González Dolores, Cubeta Marc A, Vilgalys Rytas
Departamento de Biodiversidad y Sistemática, Instituto de Ecología, A.C., Apartado Postal 63, Xalapa Veracruz 91000, México.
Mol Phylogenet Evol. 2006 Aug;40(2):459-70. doi: 10.1016/j.ympev.2006.03.022. Epub 2006 May 2.
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 species complex is not monophyletic. Six clades within R. solani (teleomorph=Thanatephorus) representing distinct anastomosis groups and five clades within binucleate Rhizoctonia (teleomorph=Ceratobasidium) were well supported in all analyses. The data suggest that clades with representatives of R. solani fungi belonging to anastomosis groups 1, 4, 6, and 8 should be recognized as phylogenetic species.
丝核菌属由多种无性型真菌组成，这些真菌在世界各地常与植物和土壤相关联。一些无性型与不同分类纲、目和科中的有性型（有性阶段）相关。该真菌可能以病原体、腐生菌或菌根共生体的形式存在，并且在地理位置、形态、寄主特异性和致病性等特征方面表现出广泛的差异。在本研究中，利用来自三个基因分区（ITS、LSU rDNA和β-微管蛋白）的单独和组合数据集，对茄丝核菌复合种进行了系统发育分析。为了探究插入缺失是否是系统发育信息特征的来源，单一位点的插入缺失被视为一种新状态，而大于一个连续核苷酸的插入缺失则通过以下方式进行分析：将其作为模糊数据纳入分析（编码A）；将其排除在分析之外（编码B），以及使用三种不同的编码方式：针对不同序列的多状态编码（编码C）；针对不同长度的多状态编码（编码D）以及针对每个不同序列的不同字符编码（编码E）。结果表明，非编码区的插入缺失包含系统发育信息，并支持茄丝核菌复合种不是单系的这一事实。在所有分析中，茄丝核菌（有性型=亡革菌属）内代表不同融合群的六个分支以及双核丝核菌（有性型=角担菌属）内的五个分支都得到了有力支持。数据表明，包含属于融合群1、4、6和8的茄丝核菌真菌代表的分支应被视为系统发育种。
