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Title: Analysis of the complete mitochondrial genome sequences of the soybean rust pathogens Phakopsora pachyrhizi and P. meibomiae

Author
item Stone, Christine
item POSADA-BUITRAGO, MARTHA - Joint Genome Institute
item BOORE, JEFFREY - Joint Genome Institute
item Frederick, Reid

Submitted to: Mycologia
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/16/2009
Publication Date: 6/23/2010
Citation: Stone, C.L., Posada-Buitrago, M.L., Boore, J.L., Frederick, R.D. 2010. Analysis of the complete mitochondrial genome sequences of the soybean rust pathogens Phakopsora pachyrhizi and P. meibomiae. Mycologia. 102(4):887-987.

Interpretive Summary: Soybean rust is a serious foliar disease in most soybean growing regions of the world including the U.S. Two closely related species of fungi, Phakopsora pachyrhizi and P. meibomiae, can cause soybean rust. In this study, the mitochondrial genomes of the two Phakopsora species were sequenced and found to contain genes that encode for 15 proteins, as well as, RNAs needed for protein synthesis. Gene order comparisons and phylogenetic analyses were made with all available fungal mitochondrial genomes, and our analysis supports current fungal taxonomy. Sequence differences were observed between the two Phakopsora species in the non-coding regions that might be useful for plant pathologists to develop molecular probes for diagnostic assays or possibly strain identification.

Technical Abstract: The mitochondrial (mt) genomes of two soybean rust pathogens, Phakopsora pachyrhizi and P. meibomiae, have been sequenced. The mt genome of P. pachyrhizi is a circular 31,825-bp molecule with a mean GC content of 34.6 percent, while P. meibomiae possesses a 32,520-bp circular molecule with a mean GC content of 34.9 percent. Both mt genomes contain the genes encoding ATP synthase subunits 6, 8, and 9 (atp6, atp8, and atp9), cytochrome oxidase subunits I, II, and III (cox1, cox2, and cox3), apocytochrome b (cob), reduced nicotinamide adenine dinucleotide ubiquinone oxidoreductase subunits (nad1, nad2, nad3, nad4, nad4L, nad5, and nad6), the large and small mt ribosomal RNA genes, one ORF coding for a ribosomal protein (rps3), and a set of 24 tRNA genes that recognize codons for all amino acids. The order of the protein-coding genes and the order and occurrence of tRNAs is identical between the two Phakopsora species, and all of the genes are transcribed from the same DNA strand in a clockwise manner. Introns were identified in the cox1, cob, and rnl genes of both species, with three of the introns having ORFs with motifs similar to the LAGLIDADG endonucleases of other fungi. Phylogenetic analysis of the 14 shared protein-coding genes agrees with commonly accepted fungal taxonomy.