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.
Highlights
Oomycetes are one of the most devastating groups of plant pathogens, resembling mostly filamentous fungi
The highest number of proteins were predicted (36,721) from P. syringae BL57G having a genome size of 74.93 Mb, whereas the lowest was predicted from P. kernoviae Chile4, Phyke_Chile4 with a genome size of ∼37 Mb
Other isolates of P. kernoviae remain the genomes with the least number of genes (
Summary
Oomycetes are one of the most devastating groups of plant pathogens, resembling mostly filamentous fungi. Phytophthora, the notorious causal agent for the infamous Irish potato famine, is the most common and pathogenic genus of oomycetes that have more than 180 formal species and are abundant in almost all ecosystems (Yang et al, 2017) They are usually soil-borne in nature and have a wide host range causing the root rot, stem rot, blight, and fruit rot of herbaceous and woody plants (Dodds and Rathjen, 2010). Many annotation pipelines are available recently, and the notable ones such as BRAKER2 (Bruna et al, 2021), funannotate, and MAKER (Cantarel et al, 2008) require proper training datasets for predicting gene models. Several oomycetes genome resources such as eumicrobedb.org (Panda et al, 2018) and FungiDB (Basenko et al, 2018) have been created and maintained by community members While both eumicrobedb and FungiDB are primarily based on the genome unified schema (Clark et al, 2005), the portability and ease of handling data are very difficult. There is a need for creating resources that can be updated
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