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Title:   Author  item
                                            Knaus, Brianitem
                                            TABIMA, JAVIER - Oregon State Universityitem
                                            DAVIS, CRISTINA - University Of Californiaitem
                                            JUDELSON, HOWARD - University Of Californiaitem
                                            Grunwald, Niklaus

                                                         - *Nik*
  Submitted to: Phytopathology
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 6/14/2016
                                    Publication  Date: 8/25/2016
                                    Citation: Knaus, B.J., Tabima, J.F., Davis, C.E., Judelson, H.S., Grunwald, N.J. 2016. Genomic analyses of dominant U.S. clonal lineages of Phytophthora infestans reveals a shared common ancestry for clonal lineages US11 and US18 and a lack of recently shared ancestry among all other U.S. lineages. Phytopathology. 106(11):1393-1403. doi: 10.1094/PHYTO-10-15-0279-R.Interpretive Summary: The populations of the potato and tomato late blight pathogen, Phytophthora infestans, in the US exist as clones that are occasionally replaced by a new clone. Clones are identified using molecular tools and by definition lack sex. These successions of dominant clones have historically been named US1-US24, in order of appearance, since their first characterization. Hypothetically, a clone can emerge by descent from a previously existing clone or as novel, independent clone. We tested these different evolutionary scenarios using whole genome sequences. In general, we found no support for emergence of any clone from a common ancestor shared with any other clone. Each of the US clones fit a model where populations of new clonal lineages emerge via migration from a source population that is sexual in nature. This work provides novel insights into how pant pathogens evolve.
                                Technical Abstract: The populations of the potato and tomato late blight pathogen, Phytophthora infestans, in the US are well known for emerging repeatedly as novel clonal lineages. These successions of dominant clones have historically been named US1-US24, in order of appearance, since their first characterization using molecular markers. Hypothetically, these lineages can emerge by descent from prior lineages or as novel, independent lineages. We tested for the presence of phylogenetic relationships using 33 whole genome sequences including dominant US clonal lineages as well as representative samples from global populations. We analyzed ancestry of the whole mitochondrial genome and samples of nuclear loci including supercontig 1.1 and 1.5 as well as several previously characterized coding regions. In general, we found no support for emergence of any lineage from a common ancestor shared with any other lineage. Each of the US clonal lineages fit a model where populations of new clonal lineages emerge via migration from a source population that is sexual in nature and potentially located in central Mexico. This work provides novel insights into patterns of emergence of clonal lineages in plant pathogen genomes.


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