Comparative Analyses of Complete Peronosporaceae (Oomycota) Mitogenome Sequences—Insights into Structural Evolution and Phylogeny

Abstract

Members of the Peronosporaceae (Oomycota, Chromista), which currently consists of 25 genera and approximately 1000 recognised species, are responsible for disease on a wide range of plant hosts. Molecular phylogenetic analyses over the last two decades have improved our understanding of evolutionary relationships within Peronosporaceae. To date, 16 numbered and three named clades have been recognised; it is clear from these studies that the current taxonomy does not reflect evolutionary relationships. Whole organelle genome sequences are an increasingly important source of phylogenetic information, and in this study we present comparative and phylogenetic analyses of mitogenome sequences from 15 of the 19 currently recognized clades of Peronosporaceae, including 44 newly assembled sequences. Our analyses suggest strong conservation of mitogenome size and gene content across Peronosporaceae but, as previous studies have suggested, limited conservation of synteny. Specifically, we identified 28 distinct syntenies amongst the 71 examined isolates. Moreover, 19 of the isolates contained inverted or direct repeats, suggesting repeated sequences may be more common than previously thought. In terms of phylogenetic relationships, our analyses of 34 concatenated mitochondrial gene sequences resulted in a topology that was broadly consistent with previous studies. However, unlike previous studies concatenated mitochondrial sequences provided strong support for higher level relationships within the family.

The genome of the oomycete Peronosclerospora sorghi, a cosmopolitan pathogen of maize and sorghum, is inflated with dispersed pseudogenes

“…4). This finding parallels a previous study examining a broader array of taxa, in particular Phytophthora species [28]. The mechanisms driving this type of genome evolution has yet to be determined.…”

“…The mitogenome is likely to be a good source for molecular marker development given its unique configuration in P. sorghi compared to other Peronosporaceae species (Fig. 4) [28] and its high-copy number relative to the nuclear genome. Variation of the mitogenome within and between Peronosclerospora species should be assayed to confirm its suitability as a diagnostic marker.…”

Report of Phytophthora capsici (mating type A1) isolates associated with crown‐rot disease of Capsicum annuum in Guatemala

“…Phytophthora ilicis (P3939) was used as an outgroup. Evolutionary reconstruction using ML and BI allowed the assignment of the six isolates into the P. capsici clade 2/subclade 2b of genus Phytophthora (Winkworth et al., 2022) with high bootstrap and posterior probability values (Figure 2). Two isolates of P. glovera grouped in the same clade together with the P. capsici isolates.…”

A Whole-Genome Assembly for Hyaloperonospora parasitica, A Pathogen Causing Downy Mildew in Cabbage (Brassica oleracea var. capitata L.)

“…However, there have been few genomic studies conducted on the causative pathogen of Brassicaceae downy mildew. Until now, only three genome sequences have been reported in this group: one for Hyaloperonospora arabidopsidis , causing Arabidopais thaliana downy mildew, and two for Hyaloperonospora brassicae , causing Brassica napus downy mildew [ 15 , 16 ].…”