Abstract
Akebia trifoliata is an important multiuse perennial plant that often suffers attacks from various pathogens due to its long growth cycle, seriously affecting its commercial value. The absence of research on the resistance (R) genes of A. trifoliata has greatly limited progress in the breeding of resistant varieties. Genes encoding proteins containing nucleotide binding sites (NBSs) and C-terminal leucine-rich repeats (LRRs), the largest family of plant resistance (R) genes, are vital for plant disease resistance. A comprehensive genome-wide analysis showed that there were only 73 NBS genes in the A. trifoliata genome, including three main subfamilies (50 coiled coil (CC)-NBS-LRR (CNL), 19 Toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) and four resistance to powdery mildew8 (RPW8)-NBS-LRR (RNL) genes). Additionally, 64 mapped NBS candidates were unevenly distributed on 14 chromosomes, most of which were assigned to the chromosome ends; 41 of these genes were located in clusters, and the remaining 23 genes were singletons. Both the CNLs and TNLs were further divided into four subgroups, and the CNLs had fewer exons than the TNLs. Structurally, all eight previously reported conserved motifs were identified in the NBS domains, and both their order and their amino acid sequences exhibited high conservation. Evolutionarily, tandem and dispersed duplications were shown to be the two main forces responsible for NBS expansion, producing 33 and 29 genes, respectively. A transcriptome analysis of three fruit tissues at four developmental stages showed that NBS genes were generally expressed at low levels, while a few of these genes showed relatively high expression during later development in rind tissues. Overall, this research is the first to identify and characterize A. trifoliata NBS genes and is valuable for both the development of new resistant cultivars and the study of molecular mechanisms of resistance.
Highlights
Akebia trifoliata (Thunb.) Koidz, belonging to the family Lardizabalaceae (Liu et al, 2007), presents great potential for use as a fruit and oil crop and a medicinal and ornamental plant (Li L. et al, 2010; Chen et al, 2017)
Wild plants will inevitably suffer from various diseases, such as kiwifruit bacterial canker (Scortichini et al, 2012), sweet potato root rot Akebia trifoliata nucleotide binding sites (NBSs) Resistance Genes disease (Ma et al, 2020) and apple fruit anthracnose (Zhou and Zhou, 2017); this is especially true for perennials, such as black cottonwood, which often suffer attacks from various pathogens or herbivores before reaching the reproductive stage because of their relatively long life cycle (Tuskan et al, 2006)
The 73 NBS protein sequences were classified into three groups (50 CNLs, 19 TNLs, and 4 RNLs) and nine subgroups according to the existence of CC, TIR and RPW8 domains, which are summarized in Table 2 and Supplementary Table 1
Summary
Akebia trifoliata (Thunb.) Koidz, belonging to the family Lardizabalaceae (Liu et al, 2007), presents great potential for use as a fruit and oil crop and a medicinal and ornamental plant (Li L. et al, 2010; Chen et al, 2017). Wild plants will inevitably suffer from various diseases, such as kiwifruit bacterial canker (Scortichini et al, 2012), sweet potato root rot Akebia trifoliata NBS Resistance Genes disease (Ma et al, 2020) and apple fruit anthracnose (Zhou and Zhou, 2017); this is especially true for perennials, such as black cottonwood, which often suffer attacks from various pathogens or herbivores before reaching the reproductive stage because of their relatively long life cycle (Tuskan et al, 2006). During the arms race between hosts and their pathogens, great numbers of variations arise in pathogens due to their short growth cycle and simple genomic sequences, requiring plants (especially perennials) to evolve a set of sophisticated and effective defense systems to combat them (Tuskan et al, 2006). By directly or indirectly recognizing pathogen-secreted effectors, these proteins confer resistance to various pathogens, including fungi, bacteria and viruses, by initiating a series of defense responses, such as hypersensitive responses, activating signaling pathways and inhibiting the plant infection process (Andersen et al, 2018)
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