Phytophthora Megakarya and Phytophthora Palmivora, Closely Related Causal Agents of Cacao Black Pod Rot, Underwent Increases in Genome Sizes and Gene Numbers by Different Mechanisms

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dc.contributor.authorAli, Shahin S.en_US
dc.contributor.authorShao, Jonathanen_US
dc.contributor.authorLary, David J.en_US
dc.contributor.authorKronmiller, Brent A.en_US
dc.contributor.authorShen, Danyuen_US
dc.contributor.authorStrem, Mary D.en_US
dc.contributor.authorAmoako-Attah, Ishmaelen_US
dc.contributor.authorAkrofi, Andrew Yawen_US
dc.contributor.authorBegoude, B. A. Didieren_US
dc.contributor.authorten Hoopen, G. Martijnen_US
dc.contributor.authorCoulibaly, Klotiolomaen_US
dc.contributor.authorKebe, Boubacar Ismaelen_US
dc.contributor.authorMelnick, Rachel L.en_US
dc.contributor.authorGuiltinan, Mark J.en_US
dc.contributor.authorTyler, Brett M.en_US
dc.contributor.authorMeinhardt, Lyndel W.en_US
dc.contributor.authorBailey, Bryan A.en_US
dc.contributor.utdAuthorLary, David J.en_US
dc.date.accessioned2018-06-01T16:15:29Z
dc.date.available2018-06-01T16:15:29Z
dc.date.created2017-03-01
dc.date.issued2017-03-01en_US
dc.descriptionIncludes supplementary materialen_US
dc.description.abstractPhytophthora megakarya (Pmeg) and Phytophthora palmivora (Ppal) are closely related species causing cacao black pod rot. Although Ppal is a cosmopolitan pathogen, cacao is the only known host of economic importance for Pmeg. Pmeg is more virulent on cacao than Ppal. We sequenced and compared the Pmeg and Ppal genomes and identified virulence-related putative gene models (PGeneM) that may be responsible for their differences in host specificities and virulence. Pmeg and Ppal have estimated genome sizes of 126.88 and 151.23Mb and PGeneM numbers of 42,036 and 44,327, respectively. The evolutionary histories of Pmeg and Ppal appear quite different. Postspeciation, Ppal underwent whole-genome duplication whereas Pmeg has undergone selective increases in PGeneM numbers, likely through accelerated transposable element-driven duplications. Many PGeneMs in both species failed to match transcripts and may represent pseudogenes or cryptic genetic reservoirs. Pmeg appears to have amplified specific gene families, some of which are virulence-related. Analysis of mycelium, zoospore, and in planta transcriptome expression profiles using neural network self-organizing map analysis generated 24 multivariate and nonlinear self-organizing map classes. Many members of the RxLR, necrosis-inducing phytophthora protein, and pectinase genes families were specifically induced in planta. Pmeg displays a diverse virulence-related gene complement similar in size to and potentially of greater diversity than Ppal but it remains likely that the specific functions of the genes determine each species' unique characteristics as pathogens.en_US
dc.description.departmentSchool of Natural Sciences and Mathematicsen_US
dc.description.sponsorshipUSDA National Institute of Food and Agriculture Hatch project 1003147en_US
dc.identifier.bibliographicCitationAli, Shahin S., Jonathan Shao, David J. Lary, Brent A. Kronmiller, et al. 2017. "Phytophthora megakarya and Phytophthora palmivora, Closely Related Causal Agents of Cacao Black Pod Rot, Underwent Increases in Genome Sizes and Gene Numbers by Different Mechanisms." Genome Biology and Evolution 9(3), doi:10.1093/gbe/evx021en_US
dc.identifier.issn1759-6653en_US
dc.identifier.issue3en_US
dc.identifier.urihttp://hdl.handle.net/10735.1/5814
dc.identifier.volume9en_US
dc.relation.urihttp://dx.doi.org/10.1093/gbe/evx021
dc.rightsOxford Academic states that this article is "open access" without further definition.en_US
dc.rights©2017 Crown.en_US
dc.sourceGenome Biology and Evolution
dc.subjectCacaoen_US
dc.subjectPhytophthora pod rot of cacaoen_US
dc.subjectPhytophthoraen_US
dc.subjectGenomesen_US
dc.titlePhytophthora Megakarya and Phytophthora Palmivora, Closely Related Causal Agents of Cacao Black Pod Rot, Underwent Increases in Genome Sizes and Gene Numbers by Different Mechanismsen_US
dc.type.genrearticleen_US

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