RESUMO
Phytophthora betacei is an oomycete plant pathogen closely related to Phytophthora infestans. It infects tree tomato (Solanum betaceum) in northern South America, but is, under natural conditions, unable to infect potatoes or tomatoes, the main hosts of its sister species P. infestans. We characterized, and compared the effector repertoires of P. betacei and other Phytophthora species. To this end, we used in silico approaches to predict and describe the repertoire of secreted proteins in Phytophthora species and determine unique and core effectors. P. betacei has the largest proteome and secretome of all Phytophthora species evaluated. We identified between 450 and 1933 candidate effector genes in Phytophthora ramorum, Phytophthora sojae, Phytophthora cactorum, Phytophthora parasitica, Phytophthora palmivora, P. infestans, and P. betacei genomes. The P. betacei 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 Phytophthora species) and 16 with a Crinkler (CRN) domain. We detected homologs of previously described avirulence gene (Avr) present in Phytophthora spp., such as Avr1, Avr3b, Avr4, and Avrblb1, suggesting a high level of effector gene conservation among Phytophthora species. Nonetheless, fewer CRN effectors were obtained in P. betacei compared to all other Phytophthora species analyzed. The comparison between P. infestans and P. betacei effector profiles shows unique features in P. betacei that might be involved in pathogenesis and host preference. Indeed, 402 unique predicted effector genes were detected in P. betacei, 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 P. betacei and the broadest comparison of predicted effector repertoires in the genus Phytophthora following a standardized prediction pipeline. The resultant P. betacei 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.
RESUMO
In Colombia, late blight is considered one of the most limiting diseases on potato and tomato production. Recently, a new Phytophthora species, P. betacei, was described infecting tree tomato crops in the south of Colombia. However, the distribution and the host range of this new emerging pathogen in the country are unknown. The main aims of this study were to determine if this novel species is confined to the south of Colombia, to assess if P. betacei represents a genetically uniform clone across Colombia and to determine if in all regions there is a clear differentiation between the two Phytophthora species. Therefore, we characterized Phytophthora isolates obtained from tree tomato and potato crops in a central region of Colombia and compared them with the strains from the south. Initially, we evaluated the genetic differentiation among Phytophthora strains obtained from tree tomato and potato crops using simple sequence repeat markers. Results showed a strong population structure between P. infestans and P. betacei. However, we did not detect any genetic differentiation within P. infestans or P. betacei populations from different regions. Furthermore, we detected significant morphological differences among the species based on growth and sporangial morphology measurements. We also showed that strains of Phytophthora spp. are predominantly of the A1 mating type and belong to EC-1 and EC-3 clonal lineages for P. infestans and P. betacei, respectively. Our results describe the expanded geographical range of the new species of P. betacei in the central region of Colombia.
Assuntos
Phytophthora infestans/genética , Solanum tuberosum , Colômbia , Repetições de Microssatélites , Doenças das PlantasRESUMO
Pathogen variation plays an important role in the dynamics of infectious diseases. In this study, the genetic variation of 279 Phytophthora infestans isolates was assessed using a combination of 12 microsatellite simple-sequence repeat markers. Isolates were collected from 11 different potato cultivars in 11 different geographic localities of the central region of Colombia. The objective of this study was to determine whether populations were differentiated by host genotype or geographic origin. Within a single clonal lineage, EC-1, 76 genotypes were detected. An analysis of molecular variance attributed most of the variation to differences within host genotypes rather than among the host genotypes, suggesting that host cultivars do not structure the populations of the pathogen. Furthermore, the lack of a genetic population structure according to the host cultivar was confirmed by all of the analyses, including the Bayesian clustering analysis and the minimum spanning network that used the Bruvo genetic distance, which suggested that there are no significant barriers to gene flow for P. infestans among potato cultivars. According to the geographic origin, the populations of P. infestans were also not structured, and most of the variation among the isolates was attributed to differences within localities. Only some but not all localities in the north and west of the central region of Colombia showed some genetic differentiation from the other regions. The absence of sexual reproduction of this pathogen in Colombia was also demonstrated. Important insights are discussed regarding the genetic population dynamics of the P. infestans populations of the central region of Colombia that were provided by the results. In Colombia, there is a high genetic variation within the EC-1 clonal lineage with closely related genotypes, none dominant, that coexist in a wide geographic area and on several potato cultivars.
