Evidence for intragenic recombination and selective sweep in an effector gene of Phytophthora infestans

Abstract

Effectors, a group of small proteins secreted by pathogens, play a critical role in the antagonistic interaction between plant hosts and pathogens through their dual functions in regulating host immune systems and pathogen infection capability. In this study, evolution in effector genes was investigated through population genetic analysis of Avr3a sequences generated from 96 Phytophthora infestans isolates collected from six locations representing a range of thermal variation and cropping systems in China. We found high genetic variation in the Avr3a gene resulting from diverse mechanisms extending beyond point mutations, frameshift, and defeated start and stop codons to intragenic recombination. A total of 51 nucleotide haplotypes encoding 38 amino acid isoforms were detected in the 96 full sequences with nucleotide diversity in the pathogen populations ranging from 0.007 to 0.023 (mean = 0.017). Although haplotype and nucleotide diversity were high, the effector gene was dominated by only three haplotypes. Evidence for a selective sweep was provided by (i) the population genetic differentiation (G ST) of haplotypes being lower than the population differentiation (F ST ) of SSR marker loci; and (ii) negative values of Tajima's D and Fu's FS. Annual mean temperature in the collection sites was negatively correlated with the frequency of the virulent form (Avr3aEM), indicating Avr3a may be regulated by temperature. These results suggest that elevated air temperature due to global warming may hamper the development of pathogenicity traits in P. infestans and further study under confined thermal regimes may be required to confirm the hypothesis.

Lack of gene flow between Phytophthora infestans populations of two neighboring countries with the largest potato production

“…Only 17 nucleotide and three amino acid haplotypes were detected in the 245 sequences. The genetic variation is substantially lower than in many functional genes in P. infestans (Yang et al, ) and other pathogens (Marisa et al, ). For example, from a subset of the same Chinese collection, 51 nucleotide haplotypes were identified in the 96 Avr3a sequences (Yang et al, ).…”

“…The genetic variation is substantially lower than in many functional genes in P. infestans (Yang et al, ) and other pathogens (Marisa et al, ). For example, from a subset of the same Chinese collection, 51 nucleotide haplotypes were identified in the 96 Avr3a sequences (Yang et al, ). The eEF‐1α is a housekeeping gene playing multifaceted roles in the biochemical and physiological processes of life (Chang et al, ; Kato, Sato, Nagayoshi, & Ikawa, ).…”

Temperature-Mediated Plasticity Regulates the Adaptation of Phytophthora infestans to Azoxystrobin Fungicide

“…SSR data of isolates collected from seven out of the nine field P. infestans populations (Ningxia, Gansu, Guizhou, Yunnan, Xiapu, Fuzhou, and Guangxi) were taken from earlier publications [22,39,40]; whereas, the genotypic data of the isolates for the remaining two populations (Inner Mongolia and Wuhan) were generated following the same protocols. In summary, mycelia (~100 mg) obtained from the individual isolates of P. infestans grown on rye B agar at 19 • C were composed and kept in 2 mL centrifuge tubes.…”

Trend of Biotechnology Applications in Pest Management: A Review

“…Table 3 describe the review of the application of some of the new genetic medication techniques (nGM) or new breeding techniques (NBTs) (i) RNAi, (ii) Cisgenics and intragenics, (iii) Gene editing in general, (iv) Genome editing specifically using CRIPR Cas9 in pest management. (Vincelli, 2016;Scott et al, 2016;Sniezko and Koch, 2017;Dong and Ronald., 2019) insect pest management (Mabubu et al, 2016;Dar et al, 2017b;Sniezko and Koch, 2017;Alphey and Bonsall, 2018) Herbicide-resistant crops (Kniss 2018;Fartyal et al, 2018) Intragenics diversity in effector genes of banana disease (Stergiopoulos et al, 2014), and potato disease (Yang et al, 2018) understanding of the evolution of insect epigenetic systems (Hunt et al, 2014) glyphosate resistance in Chilepepper (Ortegaet al, 2018), sugarcane resistance to herbicide (Dermawan et al, 2016 )…”