Evolutionary relationships of the Phytophthora 1a subclade species based on complete mitogenomes, and novel markers for their differentiation
Description
Phytophthora is a genus of oomycetes containing many aggressive pathogens that devastate farmlands and forests worldwide. As the one of the oldest and most famous species, P. cactorum is morphologically and genetically similar to other homothallic species belonging to subclade 1a, making their evolutionary relationships really confused. This study primarily compared seven P. cactorum strains of diverse origins with another three most closely related species from subclade 1a based on mitogenome sequences. The four species’ circular mitogenomes were almost identical in size, containing 38 protein-coding genes, 25 transfer ribonucleic acid genes, and 2 ribosomal RNA genes. The mitochondrial genomes had a higher percentage of A/T than G/C. All PCGs began with the standard ATG codon and concluded with TAA, TAG, or TGA codons. The majority of AT-skew and GC-skew values for the 38 PCGs were positive, where the AT-skew was stronger than the GC-skew. The Ka/Ks ratios indicated that 35 PCGs were subjected to intense purifying selection. The results of the phylogenetic analysis were consistent with the pairwise genetic distances, which revealed that P. cactorum was more closely related to P. pseudotsugae than to P. hedraiandra. In this study, we characterized the entire mitogenomes of seven P. cactorum strains, three closely related species of subclade 1a, and one subclade 1b species, using the next-generation sequencing (NGS) platform Illumina NovaSeq 6000. Then, we conducted comparative analyses examining codon usage, nucleotide composition, gene content, and gene-order arrangement. We also selected the potential marker genes for the differentiation of these species. Finally, we constructed phylogenetic trees using Bayesian Inference and Maximum-Likelihood methods and estimated the divergence of the subclade 1a species using 33 protein-coding genes. The input data (and output) for molecular divergence analyzing, maximum-likelihood tree inference, and Bayesian inference, as well as input data for selection analyses, are all included in this publication.