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

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Abstract

The sequences of the mitochondrial genomes of the oomycetes Phytophthora ramorum and P. sojae were determined during the course of complete nuclear genome sequencing (Tyler et al., Science, 313:1261,2006). Both mitochondrial genomes are circular mapping, 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, six more open reading frames (ORFs) that are conserved, presumably due to functional constraint, across Phytophthora species (P. sojae, P. ramorum, and P. infestans), six ORFs that are unique for P. sojae and one that is unique for P. ramorum. Non-coding regions comprise about 11.5 and 18.4% 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 differed in two adjacent locations due to inversions and specific regions of the genomes exhibited greater divergence than others. For example, the breakpoints for the inversions observed in P. infestans corresponded to regions of high sequence divergence in comparisons between P. ramorum and P. sojae and the location of a hypervariable microsatellite sequence (eight repeats of 24 bp) in the P. sojae genome corresponds to a site of major length variation in P. infestans. Although the overwhelming majority of each genome is conserved (81–92%), there are a number of genes that evolve more rapidly than others. Some of these rapidly evolving genes appear specific to Phytophthora, arose recently, and future evaluation of their function and the effects of their loss could prove fruitful for understanding the phylogeny of these devastating plant pathogens.

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Acknowledgments

Thanks to Susan Lucas and all of the members of the JGI Production Sequencing Department for leading the efforts to determine these sequences. Thanks for related technical support to Jarrod Chapman, Nik Putnam, Dan Rokhsar, Astrid Terry, and Harris Shapiro. This work was supported by National Science Foundation Grant MCB-0242131 and by grant 2002-35600-12747 from the National Research Initiative of the USDA Cooperative State Research, Education and Extension Service, and 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 Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under Contract No. DE-AC02-05CH11231 and Los Alamos National Laboratory under Contract No. W-7405-ENG-36.

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Author notes

  1. Douda Bensasson

    Present address: Faculty of Life Sciences, University of Manchester, Manchester, UK

  2. Jeffrey L. Boore

    Present address: SymBio Corporation, Menlo Park, CA, USA

Authors and Affiliations

  1. USDA-ARS, Salinas, CA, 93905, USA

    Frank N. Martin

  2. DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Walnut Creek, CA, USA

    Douda Bensasson & Jeffrey L. Boore

  3. Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA

    Brett M. Tyler

  4. University of California, Berkeley, CA, USA

    Jeffrey L. Boore

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  1. Frank N. Martin
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Correspondence to Frank N. Martin.

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Communicated by L. Tomaska.

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Martin, F.N., Bensasson, D., Tyler, B.M. et al. Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojae . Curr Genet 51, 285–296 (2007). https://doi.org/10.1007/s00294-007-0121-6

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