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Segmental and Tandem Duplications Driving the Recent NBS-LRR Gene Expansion in the Asparagus Genome

Department of Genetics, ETSIAM, University of Córdoba, 14071 Córdoba, Spain
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Genes 2018, 9(12), 568; https://doi.org/10.3390/genes9120568
Received: 15 September 2018 / Revised: 7 November 2018 / Accepted: 19 November 2018 / Published: 23 November 2018
(This article belongs to the Section Plant Genetics and Genomics)
Garden asparagus is an important horticultural plant worldwide. It is, however, susceptible to a variety of diseases, which can affect the potential yield, spear quality, and lifespan of production fields. Screening studies have identified resistant germplasm. The genetic resistance is usually complex, and the genes underlying that resistance are still unknown. Most often, disease resistance is determined by resistance genes (R). The most predominant R-genes contain nucleotide binding site and leucine-rich repeat (NBS-LRR) domains. Using bioinformatics and data mining approaches, we identified and characterized 68 NBS predicted proteins encoded by 49 different loci in the asparagus genome. The NBS-encoding genes were grouped into seven distinct classes based on their domain architecture. The NBS genes are unevenly distributed through the genome and nearly 50% of the genes are present in clusters. Chromosome 6 is significantly NBS-enriched and one single cluster hosts 10% of the genes. Phylogenetic analysis points to their diversification into three families during their evolution. Recent duplications are likely to have dominated the NBS expansion with both tandem genes and duplication events across multiple chromosomes. Transcriptome sequencing data provided evidence for their transcription and tissue-specific expression. The total number of cis-regulatory elements as well as their relative positions within the NBS promoters suggests a complex transcriptional network regulating defense responses. Our study provides a strong groundwork for the isolation of candidate R-genes in garden asparagus. View Full-Text
Keywords: asparagus; coiled coil; disease resistance; duplications; nucleotide binding site; plant defense; promoter; regulatory elements asparagus; coiled coil; disease resistance; duplications; nucleotide binding site; plant defense; promoter; regulatory elements
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Die, J.V.; Castro, P.; Millán, T.; Gil, J. Segmental and Tandem Duplications Driving the Recent NBS-LRR Gene Expansion in the Asparagus Genome. Genes 2018, 9, 568.

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