Intraspecific Variation and Phylogenetic Relationships Are Revealed by ITS1 Secondary Structure Analysis and Single-Nucleotide Polymorphism in Ganoderma lucidum

Abstract

Ganoderma lucidum is a typical polypore fungus used for traditional Chinese medical purposes. The taxonomic delimitation of Ganoderma lucidum is still debated. In this study, we sequenced seven internal transcribed spacer (ITS) sequences of Ganoderma lucidum strains and annotated the ITS1 and ITS2 regions. Phylogenetic analysis of ITS1 differentiated the strains into three geographic groups. Groups 1–3 were originated from Europe, tropical Asia, and eastern Asia, respectively. While ITS2 could only differentiate the strains into two groups in which Group 2 originated from tropical Asia gathered with Groups 1 and 3 originated from Europe and eastern Asia. By determining the secondary structures of the ITS1 sequences, these three groups exhibited similar structures with a conserved central core and differed helices. While compared to Group 2, Groups 1 and 3 of ITS2 sequences shared similar structures with the difference in helix 4. Large-scale evaluation of ITS1 and ITS2 both exhibited that the majority of subgroups in the same group shared the similar structures. Further Weblogo analysis of ITS1 sequences revealed two main variable regions located in helix 2 in which C/T or A/G substitutions frequently occurred and ITS1 exhibited more nucleotide variances compared to ITS2. ITS1 multi-alignment of seven spawn strains and culture tests indicated that a single-nucleotide polymorphism (SNP) site at position 180 correlated with strain antagonism. The HZ, TK and 203 fusion strains of Ganoderma lucidum had a T at position 180, whereas other strains exhibiting antagonism, including DB, RB, JQ, and YS, had a C. Taken together, compared to ITS2 region, ITS1 region could differentiated Ganoderma lucidum into three geographic originations based on phylogenetic analysis and secondary structure prediction. Besides, a SNP in ITS 1 could delineate Ganoderma lucidum strains at the intraspecific level. These findings will be implemented to improve species quality control in the Ganoderma industry.

Genetic Diversity and Demographic History of Ganoderma boninense in Oil Palm Plantations of Sarawak, Malaysia Inferred from ITS Regions

“…Intra-strain heterogeneity in the ITS sequences has been reported for species such as G. applanatum var. gibbosum , G. fornicatum , G. japonicum , G. lucidum and G. neojaponicum [45,46]. Sequence variation within strains varies and may occur within ITS1, ITS2 or the 5.8S region.…”

Effect of Strain, Wood Substrate and Cold Treatment on the Yield and β-Glucan Content of Ganoderma lucidum Fruiting Bodies

“…However, Cho et al [ 41 ] reported a lower β -glucan content (<20 g/100 g dm) for G. lucidum specimens originating from Korea, Japan, Taiwan, USA and Brazil. Considering the taxonomy confusion of G. lucidum , it is possible that these specimens differ from the European G. lucidum [ 30 ]; therefore, differences in β -glucan production could be expected between closely related species. Another possible explanation is the extraction method.…”

“…Since then, the fungus has been reported worldwide based mainly on morphological characteristics [ 33 , 34 ]. Recently, molecular and taxonomic data have confirmed that Asian ‘ G. lucidum ’ differs from the originally described species from Europe [ 28 , 29 , 30 ].…”

“…In Asian countries, ‘ Ganoderma lucidum ’ has been used to name the traditionally cultivated Reishi or Ling-Zhi mushroom [ 13 ]. However, the taxonomy of the species is not clear leading to confusion among closely related species [ 28 , 29 , 30 ]. The genus Ganoderma (P.…”

Effect of wood residues on the growth of Ganoderma lucidum

“…Studies based on morphological characteristics and molecular data have pointed out that 'G. lucidum' from Asia does not correspond with the originally described European species (Moncalvo & Ryvarden 1997;Cao et al 2012;Wang et al 2012;Zhang et al 2017).…”