Large-scale analysis of NBS domain-encoding resistance gene analogs in Triticeae

Abstract

Proteins containing nucleotide binding sites (NBS) encoded by plant resistance genes play an important role in the response of plants to a wide array of pathogens. In this paper, an in silico search was conducted in order to identify and characterize members of NBS-encoding gene family in the tribe of Triticeae. A final dataset of 199 sequences was obtained by four search methods. Motif analysis confirmed the general structural organization of the NBS domain in cereals, characterized by the presence of the six commonly conserved motifs: P-loop, RNBS-A, Kinase-2, Kinase-3a, RNBS-C and GLPL. We revealed the existence of 11 distinct distribution patterns of these motifs along the NBS domain. Four additional conserved motifs were shown to be significantly present in all 199 sequences. Phylogenetic analyses, based on genetic distance and parsimony, revealed a significant overlap between Triticeae sequences and Coiled coil-Nucleotide binding site-Leucine rich repeat (CNL)-type functional genes from monocotyledons. Furthermore, several Triticeae sequences belonged to clades containing functional homologs from non Triticeae species, which has allowed for these sequences to be functionally assigned. The findings reported, in this study, will provide a strong groundwork for the isolation of candidate R-genes in Triticeae crops and the understanding of their evolution.

Prediction and analysis of three gene families related to leaf rust (Puccinia triticina) resistance in wheat (Triticum aestivum L.)

“…This number is slightly higher than those in previous studies of the genome-wide analysis of NLR-coding genes in wheat [40, 41] but slightly lower than the 1185 NLR proteins predicted using the new gene models in the wheat genome assembly recently generated by Earlham Institute [42]. In a concurrent analysis, we predicted 249 NLR proteins in Arabidopsis and the majority of them were TNL (Tir-NBS-LRR), accounting for nearly 69% (171), compared to less than 21% (52) of CNL (Coiled-coil-NBS-LRR) proteins.…”

Accelerating the phylogenetic parsimony function on heterogeneous systems

“…From a historical perspective, this criterion has represented one of the most popular approaches for inferring phylogenies since the early 1970s. While it is true that modern phylogenetic analyses are mostly focused on the use of statistical inference methods that involve the likelihood function, parsimony still plays a significant role in the processing of complex biological data sets and large‐scale analyses …”

“…While it is true that modern phylogenetic analyses are mostly focused on the use of statistical inference methods that involve the likelihood function, parsimony still plays a significant role in the processing of complex biological data sets and large-scale analyses. 31,32 Let D be the input dataset, composed of N nucleotide sequences of length M, and T=(V, E) a phylogenetic topology inferred from D. The parsimony score of TP(T) is given by the following expression 9 :…”

Characterization, Identification and Expression Profiling of Genome-Wide R-Genes in Melon and Their Putative Roles in Bacterial Fruit Blotch Resistance

“…These domains are involved in pathogen recognition, signaling, and plant innate immunity responses [26,27,29,[31][32][33][34][35]. R-genes have been identified in the genomes of plant species including watermelon [36], cucumber [37], rice [38,39], Chinese cabbage [40], maize [41], wheat [42], Arabidopsis thaliana [43], and apple [44].…”