Assuntos
Genética Populacional , Phytophthora infestans/genética , Doenças das Plantas/microbiologia , Solanum tuberosum/genética , Teorema de Bayes , Colômbia , Variação Genética , Genótipo , Phytophthora infestans/patogenicidade , Solanum tuberosum/microbiologiaRESUMO
Cassava bacterial blight, caused by Xanthomonas axonopodis pv. manihotis (Xam), is the most important bacterial disease affecting this crop. A continuous surveillance of the pathogen population dynamics is required to develop an efficient disease management program. During the 1990s, Xam populations showed high levels of genetic variation and relevant migratory processes that were important determinants of the distribution of the pathogen diversity in Colombia. Aiming to characterize the current population structure of the pathogen and the evolutionary forces that shape these populations, sampling collections were carried out from September 2008 until November 2010 in the Colombian Caribbean Region. One hundred and sixty bacterial isolates were characterized using amplified fragment length polymorphism (AFLP) markers. Additionally, a subset of effector genes were sequenced in some isolates to determine their usefulness in Xam population studies and to provide additional information to that obtained with AFLPs. Virulence patterns of ten isolates were determined in nine cassava accessions. Our results show a complex architecture of population and confirm migratory process previously reported in the Caribbean Region. Chinú, one of the locations sampled, presented remarkable features in population dynamics such as longer genetic distances, higher diversity indices, and a genetically differentiated population when it was compared with other locations. Virulence tests showed that MCOL2215, one of the most cultivated cassava varieties in the Caribbean coast, was susceptible to the majority of Xam isolates tested. This study shows the current condition of populations of Xam in the Caribbean Region of Colombia, and it contributes to improve the existing bacterial blight control practices.
Assuntos
Genética Populacional , Manihot/microbiologia , Doenças das Plantas/microbiologia , Xanthomonas axonopodis/genética , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Colômbia , DNA Bacteriano/genética , Evolução Molecular , Genes Bacterianos , Marcadores Genéticos , Haplótipos , Polimorfismo Genético , Seleção Genética , Virulência/genética , Xanthomonas axonopodis/patogenicidadeRESUMO
Late blight caused by Phytophthora infestans is one of the most limiting diseases in solanaceous crops in the world. This pathogen is a main constraint in the highland Andes, where these plants are grown under high humidity conditions and continuous cropping. The aim of this research was to increase the available information on the biology of P. infestans, specifically on its level of genetic variation in south-western Colombia, an area where various solanaceous crops susceptible to this pathogen converge. The study was carried out by using AFLP molecular markers with the restriction enzymes EcoRI and MseI and different primer combinations. Results indicated a low level of genetic variation among the 26 isolates evaluated, with only 18 polymorphic bands out of 135 amplicons obtained (13.43%), a Nei's genetic diversity index of 0.04, and a Shannon's information index of 0.06.
Assuntos
Variação Genética , Phytophthora infestans/genética , Colômbia , Phytophthora infestans/isolamento & purificação , Solanum/microbiologiaRESUMO
La gota o tizón tardío causado por Phytophthora infestans es una de lasenfermedades más limitantes en diversos cultivos de solanáceas en el mundo.Este patógeno es especialmente problemático en las zonas andinas altas,donde dichos cultivos se desarrollan bajo condiciones de alta humedad ysiembra continua durante todo el año. El objetivo de este trabajo fue aumentarla información disponible sobre la biología de P. infestans, especialmente conrespecto a su variabilidad genética en el suroeste de Colombia, región dondeconfluyen cultivos de diferentes solanáceas susceptibles a este patógeno.La evaluación se realizó mediante la utilización de marcadores molecularesAFLP con las enzimas de restricción EcoRI y MseI y diferentes combinacionesde cebadores. Los resultados obtenidos indicaron un bajo nivel de variacióngenética entre los 26 aislamientos evaluados, presentándose sólo 18 bandaspolimórficas de los 135 amplicones obtenidos (13,43%), un índice dediversidad de Nei de 0,04 y un índice de Shannon de 0,06. A pesar del altogrado de similitud encontrado en la población, el dendrograma generado porel método UPGMA permitió dividir la población en dos grandes grupos.El primero de ellos presentaba aislamientos procedentes de papa (Solanumtuberosum y Solanum phureja), mientras que el segundo incluyó soloaislamientos obtenidos de tomate de árbol (Solanum betaceum). Uno de losaislamientos evaluados (C8) no se agrupó con ninguno de los anterioresgrupos, aunque compartió un alto nivel de similitud con éstos (0,86).Los resultados apoyan la hipótesis de la estructuración poblacional deP. infestans en función del hospedante; sin embargo, esta situación requiereser verificada con evaluaciones de patogenicidad cruzada(AU)
Late blight caused by Phytophthora infestans is one of the most limitingdiseases in solanaceous crops in the world. This pathogen is a mainconstraint in the highland Andes, where these plants are grown under highhumidity conditions and continuous cropping. The aim of this research was toincrease the available information on the biology of P. infestans, specifically onits level of genetic variation in south-western Colombia, an area where varioussolanaceous crops susceptible to this pathogen converge. The study wascarried out by using AFLP molecular markers with the restriction enzymesEcoRI and MseI and different primer combinations. Results indicated a lowlevel of genetic variation among the 26 isolates evaluated, with only 18polymorphic bands out of 135 amplicons obtained (13.43%), a Nei´s geneticdiversity index of 0.04, and a Shannon´s information index of 0.06. The UPGMA dendrogram allowed dividing the population in two main groups,the first of them having the isolates collected from potato (Solanum tuberosumand Solanum phureja), while the second one included isolates obtained fromtree tomato (Solanum betaceum). One of the isolates (C8) was located outsideof these groups, although it shared a high level of similarity with them (0.86).The results support the hypothesis of population structure of P. infestansbased on host; however, this situation needs to be verified with crosspathogenicity assays(AU)