Abstract
BackgroundPlant NBS-LRR -resistance genes tend to be found in clusters, which have been shown to be hot spots of genome variability. In melon, half of the 81 predicted NBS-LRR genes group in nine clusters, and a 1 Mb region on linkage group V contains the highest density of R-genes and presence/absence gene polymorphisms found in the melon genome. This region is known to contain the locus of Vat, an agronomically important gene that confers resistance to aphids. However, the presence of duplications makes the sequencing and annotation of R-gene clusters difficult, usually resulting in multi-gapped sequences with higher than average errors.ResultsA 1-Mb sequence that contains the largest NBS-LRR gene cluster found in melon was improved using a strategy that combines Illumina paired-end mapping and PCR-based gap closing. Unknown sequence was decreased by 70% while about 3,000 SNPs and small indels were corrected. As a result, the annotations of 18 of a total of 23 NBS-LRR genes found in this region were modified, including additional coding sequences, amino acid changes, correction of splicing boundaries, or fussion of ORFs in common transcription units. A phylogeny analysis of the R-genes and their comparison with syntenic sequences in other cucurbits point to a pattern of local gene amplifications since the diversification of cucurbits from other families, and through speciation within the family. A candidate Vat gene is proposed based on the sequence similarity between a reported Vat gene from a Korean melon cultivar and a sequence fragment previously absent in the unrefined sequence.ConclusionsA sequence refinement strategy allowed substantial improvement of a 1 Mb fragment of the melon genome and the re-annotation of the largest cluster of NBS-LRR gene homologues found in melon. Analysis of the cluster revealed that resistance genes have been produced by sequence duplication in adjacent genome locations since the divergence of cucurbits from other close families, and through the process of speciation within the family a candidate Vat gene was also identified using sequence previously unavailable, which demonstrates the advantages of genome assembly refinements when analyzing complex regions such as those containing clusters of highly similar genes.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1131) contains supplementary material, which is available to authorized users.
Highlights
Plant nucleotide-binding site leucine rich repeat (NBS-LRR) -resistance genes tend to be found in clusters, which have been shown to be hot spots of genome variability
Complex coordinated systems of responses to these stresses have evolved in different plant species
The species of the family Cucurbitaceae are of special interest for a number of reasons. They form a group of plant species with genomes of intermediate size, they are mostly diploid, and they have not undergone large genome duplications apart from those which occurred with the original diversification of flowering plants
Summary
Plant NBS-LRR -resistance genes tend to be found in clusters, which have been shown to be hot spots of genome variability. The species of the family Cucurbitaceae are of special interest for a number of reasons They form a group of plant species with genomes of intermediate size (between 300 and 450 Mbases), they are mostly diploid, and they have not undergone large genome duplications apart from those which occurred with the original diversification of flowering plants. They have a particular system of vascular development that has been related to defense mechanisms specific to these species. They are of significant economic interest and breeding of the cucurbit species is active within the seed industry
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
