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

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.

Genome-Wide Identification and Evolutionary Analysis of NBS-LRR Genes From Dioscorea rotundata

“…Genome-wide identification and evolutionary analysis has been performed in many angiosperms in the past 20 years (Bai et al, 2002;Meyers et al, 2003;Shao et al, 2016Shao et al, , 2019Zhang et al, 2016;Neupane et al, 2018a). Several evolutionary features have been documented, including frequent tandem duplication for gene expansion, cluster organization on the chromosome, rapid species-specific gene loss, and duplication (Meyers et al, 2003;Gu et al, 2015;Shao et al, 2016;Die et al, 2018;Song et al, 2019). However, most of the previous studies have concentrated on dicots, especially the rosid lineage of the angiosperms.…”

Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus

“…Most of the extensively investigated plant R genes contain NBSs 35 . The A. officinalis genome contains 49 different NBS R genes 36 . In this study, we identified 76 nonredundant R genes in the A. setaceus genome, which was greater than the number in A. officinalis.…”

Population Genetics of the Highly Polymorphic RPP8 Gene Family

“…NLR genes in many plant species are present in large, tandem arrays, which are frequently located on the ends of chromosomes, far from the pericentromeric suppression of recombination [15,16,18,20,21,22,23,24]. Ectopic crossovers are often invoked as a likely mechanism to generate NLR gene diversity in these clusters [16,20,82].…”

“…Genomic and comparative evolutionary analyses have been employed to characterize the genetic architecture and structural evolution of NLR genes. Across many plant species, traits such as the number of NLR genes, their locations within the genome, and patterns of deletion, duplication, and divergence have been probed to reveal a history of how gene family members have expanded and diverged (e.g., [1,3,14,15,16,17,18,19,20,21,22,23,24,25]). In A. thaliana , these genome-wide studies have found evidence for genomic clustering of 50%–70% of NLR genes [1].…”