Differentiation and grouping of isolates of the Ganoderma lucidum complex by random amplified polymorphic DNA-PCR compared with grouping on the basis of internal transcribed spacer sequences

Abstract

Laccate polypores of the Ganoderma lucidum species complex are widespread white rot fungi of economic importance, but isolates cannot be identified by traditional taxonomic methods. Parsimony analysis of nucleotide sequences from the internal transcribed spacers (ITS) of the ribosomal gene (rDNA) distinguished six lineages in this species complex. Each ITS lineage may represent one or more putative species. While some isolates have identical ITS sequences, all of them could be clearly differentiated by genetic fingerprinting using random amplified polymorphic DNA (RAPD). To investigate the suitability of RAPD markers for taxonomic identification and grouping of isolates of the G. lucidum complex, RAPD fragments (RAPDs) were used as phenotypic characters in numerical and parsimony analyses. Results show that data from RAPDS do not distinguish the same clades as ITS data do. Groupings based on analysis of RAPD data were very sensitive to the choice of the grouping method used, and no consistent grouping of isolates could be proposed. However, analysis with RAPDs did resolve several robust terminal clades containing putatively conspecific isolates, suggesting that RAPDs might be helpful for systematics at the lower taxonomic levels that are unresolved by ITS sequence data. The limitations of RAPDs for systematics are briefly discussed. The conclusion of this study is that ITS sequences can be used to identify isolates of the G. lucidum complex, whereas RAPDs can be used to differentiate between isolates having identical ITS sequences. The practical implications of these results are briefly illustrated.

Evaluation of different PCR-based DNA fingerprinting techniques for assessing the genetic variability of isolates of the fungus Epicoccum nigrum

“…This fact was confirmed by DNA sequencing; Arenal et al (1999) showed that the comparison of sequences reveals a percentage of nucleotide substitution in this region close to 1%, well within the range of intraspecific variation reported for other fungal species (Egger and Sigler 1993;Yan et al 1995;Harrington and Potter 1997). This observation is consistent with the idea that the ARDRA technique is more appropriate for studying the relatedness among cultures classified at taxonomic ranks above species (Hseu et al 1996).…”

Molecular profiling demonstrates limited diversity amongst geographically separate strains ofUstilago scitaminea

“…This reflects a high degree of genetic similarity between the isolates. Based on the criteria reported by Hseu et al [34], the Reunion Island isolate therefore may be the least related to the U. scitaminea group. However, it is indicated that less than 10 base differences between two organisms signify that these organisms may have only recently diverged [34].…”

Applied modern biotechnology for cultivation of Ganoderma and development of their products

“…(Anderson et al 1987;Hwang and Kim 1995). Subsequently, it was introduced to variety identification and authentication in Lingzhi (Hseu et al 1996;Shi et al 2008;Wu et al 2009b;). Some scholars tried to use the function gene such as FIPs to identify Lingzhi (Zhou et al 2008b).…”