Different scales of gene duplications occurring at different times have jointly shaped the NBS-LRR genes in Prunus species

Yan Zhong,Zong-Ming Cheng,Zhao Chen

doi:10.1007/s00438-021-01849-z

Yan Zhong, Zong-Ming Cheng + Show 1 more

Open Access

https://doi.org/10.1007/s00438-021-01849-z

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Abstract

In this study, genome-wide identification, phylogenetic relationships, duplication time and selective pressure of the NBS-LRR genes, an important group of plant disease-resistance genes (R genes), were performed to uncover their genetic evolutionary patterns in the six Prunus species. A total of 1946 NBS-LRR genes were identified; specifically, 589, 361, 284, 281, 318, and 113 were identified in Prunus yedoensis, P. domestica, P. avium, P. dulcis, P. persica and P. yedoensis var. nudiflora, respectively. Two NBS-LRR gene subclasses, TIR-NBS-LRR (TNL) and non-TIR-NBS-LRR (non-TNL), were also discovered. In total, 435 TNL and 1511 non-TNL genes were identified and could be classified into 30/55/75 and 103/158/191 multi-gene families, respectively, according to three different criteria. Higher Ks and Ka/Ks values were detected in TNL gene families than in non-TNL gene families. These results indicated that the TNL genes had more members involved in relatively ancient duplications and were affected by stronger selection pressure than the non-TNL genes. In general, the NBS-LRR genes were shaped by species-specific duplications, and lineage-specific duplications occurred at recent and relatively ancient periods among the six Prunus species. Therefore, different duplicated copies of NBS-LRRs can resist specific pathogens and will provide an R-gene library for resistance breeding in Prunus species.

Highlights

Prunus species are widely cultivated around the world for their economic and ornamental value
P. yedoensis possessed the largest number of nucleotidebinding site (NBS)-leucine-rich repeat (LRR) genes at 589
Because the assembly genome of P. yedoensis var. nudiflora was based on homozygous reads possessing half the size of P. yedoensis, leading to a distinct difference in NBS-LRR gene numbers between the two species (Baek et al 2018)

Summary

Introduction

Prunus species are widely cultivated around the world for their economic and ornamental value Such species include the cherry plum (P. cerasifera Ehrh.), sour cherry (P. cerasus L.), plums (P. domestica L. and P. insititia L.), invasive black cherry (P. serotina Ehrh.), and almond (P. communis Archang.) (Cici and Van Acker 2010). These Prunus trees can be infected by various pathogens. A large proportion of plant R genes are called NBS-LRR genes and encode a conserved nucleotidebinding site (NBS) domain and leucine-rich repeat (LRR) motifs (McHale et al 2006). The N-terminal structures of NBS-LRR proteins contribute to pathogen recognition and downstream signal transduction (Maekawa et al 2011).

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