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

Jose Die,Teresa Millán,Juan Gil,Patricia Castro

doi:10.3390/genes9120568

Abstract

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.

Highlights

Garden asparagus (Asparagus officinalis L.) is the most economically important species of the Asparagus genus and the only one cultivated worldwide as a vegetable crop, with a cultivation area similar to other vegetable crops such as garlic, carrot, and eggplant [1]
The average number of exons detected in the nucleotide binding site and leucine-rich repeat (NBS-LRR) genes was
We applied a number of computational approaches that provided an integrated framework for the analysis and comprehensive cataloging of the NBS gene family in the asparagus genome

Summary

Introduction

Garden asparagus (Asparagus officinalis L.) is the most economically important species of the Asparagus genus and the only one cultivated worldwide as a vegetable crop, with a cultivation area similar to other vegetable crops such as garlic, carrot, and eggplant [1]. Asparagus is a dioecious species with female and male individuals. Male plants are preferred for agricultural production because they have higher yields, have greater longevity than females, and are more tolerant to diseases [2,3]. Most cultivars of the species derive from the Dutch population ‘Violet Dutch’, and as a consequence, they have a narrow genetic base [4,5]. Our laboratory has been working toward increasing the genetic diversity of the cultivated species using wild relatives and the Spanish tetraploid landrace ‘Morado de Huétor’ through a combination of agronomic and genetic approaches [6,7,8,9]. We are evaluating several populations and germplasm collections for traits of agronomic importance, such as early yield, spear color, spear size, spear quality, tight heads, sex determination, or disease resistances

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