Comparative Genome Analysis Across 128 Phytophthora Isolates Reveal Species-Specific Microsatellite Distribution and Localized Evolution of Compartmentalized Genomes

Abstract

Phytophthora sp. are invasive groups of pathogens belonging to class Oomycetes. In order to contain and control them, a deep knowledge of their biology and infection strategy is imperative. With the availability of large-scale sequencing data, it has been possible to look directly into their genetic material and understand the strategies adopted by them for becoming successful pathogens. Here, we have studied the genomes of 128 Phytophthora species available publicly with reasonable quality. Our analysis reveals that the simple sequence repeats (SSRs) of all Phytophthora sp. follow distinct isolate specific patterns. We further show that TG/CA dinucleotide repeats are far more abundant in Phytophthora sp. than other classes of repeats. In case of tri- and tetranucleotide SSRs also, TG/CA-containing motifs always dominate over others. The GC content of the SSRs are stable without much variation across the isolates of Phytophthora. Telomeric repeats of Phytophthora follow a pattern of (TTTAGGG)n or (TTAGGGT)n rather than the canonical (TTAGGG)n. RxLR (arginine-any amino acid-leucine-arginine) motifs containing effectors diverge rapidly in Phytophthora and do not show any core common group. The RxLR effectors of some Phytophthora isolates have a tendency to form clusters with RxLRs from other species than within the same species. An analysis of the flanking intergenic distance clearly indicates a two-speed genome organization for all the Phytophthora isolates. Apart from effectors and the transposons, a large number of other virulence genes such as carbohydrate-active enzymes (CAZymes), transcriptional regulators, signal transduction genes, ATP-binding cassette transporters (ABC), and ubiquitins are also present in the repeat-rich compartments. This indicates a rapid co-evolution of this powerful arsenal for successful pathogenicity. Whole genome duplication studies indicate that the pattern followed is more specific to a geographic location. To conclude, the large-scale genomic studies of Phytophthora have thrown light on their adaptive evolution, which is largely guided by the localized host-mediated selection pressure.

High-Throughput Microsatellite Markers Development for Genetic Characterization of Emerging Sporothrix Species

“…It is often accepted that larger genomes harbor more SSRs than smaller ones; although, there is no clear association between SSR content and genome size [ 79 , 80 , 81 ]. This statement does not seem proper for fungi, as several fungal species have varying SSR frequencies and abundances in their genomes, despite having equivalent genome sizes [ 82 ].…”

Histone (de)acetylation in epigenetic regulation of Phytophthora pathobiology

“…Effector genes are enriched in these specific genomic compartments (Dong et al., 2015 ; Raffaele & Kamoun, 2012 ). A recent report describing 128 Phytophthora species revealed that, apart from effectors, many other virulence genes encoding carbohydrate‐active enzymes (CAZymes), transcriptional regulators, signal transduction genes, ATP‐binding cassette transporters, and ubiquitins are also present in the repeat‐rich compartments (Mandal et al., 2022 ). Effector genes display expression polymorphisms, and the growing body of evidence suggests that these gene expression polymorphisms contribute to microbial responses to environmental challenges.…”

Exploring Phytophthora agathidicida Oospore Viability and Germination

“…Unfortunately, many Phytophthora species have developed resistance to numerous compounds we use to control them. An abundance of transposable elements, mobile genetic elements, have facilitated the large expansion of many Phytophthora genomes (Gijzen, 2009;Mandal et al, 2022;Raffaele & Kamoun, 2012;Tyler et al, 2006). This has resulted in the duplication and evolution of many effector proteins (involved in virulence and pathogenicity) and detoxification enzymes that increase resistance to fungicides (Mandal et al, 2022;Tyler et al, 2006;.…”