérêt agronomique (GIRC), faculté des sciences de Tunis, université de Tunis El Manar, 2092 El Manar, Tunis, Tunisia.
authors.forename: Yosra
authors.initials: Y
authors.lastname: Khalfallah
authors.affiliation: Unité de recherche UR11ES10, Génomique des insectes ravageurs des cultures d'intérêt agronomique (GIRC), faculté des sciences de Tunis, université de Tunis El Manar, 2092 El Manar, Tunis, Tunisia; Institut supérieur de l'animation pour la jeunesse et la culture (ISAJC), université de Tunis, 2055 Bir El Bey, Tunisia.
authors.forename: Hanem
authors.initials: H
authors.lastname: Makni
authors.affiliation: Unité de recherche UR11ES10, Génomique des insectes ravageurs des cultures d'intérêt agronomique (GIRC), faculté des sciences de Tunis, université de Tunis El Manar, 2092 El Manar, Tunis, Tunisia.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Makni
authors.affiliation: Unité de recherche UR11ES10, Génomique des insectes ravageurs des cultures d'intérêt agronomique (GIRC), faculté des sciences de Tunis, université de Tunis El Manar, 2092 El Manar, Tunis, Tunisia; Institut supérieur de biotechnologie de Béja (ISBB), université de Jendouba, 9000 Béja, Tunisia. Electronic address: dhia_bouktila2000@yahoo.fr.
authors.forename: Dhia
authors.initials: D
authors.lastname: Bouktila
mesh_terms: D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D019295:Computational Biology; D057225:Data Mining; D030541:Databases, Genetic; D060467:Disease Resistance / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics*; D009711:Nucleotides / Q000235:genetics*; D010935:Plant Diseases / Q000235:genetics*; D006109:Poaceae / Q000235:genetics*; D020543:Proteome / Q000235:genetics
chemical_list: D035683:MicroRNAs; D009711:Nucleotides; D020543:Proteome
keywords: Biotic stresses; Disease resistance; Expression regulation; MicroARNs; MicroRNAs; Nucleotide-Binding Site (NBS) genes; Régulation de l’expression; Résistance aux maladies; Site de fixation nucléotidique (NBS); Stress biotiques