Identification at strain level of Rhizoctonia solani AG4 isolates by direct sequence of asymmetric PCR products of the ITS regions

Boysen, Marianne; Borja, M. Bernácer; Moral, Catalina del; Salazar, Óscar; Rubio, Virginia

doi:10.1007/s002940050033

Cited by 32 publications

(45 citation statements)

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“…It provides a relatively small amount of sequence data (ITS spacers <300 bp) with low discriminatory power, and the co-occurrence of multiple sequences present in a single individual makes its use unreliable and hinders comparative sequence analysis to answer questions at this hierarchical level (Muir and Schlötterer 1999). The occurrence of multiple sequences at the ITS1 level has been documented for AG-1 (Grosch et al 2007), AG-3 (Justesen et al 2003), and AG-4 (Boysen et al 1996). For AG-1-IE and AG-1-IF, however, this phenomenon has not been observed; on the contrary, 80 and 66%, respectively, of isolate sequences have had a 100% match (Godoy-Lutz et al 2008).…”

Section: Discussionmentioning

confidence: 90%

Assessing genetic diversity in the web blight pathogen Thanatephorus cucumeris (anamorph = Rhizoctonia solani) subgroups AG-1-IE and AG-1-IF with molecular markers

Godoy‐Lutz

Steadman

et al. 2012

J Gen Plant Pathol

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genetic diversity in the web blight pathogen Thanatephorus cucumeris (anamorph = Rhizoctonia solani) subgroups AG-1-IE and AG-1-IF with molecular markers" (2012). Papers in Plant Pathology. 273. http://digitalcommons.unl.edu/plantpathpapers/273 Abstract Web blight, an important foliar disease of dry beans in the Americas, is a challenge to manage. We studied genetic variation of 92 isolates of Rhizoctonia solani subgroups AG-1-IE and AG-1-IF using DNA fingerprinting methods and mycelial compatibility grouping. The isolates were collected over 13 years from bean fields in the Dominican Republic, Honduras and Puerto Rico. Cluster and AMOVA analysis of combined data from two universal rice primers and two internal sequence repeats revealed significant genetic variation among and within populations of both subgroups. Variation was influenced by geographic origin and sampling year for AG-1-IE isolates and geographic origin for AG-1-IF isolates. Mycelial compatibility of paired isolates was mostly scored as incompatible in both subgroups and supported many unique phenotypes. Only two isolates of AG-1-IE displayed mycelial compatibility and DNA fingerprints, suggesting clonal origin. Genetic variation in these AG-1-IE and AG-1-IF isolate populations may explain the lack of durable resistance to web blight reported in dry beans.

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Section: Discussionmentioning

confidence: 90%

Assessing genetic diversity in the web blight pathogen Thanatephorus cucumeris (anamorph = Rhizoctonia solani) subgroups AG-1-IE and AG-1-IF with molecular markers

Godoy‐Lutz

Steadman

et al. 2012

J Gen Plant Pathol

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“…On the other hand, studies based on the AFLP technique, scarcely employed in Rhizoctonia, were based on several aspects related to factors and genes involved in sexual compatibility mechanisms of R. solani (Julián et al, 1999) or investigating genetic diversity of some R. solani AG (Ceresini et al, 2002). Sequencing of ribosomal DNA has been widely employed in the complex during recent years, to reconstruct phylogenetic relationships between the different organisms of the form genus (Boysen et al, 1996;Kuninaga et al, 1997;Roberts, 1999;Salazar et al, 1999Salazar et al, , 2000González et al, 2001González et al, , 2002Pope and Carter, 2001;Shan et al, 2002) or less frequently other regions such as beta-tubuline (González et al, 2003). In the future, molecular approaches should include the sequencing of a broader range of DNA regions (e.g.…”

Section: Molecular Approaches To Study the Form Genusmentioning

confidence: 99%

Review. Biology and systematics of the form genus Rhizoctonia

García¹,

Onco

Susan

2006

Span. j. agric. res.

