Progress 09/01/01 to 09/30/05
Outputs
Nuclear and mitochondrial DNA variability was used to examine the population history of P. infestans. Multilocus sequence data from nuclear and mitochondrial loci were obtained from ninety isolates from Brazil, Bolivia, Ecuador, Peru, Costa Rica, Mexico (Toluca Valley), the United States (USA) and Ireland. Mexican populations of P. infestans from the putative center of origin in the Toluca Valley harbored less nucleotide and haplotype diversity than Andean populations, and were genetically differentiated from other populations, particularly at the mitochondrial loci. Coalescent-based genealogies of mitochondrial (rpl14, rpl5, tRna's, cox1) and nuclear loci (Intron Ras and Ras) were congruent and demonstrated the existence of two lineages leading to present day haplotypes of P. infestans on potatoes. A third lineage associated with Solanum tetrapetalum from Ecuador was identified as P. andina and evolved from a common ancestor of P. infestans. Mitocondrial lineages from
potato correspond to haplotypes I and II and share a common ancestor, but formed two lineages that have evolved independently. Nuclear and mitochondrial haplotypes found in the Toluca Valley population were derived from only one of the two lineages, whereas haplotypes from Andean populations in Peru and Ecuador were derived from both lineages and were not genetically differentiated from the USA and Ireland populations, suggesting a common ancestry. Evidence for recombination was found for Mexican and the USA populations. Our results support an Andean origin of P. infestans and also suggest that the source of inoculum for the potato famine epidemics in Ireland were from the Andean region. The mitochondrial genomes of haplotypes of the Irish Potato famine pathogen, Phytophthora infestans, were sequenced. The genome sizes were 37,922, 39,870 and 39,840 bp for the type Ia, IIa and IIb mitochondrial DNA (mtDNA) haplotypes, respectively. A large spacer flanked by the genes coding for
tRNA-Tyr and the small subunit RNA (rns) contained the largest number of polymorphic sites and corresponds to the region where a large indel that differentiates type II from type I haplotypes is located. The size of this region was 785 bp, 2,666 bp and 2,670 bp in type Ia, IIa and IIb haplotypes, respectively. Phylogenetic and coalescent analysis revealed two lineages derived from a common ancestor that corresponded to the type I and type II haplotypes. Eighty-one mutations were identified among the four haplotypes. The type II haplotypes diverged earlier and were thus, more ancestral than the type I haplotypes and do not support the previous hypotheses that the type II lineage evolved from the type I lineages. The Ia haplotype diverged earlier than the Ib and the mutations associated with this divergence were identified.
Impacts
We have identified the ancestral strain responsible for historic potato famine-era epidemics. We have also identified the pathogens center of origin in the South American Andes. We have also fully sequenced the mitochondrial genome of the pathogen and identified mutations leading to the evolution of the four extant haplotypes. This information will be useful to develop novel diagnostic assays for detection of mutational changes in the pathogen.
Publications
- Cruz Avila-Adame, Luis Gomez-Alpizar, Robin C. Buell, and Jean B. Ristaino. 2005. Mitochondrial genome sequencing of the haplotypes of the Irish Potato famine pathogen, Phytophthora infestans. Curr. Gen.: DOI10.1007/s00294-005-0016-3 (available online).
- Gomez-Alpizar, L, J. Thorne, I. Carbone, and J.B. Ristaino. 2004. Population history of Phytophthora infestans inferred from nuclear and mitochondrial DNA sequences. Phytopathology 94: S35.
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Progress 10/01/03 to 09/30/04
Outputs
Nuclear and mitochondrial DNA variability was used to examine the population history of P. infestans. DNA sequence data from three nuclear regions (Intron Ras, Ras, and beta-tubulin) and two mitochondrial regions (P3 and P4) were obtained from ninety isolates from various locations including Brazil, Bolivia, Ecuador, Peru, Costa Rica, Mexico (Toluca Valley), the United States (USA) and Ireland. Population summary statistics show that the Mexican population from the presumed center of origin of P. infestans, harbored less nucleotide and haplotype diversity than South American populations, and was genetically differentiated from other populations, particularly at the mitochondrial loci. Coalescent-based genealogies of mitochondrial loci (rpl14, rpl5, tRNAs, cox1) and nuclear loci (Intron Ras+Ras) were congruent and demonstrated the existence of two lineages leading to the present day haplotypes of P. infestans associated with potatoes. A third lineage, associated with a
group of isolates from Solanum tetrapetalum collected in the Andean Highlands of Ecuador was also found. In the mitochondrial genealogy, the two potato lineages corresponded to the mitochrondrial haplotypes Type I and Type II described elsewhere. The same mitochondrial haplotype was associated with different nuclear backgrounds. Haplotypes found in the Toluca Valley population were derived from only one of the two lineages in both mitochondrial and nuclear genealogies, whereas haplotypes found in South American populations (Peru and Ecuador) were derived from both lineages. Haplotypes found in USA and Ireland populations were also derived from both lineages and these populations were not genetically differentiated from Peruvian population, suggesting a common ancestry among these populations. Evidence for recombination was found for Mexican and the USA populations. Isolates from Solanum tetrapetalum were highly polymorphic within the regions analyzed and represent a new species.
