@article{lassiter_russ_nusbaum_zeng_saville_olarte_carbone_hu_seguin-orlando_samaniego_et al._2015, title={Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species}, volume={61}, ISSN={0172-8083 1432-0983}, url={http://dx.doi.org/10.1007/s00294-015-0480-3}, DOI={10.1007/s00294-015-0480-3}, abstractNote={Phytophthora infestans is one of the most destructive plant pathogens of potato and tomato globally. The pathogen is closely related to four other Phytophthora species in the 1c clade including P. phaseoli, P. ipomoeae, P. mirabilis and P. andina that are important pathogens of other wild and domesticated hosts. P. andina is an interspecific hybrid between P. infestans and an unknown Phytophthora species. We have sequenced mitochondrial genomes of the sister species of P. infestans and examined the evolutionary relationships within the clade. Phylogenetic analysis indicates that the P. phaseoli mitochondrial lineage is basal within the clade. P. mirabilis and P. ipomoeae are sister lineages and share a common ancestor with the Ic mitochondrial lineage of P. andina. These lineages in turn are sister to the P. infestans and P. andina Ia mitochondrial lineages. The P. andina Ic lineage diverged much earlier than the P. andina Ia mitochondrial lineage and P. infestans. The presence of two mitochondrial lineages in P. andina supports the hybrid nature of this species. The ancestral state of the P. andina Ic lineage in the tree and its occurrence only in the Andean regions of Ecuador, Colombia and Peru suggests that the origin of this species hybrid in nature may occur there.}, number={4}, journal={Current Genetics}, publisher={Springer Science and Business Media LLC}, author={Lassiter, Erica S. and Russ, Carsten and Nusbaum, Chad and Zeng, Qiandong and Saville, Amanda C. and Olarte, Rodrigo A. and Carbone, Ignazio and Hu, Chia-Hui and Seguin-Orlando, Andaine and Samaniego, Jose A. and et al.}, year={2015}, month={Mar}, pages={567–577} }
 @article{ristaino_hu_fitt_2013, title={Evidence for presence of the founder Ia mtDNA haplotype of Phytophthora infestans in 19th century potato tubers from the Rothamsted archives}, volume={62}, ISSN={["0032-0862"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84876811780&partnerID=MN8TOARS}, DOI={10.1111/j.1365-3059.2012.02680.x}, abstractNote={Late blight remained a significant disease for potato growers in Europe long after the famine of the 1840s. Of the four mitochondrial haplotypes of Phytophthora infestans, only the Ia mitochondrial DNA (mtDNA) haplotype has been identified previously in infected potato leaves from famine‐era herbarium specimens collected in England, Ireland and Europe in the 19th century. Long‐term soil fertility experiments were conducted on potato between 1876 and 1901 in Rothamsted to investigate effects of combinations of organic manures and mineral fertilizers on disease and yield. This report identifies for the first time the same Ia mtDNA haplotype of P. infestans in three diseased tubers from 1877 from the long‐term Rothamsted trials, thus providing the earliest evidence of the presence of the founder Ia mtDNA haplotype of P. infestans in potato tubers in England. Soil amendments had a significant impact on disease and yield. A real‐time PCR assay was used to detect and quantify P. infestans in tubers. The level of pathogen DNA was greatest in tubers from highest yielding plots that received combinations of inorganic nitrogenous and mineral fertilizers and least in tubers from plots with organic farmyard manures or non‐nitrogenous mineral fertilizers. The Ia mtDNA haplotype was also confirmed from diseased potato leaves during the same time period. Thus, the founder Ia mtDNA haplotype survived in potato tubers after 1846 and was present over 30 years later in the UK.}, number={3}, journal={PLANT PATHOLOGY}, author={Ristaino, J. B. and Hu, C. H. and Fitt, B. D. L.}, year={2013}, month={Jun}, pages={492–500} }