205

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Members of the form genus Rhizoctonia D.C. are considered as a complex mixture of filamentous fungi, having in common the possession of a non-spored imperfect state, usually referred to as the Rhizoctonia anamorph. The group includes several of the most devastating crop pathogens like Thanatephorus cucumeris (Frank) Donk (anamorph = Rhizoctonia solani Kühn), the majority of orchid mycorrhizal symbionts (mainly belonging to genus Ceratobasidium D.P. Rogers) and a collection of saprotrophic organisms of different systematic placement. The Rhizoctonia anamorph is characterized by several common features present among members of the entire Rhizoctonia species complex. Taxa from the group have been rearranged into several groups of higher fungi, including both Ascomycota and Basidiomycota, and split into several genera, employing criteria such as the analysis and ultrastructural comparison of septal apparatus. Until very recently, classification for some of the groups within the complex has been exclusively based on criteria such as hyphal anastomosis, since other types of diagnostic features are usually scarce in these fungi. Phytopathological studies in the complex have represented the major contingent of contributions in the group, especially in the case of R. solani. Some members of the complex have been reported to be protective isolates against pathogenic members of Rhizoctonia and some other fungal pathogens. This review focuses on the knowledge of several aspects of the species of Rhizcotonia s. lato, such as its current taxonomic placement, the biology and systematics of some groups of the complex, and a revision of the methodologies employed in studying it.Additional key words: Basidiomycetes, biocontrol, Ceratobasidiaceae, Ceratobasidium, fungal diseases, methodology, taxonomy, Thanatephorus. Resumen Biología y Sistemática del género forma RhizoctoniaLos miembros del género forma Rhizoctonia D.C. son considerados como un complejo de hongos filamentosos, presentando en común una fase asexual no productora de esporas, denominada anamorfo tipo Rhizoctonia. El grupo incluye algunos importantes patógenos como Thanatephorus cucumeris (Frank) Donk (anamorfo=Rhizoctonia solani Kühn), la mayoría de especies micorrícicas de orquídeas (principalmente del género Ceratobasidium D.P. Rogers), y algunos taxones de posición taxonómica variada. El anamorfo tipo Rhizoctonia es definido por una serie de características, presentes y comunes en todos los taxones del complejo. Los taxones del grupo han sido distribuidos entre varios grupos de hongos, incluyendo Ascomicetes y Basidiomicetes, y reubicados en varios géneros de ambas clases, empleando criterios de clasificación tales como el análisis y comparación de la ultraestructura del aparato septal. Habitualmente, la clasificación en algunos de los grupos del complejo ha estado basada en la aplicación de criterios tales como la anastomosis hifal, debido a que en este tipo de hongos es escasa la presencia de un número aceptable de caracteres diagnósticos. Los trabajos ...

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“…Other, less host-specific AGs may also infect potato but they show usually rather poor or no formation of sclerotia on tubers (Sneh et al 1996;our unpublished data). Phylogenetic analysis of primary ITS sequences can be used to determine the AGs with a reasonable accuracy (Kuninaga and Yokosawa 1985;Boysen et al 1996;Mazzola et al 1996;Kuninaga et al 1997;Carling et al 2002a;Sharon et al 2008). Also, subgroups within AG-2 have been detected (Salazar et al 1999;2000;Carling et al 2002b) and the evolution of AG-1 IA analyzed using ITS sequences (Ciampi et al 2005).…”

Section: Introductionmentioning

confidence: 99%

Evolutionary Diversification Indicated by Compensatory Base Changes in ITS2 Secondary Structures in a Complex Fungal Species, Rhizoctonia solani

et al. 2009

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The rRNA cistron (18S-ITS1-5.8S-ITS2-28S) is used widely for phylogenetic analyses. Recent studies show that compensatory base changes (CBC) in the secondary structure of ITS2 correlate with genetic incompatibility between organisms. Rhizoctonia solani consists of genetically incompatible strain groups (anastomosis groups, AG) distinguished by lack of anastomosis between hyphae of strains. Phylogenetic analysis of internal transcribed spacer (ITS) sequences shows a strong correlation with AG determination. In this study, ITS sequences were reannotated according to the flanking 5.8S and 28S regions which interact during ribogenesis. One or two CBCs were detected between the ITS2 secondary structure of AG-3 potato strains as compared to AG-3 tobacco strains, and between these two strains and all other AGs. When a binucleate Rhizoctonia species related to Ceratobasidiaceae was compared to the AGs of R. solani, which were multinucleate (3-21 nuclei per cell), 1-3 CBCs were detected. The CBCs in potato strains of AG-3 distinguish them from AG-3 tobacco strains and other AGs yielding further evidence that the potato strains of AG-3 originally described as R. solani are a species distinct from other AGs. The ITS1-5.8S-ITS2 sequences were analyzed by direct sequencing of PCR products from 497 strains of AG-3 isolated from potato. The same 10 and 4 positions in ITS1 and ITS2, respectively, contained variability in 425 strains (86%). Nine different unambiguous ITS sequences (haplotypes) could be detected in a single strain by sequencing cloned PCR products indicating that concerted evolution had not homogenized the rRNA cistrons in many AG-3 strains. Importantly, the sequence variability did not affect the secondary structure of ITS2 and CBCs in AG-3.

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Identification at strain level of Rhizoctonia solani AG4 isolates by direct sequence of asymmetric PCR products of the ITS regions

Cited by 32 publications

References 0 publications

Assessing genetic diversity in the web blight pathogen Thanatephorus cucumeris (anamorph = Rhizoctonia solani) subgroups AG-1-IE and AG-1-IF with molecular markers

Assessing genetic diversity in the web blight pathogen Thanatephorus cucumeris (anamorph = Rhizoctonia solani) subgroups AG-1-IE and AG-1-IF with molecular markers

Review. Biology and systematics of the form genus Rhizoctonia

Evolutionary Diversification Indicated by Compensatory Base Changes in ITS2 Secondary Structures in a Complex Fungal Species, Rhizoctonia solani

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