Impacts
This work represents some of the first to use historic herbarium specimens and modern gene genealogies to identify genetic haplotypes from 19th century epidemics from the Irish potato famine and track origins and migrations. We found that the Ia haplotype was responsible for 19th century epidemics, whereas, the Ib haplotype was dispersed later from South America during the early part of the 20th century. We conducted coalescent and maximum likelihood analyses to study migration patterns of the pathogen and found that the 19th century late blight epidemics in Ireland were derived from a South American source. South American populations of P. infestans also harbored more nuclear and mitochondrial gene diversity and were genetically substructured from Mexican populations. The results support a South American center of origin of P. infestans.
Publications
- May, K. J. and Ristaino, J. B. 2003. The mitochondrial DNA haplotype of Phytophthora infestans in 19th century herbarium specimens. International Congress of Plant Pathology, Christchurch, New Zealand.
- Ristaino, J. B. 2003. Dispersal of oomycete plant pathogens: modern tools and historical epidemics. International Congress of Plant Pathology, Christchurch, New Zealand.
- Avila-Adame, C., L. Gomez-Alpizar, J. B. Ristaino, and C. R. Buell. 2004. A population genomics approach to the study of molecular evolution in Phytophthora infestans. Phytophthora Molecular Genetics Network Meeting, May 2004, New Orleans, LA.
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Progress 10/01/02 to 09/30/03
Outputs
The center of origin of P. infestans as well as the source of inoculum for the epidemic that caused the Irish potato famine in 1845 is an intriguing subject. Nuclear and mitochondrial DNA variability is being used to examine the population history of P. infestans in an attempt to answer two questions: 1) What is the phylogeographic pattern of molecular variation in P. infestans? 2) Does mitochondrial and nuclear DNA sequence evidence justify the specific hypothesis that a common ancestor of P. infestans originated in South American or Mexican populations? DNA sequence data from three nuclear regions and one mitochondrial region were collected from fifty-two isolates obtained from various locations including Brazil, Bolivia, Ecuador, Peru, Costa Rica, Mexico, USA, and Ireland. Gene genealogies were constructed for the Ras, Intron Ras, and beta-tubulin nuclear regions as well as for the mitochondrial P4 region (Cox I). Ras and Intron-Ras genealogies consisted of three
haplotypes; and beta-tubulin of two haplotypes. For the P4 region two main haplotypes were resolved corresponding to the I and II mtDNA haplotypes described elsewhere. Peruvian, USA and Irish populations shared the same haplotypes across the regions sequenced suggesting a common ancestry among these populations. A combined analysis as well as the reconstruction of the evolutionary history of the haplotyes are in progress using a combination of parsimony, maximum likelihood and coalescent methods.
Impacts
Our work represents some of the first to use historic herbarium specimens to diagnose a plant disease and identify the haplotype. We are also applying coalescent and maximum liklihood analyses to understand migration patterns in the pathogen and to identify potential sources of inoculum for 19th century epidemics. Our work has refuted previous hypotheses that the Ib haplotype was the causal agent of 19th century late blight epidemics. In addtion, we have found multiple mtDNA haplotypes in early 20th century samples from Central America, indicating that the historic populations were more diverse than previously believed.
Publications
- May, K. J. and Ristaino, J. B. 2003. Identify of the Mitochondrial DNA Haplotype(s) of Phytophthora infestans in Historical Specimens from the Irish Potato Famine. Mycological Res.:submitted.
- Gomez. L., Thorne, J., Carbone, I., and Ristaino, J.B. 2003. Population history of Phytophthora infestans inferred from nuclear and mitochondrial DNA sequences. Phytopathology 93:S30.