 @article{hu_perez_donahoo_mcleod_myers_ivors_secor_roberts_deahl_fry_et al._2012, title={Recent Genotypes of Phytophthora infestans in the Eastern United States Reveal Clonal Populations and Reappearance of Mefenoxam Sensitivity}, volume={96}, ISSN={["1943-7692"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84866163472&partnerID=MN8TOARS}, DOI={10.1094/pdis-03-11-0156-re}, abstractNote={ Isolates of Phytophthora infestans (n = 178) were collected in 2002 to 2009 from the eastern United States, Midwestern United States, and eastern Canada. Multilocus genotypes were defined using allozyme genotyping, and DNA fingerprinting with the RG-57 probe. Several previously described and three new mulitilocus genotypes were detected. The US-8 genotype was found commonly on commercial potato crops but not on tomato. US-20 was found on tomato in North Carolina from 2002 through 2007 and in Florida in 2005. US-21 was found on tomato in North Carolina in 2005 and Florida in 2006 and 2007. US-22 was detected on tomato in 2007 in Tennessee and New York and became widespread in 2009. US-22 was found in 12 states on tomato and potato and was spread on tomato transplants. This genotype accounted for about 60% of all the isolates genotyped. The US-23 genotype was found in Maryland, Virginia, Pennsylvania, and Delaware on both tomato and potato in 2009. The US-24 genotype was found only in North Dakota in 2009. A1 and A2 mating types were found in close proximity on potato and tomato crops in Pennsylvania and Virginia; therefore, the possibility of sexual reproduction should be monitored. Whereas most individuals of US-8 and US-20 were resistant to mefenoxam, US-21 appeared to be intermediately sensitive, and isolates of US-22, US-23, and US-24 were largely sensitive to mefenoxam. On the basis of sequence analysis of the ras gene, these latter three genotypes appear to have been derived from a common ancestor. Further field and laboratory studies are underway using simple sequence repeat genotyping to monitor current changes in the population structure of P. infestans causing late blight in North America. }, number={9}, journal={PLANT DISEASE}, author={Hu, Chia-Hui and Perez, Frances G. and Donahoo, Ryan and McLeod, Adele and Myers, Kevin and Ivors, Kelly and Secor, Gary and Roberts, Pamela D. and Deahl, Kenneth L. and Fry, William E. and et al.}, year={2012}, month={Sep}, pages={1323–1330} }
 @article{robideau_cock_coffey_voglmayr_brouwer_bala_chitty_desaulniers_eggertson_gachon_et al._2011, title={DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer}, volume={11}, number={6}, journal={Molecular Ecology Resources}, author={Robideau, G. P. and Cock, A. W. A. M. and Coffey, M. D. and Voglmayr, H. and Brouwer, H. and Bala, K. and Chitty, D. W. and Desaulniers, N. and Eggertson, Q. A. and Gachon, C. M. M. and et al.}, year={2011}, pages={1002–1011} }
 @article{guo_zhu_hu_ristaino_2010, title={Genetic Structure of Phytophthora infestans Populations in China Indicates Multiple Migration Events}, volume={100}, ISSN={["1943-7684"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77958041881&partnerID=MN8TOARS}, DOI={10.1094/phyto-05-09-0126}, abstractNote={ One hundred isolates of Phytophthora infestans collected from 10 provinces in China between 1998 and 2004 were analyzed for mating type, metalaxyl resistance, mitochondrial DNA (mtDNA) haplotype, allozyme genotype, and restriction fragment length polymorphism (RFLP) with the RG-57 probe. In addition, herbarium samples collected in China, Russia, Australia, and other Asian countries were also typed for mtDNA haplotype. The Ia haplotype was found during the first outbreaks of the disease in China (1938 and 1940), Japan (1901, 1930, and 1931), India (1913), Peninsular Malaysia (1950), Nepal (1954), The Philippines (1910), Australia (1917), Russia (1917), and Latvia (1935). In contrast, the Ib haplotype was found after 1950 in China on both potato and tomato (1952, 1954, 1956, and 1982) and in India (1968 and 1974). Another migration of a genotype found in Siberia called SIB-1 (Glucose-6-phosphate isomerase [Gpi] 100/100, Peptidase [Pep] 100/100, IIa mtDNA haplotype) was identified using RFLP fingerprints among 72% of the isolates and was widely distributed in the north and south of China and has also been reported in Japan. A new genotype named CN-11 (Gpi 100/111, Pep 100/100, IIb mtDNA haplotype), found only in the south of China, and two additional genotypes (Gpi 100/100, Pep 100/100, Ia mtDNA haplotype) named CN-9 and CN-10 were identified. There were more diverse genotypes among isolates from Yunnan province than elsewhere. The SIB-1 (IIa) genotype is identical to those from Siberia, suggesting later migration of this genotype from either Russia or Japan into China. The widespread predominance of SIB-1 suggests that this genotype has enhanced fitness compared with other genotypes found. Movement of the pathogen into China via infected seed from several sources most likely accounts for the distribution of pathogen genotypes observed. MtDNA haplotype evidence and RFLP data suggest multiple migrations of the pathogen into China after the initial introduction of the Ia haplotype in the 1930s. }, number={10}, journal={PHYTOPATHOLOGY}, author={Guo, Liyun and Zhu, Xiao-Qiong and Hu, Chia-Hui and Ristaino, Jean Beagle}, year={2010}, month={Oct}, pages={997–1006} }
