|Genomic signatures of host jumping onto raspberry and strawberry in two Phytophthora sister taxa|
J. F. TABIMA (1), D. Shen (2), B. Kronmiller (1), B. J. Knaus (3), C. M. Press (3), I. A. Zasada (1), B. M. Tyler (1), N. J. Grünwald (3). (1) Oregon State University, Corvallis, OR, U.S.A.; (2) Nanjing Agricultural University, Nanjing, Chile; (3) USDA ARS, Corvallis, OR, U.S.A.
Contrasting the genomes of sister taxa with narrow but different host ranges provides an ideal system for studying host adaptation. Selection pressures imposed by different hosts are expected to lead to adaptation by gradual divergence of populations and eventual speciation due to reproductive isolation. This process of host-mediated speciation is expected to leave signatures (such as mutations, recombination, indels, or duplications) in the corresponding pathogen genomes. We sequenced and annotated the genomes of two sister species in the plant pathogen genus<i> Phytophthora</i>, <i>P. rubi</i> and <i>P. fragariae</i>, to study which genomic signatures are involved in host adaptation (<i>P. rubi</i> and <i>P. fragariae</i> exclusively infects the genus <i>Rubus</i> or <i>Fragariae</i>, respectively). Genomes were assembled using SOAPdenovo version 1.05. Gene calling was performed using MAKER. The genomes of <i>P. rubi </i>and <i>P. fragariae</i> yielded 9,434 scaffolds and an estimated 18,268 genes for <i>P. rubi </i>and 8,511 scaffolds and 17,832 genes for <i>P. fragariae</i>. Functional annotation showed a similar number of genes involved in different biochemical pathways, such as sugar processing, metabolism, and amino acid synthesis between the two species. Positive selection (dN/dS) was detected for three pairs of orthologous effector proteins in the RxLR class. Work is ongoing to identify other candidate genes under selection and genomic signatures that may have been involved in the process of speciation via host jumping.