Phylogenetic utility of indels within ribosomal DNA and beta-tubulin sequences from fungi in the Rhizoctonia solani species complex

Molecular Phylogenetics and Evolution
Dolores GonzálezR Vilgalys

Abstract

The genus Rhizoctonia consists of a diverse assemblage of anamorphic fungi frequently associated with plants and soil throughout the world. Some anamorphs are related with teleomorphs (sexual stage) in different taxonomic classes, orders, and families. The fungus may exist as pathogen, saprophyte, or mycorrhizal symbiont and shows extensive variation in characteristics such as geographic location, morphology, host specificity, and pathogenicity. In this study, phylogenetic analyses were performed in the Rhizoctonia solani species complex with individual and combined data sets from three gene partitions (ITS, LSU rDNA, and beta-tubulin). To explore whether indels were a source of phylogenetically informative characters, single-site indels were treated as a new state, while indels greater than one contiguous nucleotide were analyzed by including them as ambiguous data (Coding A); excluding them from the analyses (Coding B), and with three distinct codes: multistate for different sequence (Coding C); multistate for different length (Coding D) and different characters for each distinct sequence (Coding E). Results suggest that indels in noncoding regions contain phylogenetic information and support the fact that the R. solani speci...Continue Reading

Citations

Jun 22, 2007·Mycorrhiza·John D W Dearnaley
Mar 30, 2016·Fungal Biology·Dolores GónzalezMarc A Cubeta
Sep 1, 2009·Fungal Genetics and Biology : FG & B·Kerry O'DonnellBrice A J Sarver
May 17, 2015·Revista Argentina de microbiología·Viviana A BarreraAmelia L Gasoni
Oct 7, 2008·Mycologia·Nikki D CharltonMarc A Cubeta
Jan 11, 2011·BMC Bioinformatics·Robert LückingReed A Cartwright
Oct 28, 2010·Environmental Microbiology·J V F CoumansL Pereg
Sep 1, 2013·Plant Disease·Carl A StrausbaughLeonard W Panella
Jan 24, 2019·Plant Disease·Angel José Vieira BlancoMurillo Lobo Junior
Apr 1, 2017·Plant Disease·Olutoyosi O Ajayi-Oyetunde, Carl A Bradley
Aug 1, 2016·Plant Disease·Loukas KanetisMichalakis Christoforou

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