 @article{haas_kamoun_zody_jiang_handsaker_cano_grabherr_kodira_raffaele_torto-alalibo_et al._2009, title={Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans}, volume={461}, ISSN={["1476-4687"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-70349281388&partnerID=MN8TOARS}, DOI={10.1038/nature08358}, abstractNote={The genome of Phytophthora infestans, the pathogen that triggered the Irish potato famine in the nineteenth century, has been sequenced. It remains a devastating pathogen, with late blight destroying crops worth billions of dollars each year. Blight is difficult to control, in part because it adapts so quickly to genetically resistant potato strains. Comparison with two other Phytophthora genomes shows rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes induced during infection that have activities thought to alter host physiology. These fast evolving effector genes are found in highly dynamic and expanded regions of the genome, a factor that may contribute to its rapid adaptability to host plants. The P. infestans genome is the biggest so far sequenced, at about 240 megabases, with an extremely high repeat content of close to 75%. It is a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes related to organisms such as brown algae and diatoms. Phytophthora infestans is a fungus-like eukaryote and the most destructive pathogen of potato, with current annual worldwide potato crop losses due to late blight estimated at $6.7 billion. Here, the sequence of the P. infestans genome is reported. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of certain secreted disease effector proteins, probably explaining the rapid adaptability of the pathogen to host plants. Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement1. To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world’s population1. Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion2. Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars3,4. Here we report the sequence of the P. infestans genome, which at ∼240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for ∼74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.}, number={7262}, journal={NATURE}, publisher={Nature Publishing Group}, author={Haas, Brian J. and Kamoun, Sophien and Zody, Michael C. and Jiang, Rays H. Y. and Handsaker, Robert E. and Cano, Liliana M. and Grabherr, Manfred and Kodira, Chinnappa D. and Raffaele, Sylvain and Torto-Alalibo, Trudy and et al.}, year={2009}, month={Sep}, pages={393–398} }
 @article{gomez-alpizar_hu_oliva_forbes_ristaino_2008, title={Phylogenetic relationships of Phytophthora andina, a new species from the highlands of Ecuador that is closely related to the Irish potato famine pathogen Phytophthora infestans}, volume={100}, ISSN={["1557-2536"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-54049104885&partnerID=MN8TOARS}, DOI={10.3852/07-074R1}, abstractNote={Phylogenetic relationships of Phytophthora infestans sensu lato in the Andean highlands of South America were examined. Three clonal lineages (US-1, EC-1, EC-3) and one heterogeneous lineage (EC-2) were found in association with different host species in genus Solanum. The EC-2 lineage includes two mitochondrial (mtDNA) haplotypes, Ia and Ic. Isolates of P. infestans sensu lato EC-2 fit the morphological description of P. infestans but are different from any genotypes of P. infestans described to date. All isolates of P. infestans sensu lato from Ecuador were amplified by a P. infestans specific primer (PINF), and restriction fragment length patterns were identical in isolates amplified with ITS primers 4 and 5. The EC-1 clonal lineage of P. infestans sensu lato from S. andreanum, S. columbianum, S. paucijugum, S. phureja, S. regularifolium, S. tuberosum and S. tuquerense was confirmed to be P. infestans based on sequences of the cytochrome oxidase I (cox I) gene and intron 1 of ras gene. The EC-2 isolates with the Ic haplotype formed a distinct branch in the same clade with P. infestans and P. mirabilis, P. phaseoli and P. ipomoeae for both cox I and ras intron 1 phylogenies and were identified as the newly described species P. andina. Ras intron 1 sequence data suggests that P. andina might have arisen via hybridization between P. infestans and P. mirabilis.}, number={4}, journal={MYCOLOGIA}, author={Gomez-Alpizar, Luis and Hu, Chia-Hui and Oliva, Ricardo and Forbes, Gregory and Ristaino, Jean Beagle}, year={2008}, pages={590–602} }