In silico survey of resistance (R) genes in Eucalyptus transcriptome

Abstract

A major goal of plant genome research is to recognize genes responsible for important traits. Resistance genes are among the most important gene classes for plant breeding purposes being responsible for the specific immune response including pathogen recognition, and activation of plant defence mechanisms. These genes are quite abundant in higher plants, with 210 clusters found in Eucalyptus FOREST database presenting significant homology to known R-genes. All five gene classes of R-genes with their respective conserved domains are present and expressed in Eucalyptus. Most clusters identified (93) belong to the LRR-NBS-TIR (genes with three domains: Leucine-rich-repeat, Nucleotide-binding-site and Toll interleucine 1-receptor), followed by the serine-threoninekinase class (49 clusters). Some new combinations of domains and motifs of R-genes may be present in Eucalyptus and could represent novel gene structures. Most alignments occurred with dicots (94.3%), with emphasis on Arabidopsis thaliana (Brassicaceae) sequences. All best alignments with monocots (5.2%) occurred with rice (Oryza sativa) sequences and a single cluster aligned with the gymnosperm Pinus sylvestris (0.5%). The results are discussed and compared with available data from other crops and may bring useful evidences for the understanding of defense mechanisms in Eucalyptus and other crop species.

An overall evaluation of the resistance (R) and pathogenesis-related (PR) superfamilies in soybean, as compared with Medicago and Arabidopsis

“…Similar results were observed in previous studies regarding R genes of eucalyptus (Barbosa-da-Silva et al , 2005) and sugarcane (Wanderley-Nogueira et al , 2007). This occurs due to the common domains shared by R genes, as for example the LRR domain that is present in the LRR, NBS-LRR and LRR-kinase gene families, facilitating alignments with more than one gene.…”

“…The selected protein sequences were related to the 42 R and 17 PR gene classes described above. The R genes were previously compiled by Barbosa-da-Silva et al (2005) and Wanderley-Nogueira et al (2007), and PR seed sequences are available in Table S1 (Supplementary Material). All 59 seed sequences regarded full cDNAs that were obtained from the NCBI database and conceptually translated to improve search strategies.…”

“…It is characterized by a serine/threonine-kinase (ser/thre-kinase) domain, able to interact with the avrPto gene (Tang et al , 1999). This gene was also identified in other plants, such as Arabidopsis thaliana , Phaseolus vulgaris (Melotto et al , 2004), eucalyptus (Barbosa-da-Silva et al , 2005) and sugarcane (Wanderley-Nogueira et al , 2007). …”

Comparative analysis of soybean genotype resistance to Heterodera glycines and Meloidogyne species via resistance gene analogs

“…For resistance to the nematodes of this genus, the RGAs were able to discriminate between resistant and susceptible genotypes, without differentiation for resistance between species of M. incognita, M. javanica, and M. enterolobi. These data indicate that, for resistance to Meloidogyne spp, some factor related to the NBS domain confers ample resistance to the nematode, which is supported by reports showing that a small number of genes of greater effect control such resistance (Barbosa-da-Silva et al, 2005).…”

Pathogenesis-related genes and proteins in forest tree species

“…Another group of R genes, the ser-thr-kinase with strong homology to tomato pto was identified and their number was comparable to Arabidopsis, where 50 such genes were reported in the genome. An important finding of the study was the presence of gene with similar motifs like MIX class I with LRR and LRRkinase motifs suggesting an evolutionary link between different classes of R genes (Barbosa da Silva et al 2005).…”