Comparative Genomic and Proteomic Analyses of Three Widespread Phytophthora Species: Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae

Abstract

The Phytophthora genus includes some of the most devastating plant pathogens. Here we report draft genome sequences for three ubiquitous Phytophthora species—Phytophthora chlamydospora, Phytophthora gonapodyides, and Phytophthora pseudosyringae. Phytophthora pseudosyringae is an important forest pathogen that is abundant in Europe and North America. Phytophthora chlamydospora and Ph. gonapodyides are globally widespread species often associated with aquatic habitats. They are both regarded as opportunistic plant pathogens. The three sequenced genomes range in size from 45 Mb to 61 Mb. Similar to other oomycete species, tandem gene duplication appears to have played an important role in the expansion of effector arsenals. Comparative analysis of carbohydrate-active enzymes (CAZymes) across 44 oomycete genomes indicates that oomycete lifestyles may be linked to CAZyme repertoires. The mitochondrial genome sequence of each species was also determined, and their gene content and genome structure were compared. Using mass spectrometry, we characterised the extracellular proteome of each species and identified large numbers of proteins putatively involved in pathogenicity and osmotrophy. The mycelial proteome of each species was also characterised using mass spectrometry. In total, the expression of approximately 3000 genes per species was validated at the protein level. These genome resources will be valuable for future studies to understand the behaviour of these three widespread Phytophthora species.

Evolutionary dynamics of transposable elements in bdelloid rotifers

“…For genomes from species with very high intragenomic homologous divergence ( A. ricciae and A. vaga ), redundancy among multiple BUSCO gene copies was removed by selecting the copy with the highest BUSCO score, using the script ‘BUSCO_collapse_multicopy.pl’ ( Nowell, 2020 ). One-to-one co-orthologs found in at least 95% of the samples were then identified using the script ‘BUSCO_phylogenomics.py’ ( McGowan et al, 2020 ). Protein sequences were aligned using Clustalo ( Sievers et al, 2011 ) and concatenated in Geneious Prime v2020.1.2 ( Kearse et al, 2012 ).…”

Trichoderma Counteracts the Challenge of Phytophthora nicotianae Infections on Tomato by Modulating Plant Defense Mechanisms and the Expression of Crinkler, Necrosis-Inducing Phytophthora Protein 1, and Cellulose-Binding Elicitor Lectin Pathogenic Effectors

“…Phytophthora species also secrete a large array of effectors during infection of the plant hosts ( Stam et al, 2013 ). Effectors of several species of Phytophthora have been identified ( Chepsergon et al, 2020 ; McGowan et al, 2020 ). Among these, the Crinkler (CRN) proteins are a family of effectors that cause necrosis in the cells of the host and also induce further intracellular effectors that target the host nucleus during infection ( Stam et al, 2013 ).…”

The mitogenome of Phytophthora agathidicida: Evidence for a not so recent arrival of the “kauri killing” Phytophthora in New Zealand

“…Mitogenome size and gene content is also broadly similar to those reported for other Phytophthora species. For example, all available Phytophthora mitogenomes contain the same 35 protein-coding genes of known function (i.e., 18 respiratory chain proteins, 16 ribosomal proteins, and an import protein) and two ribosomal RNA genes (e.g., [ 59 , 60 ]). However, despite these similarities no previously reported Phytophthora mitogenome has the same structural arrangement as that identified for the clade 5 taxa.…”