AUTHOR=Rojas-Estevez Paola , Urbina-Gómez David A. , Ayala-Usma David A. , Guayazan-Palacios Natalia , Mideros Maria Fernanda , Bernal Adriana J. , Cardenas Martha , Restrepo Silvia 

TITLE=Effector Repertoire of Phytophthora betacei: In Search of Possible Virulence Factors Responsible for Its Host Specificity

JOURNAL=Frontiers in Genetics

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.00579

DOI=10.3389/fgene.2020.00579

ISSN=1664-8021

ABSTRACT=<p><italic>Phytophthora betacei</italic> is an oomycete plant pathogen closely related to <italic>Phytophthora infestans.</italic> It infects tree tomato (<italic>Solanum betaceum</italic>) in northern South America, but is, under natural conditions, unable to infect potatoes or tomatoes, the main hosts of its sister species <italic>P. infestans</italic>. We characterized, and compared the effector repertoires of <italic>P. betacei</italic> and other <italic>Phytophthora</italic> species. To this end, we used <italic>in silico</italic> approaches to predict and describe the repertoire of secreted proteins in <italic>Phytophthora</italic> species and determine unique and core effectors. <italic>P. betacei</italic> has the largest proteome and secretome of all <italic>Phytophthora</italic> species evaluated. We identified between 450 and 1933 candidate effector genes in <italic>Phytophthora ramorum, Phytophthora sojae, Phytophthora cactorum, Phytophthora parasitica, Phytophthora palmivora, P. infestans</italic>, and <italic>P. betacei</italic> genomes. The <italic>P. betacei</italic> predicted secretome contains 5653 proteins, 1126 of which are apoplastic effectors and 807cytoplasmic effectors. Genes encoding cytoplasmic effectors include 791 genes with an RxLR domain (the largest number known so far in a <italic>Phytophthora</italic> species) and 16 with a Crinkler (CRN) domain. We detected homologs of previously described avirulence gene (Avr) present in <italic>Phytophthora</italic> spp., such as Avr1, Avr3b, Avr4, and Avrblb1, suggesting a high level of effector gene conservation among <italic>Phytophthora</italic> species. Nonetheless, fewer CRN effectors were obtained in <italic>P. betacei</italic> compared to all other <italic>Phytophthora</italic> species analyzed. The comparison between <italic>P. infestans</italic> and <italic>P. betacei</italic> effector profiles shows unique features in <italic>P. betacei</italic> that might be involved in pathogenesis and host preference. Indeed, 402 unique predicted effector genes were detected in <italic>P. betacei</italic>, corresponding to 197 apoplastic effector genes, 203 RxLR cytoplasmic effector genes, and 2 effector genes with CRN domain. This is the first characterization of the effector profile of <italic>P. betacei</italic> and the broadest comparison of predicted effector repertoires in the genus <italic>Phytophthora</italic> following a standardized prediction pipeline. The resultant <italic>P. betacei</italic> putative effector repertoire provides a reasonable set of proteins whose experimental validation could lead to understand the specific virulence factors responsible for the host specificity of this species.</p>