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Phytophthora nicotianae  is one of the most destructive plant pathogens affecting a variety of plants, causing black shank of tobacco, among several other devastating diseases. Herein, we assembled the mitochondrial genome of  P. nicotianae  and analyzed its gene content and genome structure, performed comparative mitochondrial genomics analysis, and assessed phylogenetic relationships among oomycetes species. The circular mitogenome is 37,561 bp long, with 38 protein-coding genes, 25 transfer RNA (tRNA) genes, and 2 ribosomal RNA genes (rrnl and rrns). The mitochondrial genome showed a biased A/T usage versus G/C. The overall gene content and size of the  P. nicotianae  mitogenome are identical to those of other published  Phytophthora  mitogenomes. Interestingly, collinearity analysis using an existing ∼10 k inversion region (including 11 genes and 8 tRNAs) revealed that  Phytophthora andina ,  Phytophthora infestans ,  Phytophthora mirabilis ,  Phytophthora ipomoeae , and  Phytophthora phaseoli  differed from  Phytophthora nicotianae ,  Phytophthora sojae ,  Phytophthora ramorum , and  Phytophthora polonica . Moreover, inverted repeat regions were found to be absent among species of the Peronosporales when compared with species from the Pythiales and Saprolegniales. A phylogenomic investigation based on 29 protein-coding genes demonstrated that  Phytophthora  is monophyletic, and placed  P. nicotianae  close to the clade including  P. mirabilis ,  P. ipomoeae ,  P. andina ,  P. infestans , and  P. phaseoli . Furthermore, we discovered six new candidate DNA molecular markers ( rpl6 ,  atp8 ,  nad11 ,  rps2 ,  rps3 , and  rps4 ) based on these mitogenomes that would be suitable for species identification in the oomycetes, which have the same identification level as the whole mitogenome and ribosomal DNA sequences. These new molecular markers can not only provide a quick preview of the species without mitogenome information, but will also help to gain better understanding of the oomycetes pathogens and developing treatment or monitoring strategies.

Complete Mitochondrial Genome of Phytophthora nicotianae and Identification of Molecular Markers for the Oomycetes