Evidence of extensive positive selection acting on cherry (Prunus avium L.) resistance gene analogs (RGAs)

Abstract

The cherry tree (Prunus avium L.), is an important tree species which is intensively plagued by many phytopathogenic fungal species. Resistance gene analogs (RGAs) are the largest class of resistance (R) genes and are pivotal components at breeding projects, serving as useful functional markers linked to R genes. In order to assess the evolutionary pressures acting upon P. avium RGAs candidates, their 173 homologues that have previously been deposited in GenBank were mined. Their proteins were clustered according to their blast(p) similarities in 12 MCL (Markov Cluster Algorithm) tribes, resulting in unique and well supported paralogous gene groups (PGGs). The extent to which these genes exhibit evidence of adaptive, positive selective pressures, which are causing excessive fixation of non-synonymous mutations, was determined using a series of maximum likelihood analyses using the PAML package. The results postulate existence of robust evidence of positive selection, acting in almost all of the clustered PGGs across their phylogenies. Furthermore, analyses revealed that the majority of the positively selected amino acid residues sites are localized widely across these RGAs sequences. We speculate that the clustered distribution of these RGAs might also be pronounced of high birth and death genes rates with diversifying episodes acting on their NB-ARC domains, putatively affecting their ligandbinding specificities. Such evolutionary insights shed light on how these NBS-encoding RGAs in P. avium are being evolved, assigning them as the foremost surveillance mechanism against rapidly evolving fungal pathogens, and providing breeders with effective tools for fast-tracking the development of varieties with more durable resistance.

Identification and evidence of positive selection upon resistance gene analogs in cotton (Gossypium hirsutum L.)

“…Previously, comparative analyses of R genes at Rosaceae species revealed that the solvent-exposed amino acid residues of the LRRs domains were significantly variable with intensive positive selective pressures acting upon them (Perazzolli et al 2014). Similar results were also observed in a genome wide analysis of the RGA in cherry (Zambounis et al 2016). Such evidences are interpreted as an additional indication of the active involvement of these regions in fungal pathogens recognition pathways (Zambounis et al 2012b), which is accurately consistent with the host-pathogen co-evolution processes leading to acquisition of disease resistance specificities (Mondragón-Palomino et al 2002).…”

Targeted plant improvement through genome editing: from laboratory to field

“…The ETI system activates complex plant immune reactions for defence against pathogens (Win et al 2012;Zhang et al 2017a). Plant defence mechanisms are constantly evolving to early respond against new diseases (Whitham et al 2016;Zambounis et al 2016). However, adaptation of pathogens to altering environment conditions happens quite faster than in plants.…”

Breeding Climate-Resilient Bananas

“…Plant defence mechanisms are constantly evolving to respond on time against new diseases-causing treats (Zambounis et al 2016a), such as evolving pathogen isolates and climate changes (Whitham et al 2016). Climate change alters dramatically the susceptibility of the plant host, and unfortunately, adaptation of pathogen genome to new environment progresses happens faster than in plant genome in a given pathosystem.…”

“…Therefore, increasing resistance to the major diseases by deciphering the genetic basis of resistance and subsequently creating genotypes with durable disease resistance is one of the basic prerequisites of sweet cherry breeders in the upcoming changes in climate. As a consequence, the assessment of disease resistance in cherry breeding germplasm is a prerequisite in terms of maintaining and enhancing the utility, durability and acceptance of new cultivars, besides the establishment of disease management strategies (Zambounis et al 2016a). Despite that this procedure is rather a time-consuming approach, previous studies have evaluated continuously the resistance of sweet cherry cultivars to economically important pathogens including the causal agents of powdery mildew and bacterial canker (Olmstead and Lang 2002;Mgbechi-Ezeri et al 2017).…”

“…In plants, pathogen recognition is the first step of defence reactions and is often mediated by a plethora of rapidly evolving receptors. The majority of them contain specific ligand-binding and signal transduction domains, such as leucine-rich repeats (LRRs) and NB-ARC domains, respectively, the most highly expanded group of genes linked directly to R-genes' functions (Debener and Byrne 2014;Zambounis et al 2016a). Besides, in plants, MAS approaches employing innovative molecular mapping technologies, besides traditional breeding practices towards the selection of resistant germplasms were targeted mainly the family of NBS (nucleotide-binding site)/LRRs-containing genes, however, without assigning an exact functional confirmation to individual genes (Dangl et al 2013).…”