Mitochondrial Haplotype Determination in the Oomycete Plant Pathogen Phytophthora Ramorum

Overview

Journal Curr Genet

Specialty Genetics

Date 2008 May 20

PMID 18488228

Citations 10

Authors

Frank N Martin

Affiliations

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Abstract

The mitochondrial genome of an isolate of Phytophthora ramorum from Europe (EU) was sequenced and compared to the previously published genome sequence of an isolate from California (NA). The EU mitochondrial genome had the identical gene order and encoded for the same suite of genes as the NA mitochondrial genome, but had 13 single nucleotide polymorphisms (SNPs) and at 39,494 bp was 180 bp longer. This length difference was due to an increase in the size of the spacer region between the nad5 and nad6 genes caused by a chimeric region containing duplication of the spacer sequence and additional sequences from the flanking genes. Recombination between the 1,150 bp-inverted repeats (IR) generated orientational isomers where the gene order was reversed between the IR. A total of seven primer pairs were developed for amplification of regions where the SNPs were located and two other regions where additional SNPs were encountered when a larger number of isolates were examined. Sequence data for a total of 5,743 bp for 40 isolates collected from a range of geographic areas was compared and 28 loci were found to be polymorphic. The combination of these polymorphisms revealed a total of 4 mitochondrial haplotypes; the traditional EU (haplotype I), the traditional NA (haplotype IIa), the third nuclear lineage of the pathogen recovered from a nursery in Washington State (haplotype III) and a new haplotype representing a subgroup of NA isolates from an Oregon forest (haplotype IIb). Phylogenetic analysis using the sequences generated from the haplotype analysis supported a high affinity for haplotypes IIa and IIb, both of which were distinct from haplotype I, with haplotype I basal to these and haplotype III representing the ancestral state.

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References

Brasier C . Sudden oak death: Phytophthora ramorum exhibits transatlantic differences. Mycol Res. 2003; 107(Pt 3):258-9. DOI: 10.1017/s0953756203227660. View

Martin F, Bensasson D, Tyler B, Boore J . Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojae. Curr Genet. 2007; 51(5):285-96. DOI: 10.1007/s00294-007-0121-6. View

Grayburn W, Hudspeth D, Gane M, Hudspeth M . The mitochondrial genome of Saprolegnia ferax: organization, gene content and nucleotide sequence. Mycologia. 2010; 96(5):981-9. View

Martin F, Tooley P . Phylogenetic relationships among Phytophthora species inferred from sequence analysis of mitochondrially encoded cytochrome oxidase I and II genes. Mycologia. 2010; 95(2):269-84. View

Ivors K, Garbelotto M, Vries I, Ruyter-Spira C, Te Hekkert B, Rosenzweig N . Microsatellite markers identify three lineages of Phytophthora ramorum in US nurseries, yet single lineages in US forest and European nursery populations. Mol Ecol. 2006; 15(6):1493-505. DOI: 10.1111/j.1365-294X.2006.02864.x. View

Paquin B, Laforest M, Forget L, Roewer I, Wang Z, Longcore J . The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression. Curr Genet. 1997; 31(5):380-95. DOI: 10.1007/s002940050220. View

Kroon L, Verstappen E, Kox L, Flier W, Bonants P . A Rapid Diagnostic Test to Distinguish Between American and European Populations of Phytophthora ramorum. Phytopathology. 2008; 94(6):613-20. DOI: 10.1094/PHYTO.2004.94.6.613. View

Ivors K, Hayden K, Bonants P, Rizzo D, Garbelotto M . AFLP and phylogenetic analyses of North American and European populations of Phytophthora ramorum. Mycol Res. 2004; 108(Pt 4):378-92. DOI: 10.1017/s0953756204009827. View

Schena L, Cooke D . Assessing the potential of regions of the nuclear and mitochondrial genome to develop a "molecular tool box" for the detection and characterization of Phytophthora species. J Microbiol Methods. 2006; 67(1):70-85. DOI: 10.1016/j.mimet.2006.03.003. View

10.

Brudno M, Do C, Cooper G, Kim M, Davydov E, Green E . LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 2003; 13(4):721-31. PMC: 430158. DOI: 10.1101/gr.926603. View

11.

Avila-Adame C, Gomez-Alpizar L, Zismann V, Jones K, Buell C, Ristaino J . Mitochondrial genome sequences and molecular evolution of the Irish potato famine pathogen, Phytophthora infestans. Curr Genet. 2005; 49(1):39-46. DOI: 10.1007/s00294-005-0016-3. View

12.

Frazer K, Pachter L, Poliakov A, Rubin E, Dubchak I . VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004; 32(Web Server issue):W273-9. PMC: 441596. DOI: 10.1093/nar/gkh458. View

13.

Prospero S, Hansen E, Grunwald N, Winton L . Population dynamics of the sudden oak death pathogen Phytophthora ramorum in Oregon from 2001 to 2004. Mol Ecol. 2007; 16(14):2958-73. DOI: 10.1111/j.1365-294X.2007.03343.x. View

14.

Mayor C, Brudno M, Schwartz J, Poliakov A, Rubin E, Frazer K . VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinformatics. 2001; 16(11):1046-7. DOI: 10.1093/bioinformatics/16.11.1046. View

15.

Lowe T, Eddy S . tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997; 25(5):955-64. PMC: 146525. DOI: 10.1093/nar/25.5.955. View

16.

Gordon D, Abajian C, Green P . Consed: a graphical tool for sequence finishing. Genome Res. 1998; 8(3):195-202. DOI: 10.1101/gr.8.3.195. View

17.

Martin F, Tooley P, Blomquist C . Molecular Detection of Phytophthora ramorum, the Causal Agent of Sudden Oak Death in California, and Two Additional Species Commonly Recovered from Diseased Plant Material. Phytopathology. 2008; 94(6):621-31. DOI: 10.1094/PHYTO.2004.94.6.621. View

18.

Hudspeth M, Shumard D, Bradford C, Grossman L . Organization of Achlya mtDNA: a population with two orientations and a large inverted repeat containing the rRNA genes. Proc Natl Acad Sci U S A. 1983; 80(1):142-6. PMC: 393326. DOI: 10.1073/pnas.80.1.142. View