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Progress 09/30/01 to 10/01/02
Outputs
In this project, we are using mtDNA and nuclear gene sequences to unravel the genealogical history of the potato blight pathogen, Phytophtora infestans. The mitochondrial DNA (mtDNA) haplotype(s) of Phytophthora infestans present in dried potato and tomato leaves from herbarium specimens collected during 19th and early 20th century epidemics were identified. A 100bp fragment of rDNA specific for P. infestans was amplified from 90% of the specimens (n=186) and confirmed infection by P. infestans. Mitochondrial DNA primers were designed that distinguish four extant haplotypes. All the oldest leaves (n=60) from famine-era epidemics were infected with the Ia mtDNA haplotype. Two early 20th century potato leaves from Ecuador (1967) and Bolivia (1944) were infected with the Ib mtDNA haplotype. Two haplotypes were found in Nicaragua in the 1950's including a Ia and a IIb mtDNA haplotype. Our data indicate that the Ia haplotype of P. infestans was responsible for the historic
epidemics during the 19th century from the UK, Europe, and the US. The Ib mtDNA haplotype may have been dispersed worldwide in the early 20th century from the Andean region of South America. Work is now underway to amplify multiple nuclear and mtDNA genes from a range of modern US, UK, Central and South American isolates and to conduct phylogenetic analyses to determine the pathogens center of origin.
Impacts
This is the first time that nuclear and mtDNA of a plant pathogen has been amplified and sequenced from lesions from historic epidemics and represents an important breakthrough in the science. Sequence data from the mtDNA indicated that the Ib haplotype did not cause the lesions in the samples assayed. Our work has documented that the strain was in fact a Ia mtDNa haplotype. Our data are not consistent with present day theories that suggest that the US-1 genotype was solely responsible for epidemics of potato late blight during the Irish potato famine and later in the 19th and early 20th century in the US and Europe. Herbarium collections have not been used previously to understand epidemics of the past and track pathogen migrations. In fact, many important natural history collections have recently been critically under funded and are in jeopardy of being lost. Our work indicates that these historic collections can be valuable to epidemiologists and population
geneticists who study plant diseases. Misleading data can be derived from studies that examine only extant phylogeographic patterns of genotypes of plant pathogens. Our work emphasizes the importance of looking back with actual historic specimens when making inferences about historic populations.
Publications
- Ristaino, J. B., Groves, C. T., and Parra, G. 2001. PCR amplification of the Irish potato famine pathogen from historic specimens. Nature 41:695-697.
- Ristaino. J. B. 2002. Tracking historic migrations of the Irish potato famine Pathogen Phytophthora infestans. Microbes and Infection. 4:1369-1377.
- Wangsomboondee, T., Groves, C. T., Shoemaker, P. B., Cubeta, M. A., and Ristaino, J. B. 2002. Phytophthora infestans populations from Tomato and Potato in North Carolina differ in the genetic diversity and structure. Phytopathology 92: 1189-1195.
- May, K. J. and Ristaino, J. B. 2002. The mitochondrial DNA haplotype of Phytophthora infestans in 19th century herbarium specimens revealed. Phytopathology 92:S53.
- Gomez, L. Cafe-Filho, A. C., and Ristaino, J. B. 2002. Genetic structure of Phytophthora infestans populations from Costa Rica. Phytopathology 92:S30.
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Progress 10/01/00 to 09/30/01
Outputs
In this project, we will use mtDNA and nuclear DNA gene sequences to unravel the genealogical history of the potato late blight pathogen. Late blight caused by the pathogen Phytophthora infestans causes a devastating disease of potato and tomato in the U.S. and worldwide and epidemics in 1845 led to the Irish potato famine and the mass migration and death of over 3 million people in Ireland. Our objectives are to ask the following questions: 1) What ancestral strain was responsible for late blight epidemics that caused disease in 1845 in Ireland and Europe? Did the initial migrations of P. infestans into Europe, Ireland, and England in the 1840's contain one or multiple mtDNA types of P. infestans? 2) Does mtDNA and nuclear DNA gene sequence evidence justify the specific hypothesis that a common ancestor of P. infestans originated in South American populations? This hypothesis will be tested first by examining gene sequence evolution in the pathogen by construction of
phylogenetic trees for several genes of interest in the mitochondrial and nuclear genome in a range of isolates from a modern collection from different geographical areas in the US, Ireland, UK, Europe, Mexico, Central and South America, and in samples from historic herbarium specimens.
Impacts
The late blight research that has been conducted in my laboratory will have broad impacts on a number of disciplines. Most previous studies of plant microbe associations have been done on extant samples. First, the work is pioneering and will certainly lead to a new area of research that links forensics and molecular evolution with the science of Plant Pathology. More importantly, our research has demonstrated the importance of using actual historic materials when making inferences about historical populations. Currently, many of the population genetic studies of plant pathogens rely totally on studies of modern populations, and inferences are made about historic populations. Our work takes the unusual approach of using both modern and historic populations to study pathogen migration.
Publications
- Ristaino, J. B., Groves, C. T., and Parra, G. 2001. PCR Amplification of the Irish Potato Famine Pathogen from Historic Specimens. Nature 41:695-697.
- K. J. May, J. B. Ristaino, G. P. Parra. 2001. Identification of the mitochondrial DNA haplotype of Phytophthora infestans in 19th century herbarium specimens. Phytopathology 91:S56.
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