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United States Department of Agriculture

Agricultural Research Service

Title: Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojae

Authors
item Martin, Frank
item Bensasson, D. - GEN.INST.BERK.NATL.LAB
item Tyler, B - VPI, BLACKSBURG, VA
item Boore, J - GEN.INST.BERK.NATL.LAB

Submitted to: Current Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 19, 2007
Publication Date: February 20, 2007
Citation: Martin, F.N., Bensasson, D., Tyler, B.M., Boore, J.L. 2007. Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojae. Current Genetics 51:285-296. DOI 10.1007/s00294-007-0121-6

Interpretive Summary: This research paper is a report on the DNA sequence analysis of the mitochondrial genomes of two important species of Phytophthora; Phytophthora ramorum (the cause of Sudden Oak Death) and Phytophthora sojae (the cause of root and stem rot of soybean). As part of this sequence analysis basic information about the mitochondrial genome was obtained, such as its size, identification of the genes that are encoded, and the order of the genes. Comparative genomics was done to evaluate the differences between the two genomes as well as with other published sequences of mitochondrial genomes of related species. This information will provide basic data on genome evolution as well as sequence information that will be useful for developing isolate and species-specific molecular markers.

Technical Abstract: The complete sequences of the mitochondrial genomes of the oomycetes Phytophthora ramorum and P. sojae were determined during the course of their complete nuclear genome sequencing (Tyler et al. 2006). Both are circular, with sizes of 39,314 bp for P. ramorum and 42,977 bp for P. sojae. Each contains a total of 37 recognizable protein-encoding genes, 26 or 25 tRNAs (P. ramorum and P. sojae, respectively) specifying 19 amino acids, 6 functionally constrained ORFs conserved across Phytophthora species (P. sojae, P. ramorum and P. infestans), 6 ORFs that are specific for P. sojae and one that is seen only in P. ramorum. Non-coding regions comprise approximately 11.5 percent and 18.4 percent of the genomes of P. ramorum and P. sojae, respectively. Relative to P. sojae, there is an inverted repeat of 1,150 bp in P. ramorum that includes an unassigned unique ORF, a tRNA gene, and adjacent non-coding sequences, but otherwise the gene order in both species is identical. Comparisons of these genomes with published sequences of the P. infestans mitochondrial genome reveals a number of similarities, but the gene order in P. infestans differs in two adjacent locations due to inversions. The location of a hypervariable microsatellite sequence in the P. sojae genome corresponds to a site of major length variation in P. infestans, but there is no sequence similarity between the sites. After taking into consideration the inversions in P. infestans, sequence alignments of the three genomes reveals that 75 to 85 percent of each genome is conserved and that specific regions evolve more rapidly than others.

Last Modified: 11/28/2014
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