Analysis of the melon genome in regions encompassing TIR-NBS-LRR resistance genes

Abstract

Plant genomes contain numerous genes (R-genes) that play a role in initiating defence measures against their particular pathogens. Defence mechanisms controlled by R-genes have been the focus of extensive research over the past several years. The majority of the R-genes described so far belong to a super-family of genes (150-600 members) that encode proteins with a nucleotide binding site (NBS), some leucine-rich repeats (LRR) and an N-terminal domain that shows similarity to the Toll and Interleukin-1 receptors (TIR) or a N-terminal coiled-coil (CC) domain. Analysis of four regions of the melon (Cucumis melo) genome, including two sequenced BACs, identified 14 TIR-NBS-LRR genes. Known disease resistance genes have been mapped in three of these regions. Transcriptional expression was detected for predicted genes that are possibly involved in defence responses to pathogen attack. TIR-NBS-LRR genes appear to be clustered in the melon genome. They contain all the conserved motifs that have previously been described for their counterparts in other species, although differences were also detected. The results presented here may contribute to a better understanding of the genomic distribution and evolution of this group of resistance gene homologues and their variability.

Mutator-like elements identified in melon, Arabidopsis and rice contain ULP1 protease domains

“…Analysis of the melon 31O16 BAC sequence (van Leeuwen et al 2005) produced, among other gene sequences, a putative protein with high similarity to the MuDR family of transposases (conserved protein family domain pfam03108), as detected with RPSBLAST at NCBI (Marchler-Bauer and Bryant 2004) (E-value of 3E-33 with an alignment coverage of 87.7%). Full length elements (MuDR) in maize encode two proteins: the MURA protein with a transposase function, and the MURB protein of unknown function.…”

“…The 31O16 BAC sequence (van Leeuwen et al 2005) was analyzed for localization of repeated sequences with the JDotter software (Brodie et al 2004). The Arabidopsis genome sequence was screened with the TBLASTN program (Altschul et al 1997) at the TAIR BLAST web site (http://www.arabidopsis.org/Blast/) with the melon MURA (GenBank AAU04773), ULP1-1 (GenBank AAU04774) and ULP1-2 (GenBank AAU04775) sequences, and the Arabidopsis protein sequences AT2G05690 (MURA-like), AT5G45570 (ULP1-like) and ESD4 (ULP1-like) with the parameters: AGI whole genome (BAC clones) (DNA), no Wlter and an arbitrarily chosen, E-value of 0.001.…”

“…In the course of studying the genomic structure in a region of Cucumis melo, rich in homologues to resistance genes (van Leeuwen et al 2005), a sequence with the features of a MULE transposon was found and compared to the Arabidopsis and maize elements. This element, named CUMULE, contains sequences related to the ULP1 protease besides the MURA-like transposase.…”

Research tools for functional genomics in melon (<i>Cucumis melo</i> L.): Current status and prospects

“…Using this BAC library, a contig of four BACs around the MRGH63 (Garcia-Mas et al 2001) resistance gene homolog fragment was created (van Leeuwen et al 2005). A detailed analysis of four regions of the melon genome, including two sequenced BACs, identified 14 TIR/NBS/LRR genes, which appear to be clustered in the melon genome.…”

Breeding melon for resistance to Fusarium wilt: recent developments

“…chinensis, conomon and makuwa. Tezuka et al (2011) developed a SCAR marker (S-MRGH9) and three CAPS markers (CAPS3, C-MRGH12 and C-MRGH13) based on the published BAC 31O16 sequence (Van Leeuwen et al 2005), which contains a cluster of melon RGH and maps around the Fom-1 locus (Table 3).…”