Concerted evolution of a tandemly arrayed family of mating-specific genes in Phytophthora analyzed through inter- and intraspecific comparisons

Abstract

Multigene families are features of most eukaryotic genomes, which evolve through a variety of mechanisms. This study describes the structure, expression, and evolution of a novel family in the oomycete Phytophthora. In the heterothallic species P. infestans, M96 is expressed specifically during sexual sporogenesis, and encodes a low-complexity extracellular protein that may be a component of oospore walls. Intriguingly, M96 exists in P. infestans as 22 relatively homogeneous loci tandemly repeated at a single site, which is partitioned by inversions and retroelements into subclusters exhibiting semi-independent evolution. M96 relatives were detected in other heterothallic and homothallic oomycetes including species closely (P. mirabilis, P. phaseoli) or distantly (P. ramorum, P. sojae) related to P. infestans. Those M96 relatives also exhibit oosporogenesis-specific expression and are arrayed multigene families. Nucleotide changes and repeat expansion diversify M96 in each species, however, paralogues are more related than orthologues. Concerted evolution through gene conversion and not strong purifying selection appears to be the major contributor to intraspecific homogenization. Divergence and concerted evolution was also detected between isolates of P. infestans. The divergence of M96 proteins between P. infestans, P. ramorum, and P. sojae exceeds that of typical proteins, reflecting trends in reproductive proteins from other kingdoms.

A multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences

“…In addition, some newly described Phytophthora species have been placed in an unresolved, basal group that appears to be outside the main radiation of the genus (Belbahri et al, 2006;Brasier et al, 2005;Dick et al, 2006). Establishing a well-resolved phylogeny of the genus Phytophthora is important not only for validating diagnostic methods of species identification (e.g., Kong et al, 2004;Lees et al, 2006;Martin et al, 2004;Schena et al, 2006;Tooley et al, 2006), but also for interpreting the evolutionary history of various genetic traits of interest, such as pathogenicity factors Liu et al, 2005;Whisson et al, 2004), transposable elements (Ah Fong and Judelson, 2004;Judelson, 2002), and mating types (Cvitanich et al, 2006;Qi et al, 2005).…”

Dynamics and Innovations within Oomycete Genomes: Insights into Biology, Pathology, and Evolution

“…Some clusters of repeated genes can nevertheless be found in gene-dense regions, including some protein kinases and genes involved in sexual development (14,34). P. infestans encodes 354 proteins with classic eukaryotic protein kinase domains, with other members of the genus having similar numbers.…”

Minimum Structural Requirements for Fungicidal Evaluation of N-Phenyl-O-phenylthionocarbamates against the Capsicum Phytophthora Blight (Phyophthora capsici) Based on the 3D-QSARs

“…18 In addition, we included clogP values as an additional descriptor in order to consider the hydrophobic field. The four 3D-QSAR models derived under the combination of alignments (atom based fit: AF and field fit: FF), grid Å (1-3; 0.50 Å interval), major components (3)(4)(5), and characteristic 3D-QSAR fields showed the best statistical qualities.…”

“…However, it seems that disinfectants from the phenylamide family and compounds of the metalaxy family may inhibit the permeability of the pathogen. 5,6 Because of the abuse of agrochemicals, the resistant pathogen of Phytophthora has appeared quickly and spread at a fast rate. For this reason, it now causes great damage to crops of tomatoes, calabash, red peppers, and etc.…”