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

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%, while P. meibomiae possesses a 32 520-bp circular molecule with a mean GC content of 34.9%. 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 tRNA is identical in the two Phakopsora species, and all genes are transcribed from the same DNA strand clockwise. 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.

• Basidiomycota
• codon usage
• comparative genomics
• gene order
• genome organization
• intron
• LAGLIDADG motif
• mitochondrial DNA

We thank Paul Tooley and Doug Luster for their critical review of this manuscript. The use of trade, firm or corporation names in thisPUBLICation is for the information and benefit of the reader. Such use does not constitute an official endorsement or approval by the USDA Agricultural Research Service of any product or service to the exclusion of others that may be suitable. This work was performed partly under the auspices of the US Department of Energy’s Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory, under contract No. DE-AC02-05CH11231.