Comparative analysis of resistance gene analogues encoding NBS‐LRR domains in cotton

Abstract

The allotetraploid genome of cotton, after separating from its diploid parents, experienced polyploidisation, natural and artificial selection, hybrid necrosis, duplication and recombination which became the reason to shed off and evolve new genes for its survival. These driving forces influenced the development of genomic architecture that make it susceptible to diseases and pathogens as compared to donor parents.

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

“…We assume that recent episodes of positive selection events have been occurred, overlapping similar more ancient events among these RGAs. Constantly with our results, similar existences of positive selective pressures acting on plant RGAs have been recently reported (Khan et al 2015;Perazzolli et al 2014). Finally, using the CODEMLSITES program and various selection models, we tested whether positive selection was acting at individual amino acid sites.…”

In silico analysis of the LRR receptor-like serine threonine kinases subfamily in Morus notabilis

“…Comparative analyses among Rosaceae trees species regarding their resistance (R) genes have revealed that solvent-exposed residues of the LRRs domains are hyper-variable, with intensive positive selective pressures acting on them (Perazzolli et al, 2014). Similar results were constantly observed in a range of plant species (Li et al, 2010;Zambounis et al, 2012;Yang et al, 2013;Khan et al, 2015). We hypothesize that these positive selective pressures acting upon LRRs of the LRR-RSTK subfamily in M. notabilis might being associated mainly with a continual selective demand for their functional diversification in terms of increasing fungal disease resistance.…”

“…Our findings postulate also that LRRs of LRR-RSTKs exhibit signs of positive selection. Such a selective mode is promoting a rapid alteration of gene sequences in different alleles or species by a non-directional mode without altering the main functions, which in cases of fungal attacks, often increases the reservoir of the ligands that can be recognized in these interactions (Delph and Kelly, 2014).Positive selection on NBS-containing gene families in plants and especially among their LRRs domains, were reported in various studies Perazzolli et al, 2014;Khan et al, 2015), supporting the view that selection upon them for durable disease resistance might be a crucial component of nearly all plant breeding programs (Mace et al, 2014). Comparative analyses among Rosaceae trees species regarding their resistance (R) genes have revealed that solvent-exposed residues of the LRRs domains are hyper-variable, with intensive positive selective pressures acting on them (Perazzolli et al, 2014).…”

“…Even, the location of positively selected amino acid residues is crucial for obtaining novel gene functions (Mondragon-Palomino et al, 2002); Thus, previous studies have reported that solvent-exposed regions of the LRRs repeats are under strong positive selection. Such evidence has been interpreted as an additional sign of the involvement of these regions in fungal pathogens recognition (Khan et al, 2015;Parniske et al, 1997;Zambounis at al., 2012).…”

“…These LRRs domains evolve novel ligandbinding specificities through a wealth of various mechanisms, such as point mutations at variable residues, variations in their repeat numbers, tandem gene duplications and conversions events, unequal crossing-over and other short rearrangements (Friedman and Baker, 2007;Meyers et al, 2003;Yang et al, 2008;Zambounis et al, 2012). Therefore, the evolution patterns of plant LRRs-containing genes appears to be rather a complex process (Sekhwal et al, 2015;Zhou et al, 2004), where signatures of positive selective pressures acting upon them are often quite evident (Khan et al, 2015). Positive selection is defined as the rapid fixation of beneficial non-synonymous mutations and is an important evolutionary force for a number of defense-related genes towards their functional diversification, which may be selectively favored in plants under intensive biotic pressures (Delph and Kelly, 2014).…”