Distinct Evolutionary Patterns of NBS-Encoding Genes in Three Soapberry Family (Sapindaceae) Species.

Guang-Can Zhou,Guo-Qing Meng,Ming Zhang,Yi-Lei Wang,Yang Liu,Yan-Mei Zhang,Wen Li,Min Li

doi:10.3389/fgene.2020.00737

Abstract

Nucleotide-binding site (NBS)-type disease resistance genes (R genes) play key roles in plant immune responses and have co-evolved with pathogens over the course of plant lifecycles. Comparative genomic studies tracing the dynamic evolution of NBS-encoding genes have been conducted using many important plant lineages. However, studies on Sapindaceae species have not been performed. In this study, a discrepant number of NBS-encoding genes were identified in the genomes of Xanthoceras sorbifolium (180), Dinnocarpus longan (568), and Acer yangbiense (252). These genes were unevenly distributed and usually clustered as tandem arrays on chromosomes, with few existed as singletons. The phylogenetic analysis revealed that NBS-encoding genes formed three monophyletic clades, RPW8-NBS-LRR (RNL), TIR-NBS-LRR (TNL), and CC-NBS-LRR (CNL), which were distinguished by amino acid motifs. The NBS-encoding genes of the X. sorbifolium, D. longan, and A. yangbiense genomes were derived from 181 ancestral genes (three RNL, 23 TNL, and 155 CNL), which exhibited dynamic and distinct evolutionary patterns due to independent gene duplication/loss events. Specifically, X. sorbifolium exhibited a “first expansion and then contraction” evolutionary pattern, while A. yangbiense and D. longan exhibited a “first expansion followed by contraction and further expansion” evolutionary pattern. However, further expansion in D. longan was stronger than in A. yangbiense after divergence, suggesting that D. longan gained more genes in response to various pathogens. Additionally, the ancient and recent expansion of CNL genes generated the dominance of this subclass in terms of gene numbers, while the low copy number status of RNL genes was attributed to their conserved functions.

Highlights

Nucleotide-binding site (NBS)-encoding genes are the largest type (∼80%) of disease resistance genes (R genes) found in plants and are responsible for the protection against various pathogens (Liu et al, 2007; Dangl et al, 2013)
A total of 180, 252, and 568 non-redundant NBS-encoding genes were identified from the genomes of X. sorbifolium, A. yangbiense, and D. longan, respectively (Table 1 and Supplementary Table S1), accounting for 0.73, 0.89, and 1.83% of the 24,672, 28,320, and 31,007 annotated protein-coding
D. longan possessed the largest number of NBS-encoding genes and was 3.16- and 2.25-times greater than X. sorbifolium and A. yangbiense, respectively

Summary

Introduction

Nucleotide-binding site (NBS)-encoding genes are the largest type (∼80%) of disease resistance genes (R genes) found in plants and are responsible for the protection against various pathogens (Liu et al, 2007; Dangl et al, 2013). According to the structure of N-terminal domains that possess a coiled-coil (CC), Drosophila toll and mammalian interleukin-1 receptor-like (TIR), or resistance to powdery mildew (RPW8) domain, NBSencoding genes can be classified into three subclasses: CC-NBSLRR (CNL), TIR-NBS-LRR (TNL), and RPW8-NBS-LRR (RNL) (Meyers et al, 2003; Shao et al, 2014, 2016, 2019; Zhang et al, 2016, 2020; Qian et al, 2017; Xue et al, 2020). As an example of function, the CNL gene, RPP8, in Arabidopsis thaliana provides resistance against downy mildew after Peronospora parasiticia infection (Mcdowell et al, 1998). Another CNL gene, Pik, confers resistance to rice blast caused by Magnaporthe grisea infection (Zhai et al, 2011). NBS-encoding R genes are of great importance to plant growth and would tangibly benefit humankind if properly used in disease resistance breeding

Methods

Results

Conclusion