Molecular characterization of Monascus strains based on the D1/D2 regions of LSU rRNA genes

Abstract

The D1/D2 regions of the large subunit (LSU) rRNA genes of 65 strains of Monascus and Xeromyces were PCR amplified and sequenced in both directions. Maximum-parsimony analysis produced five most parsimonious trees. The strict consensus tree of these five parsimonious trees clustered M. eremophilus, M. ruber, M. pilosus, M. purpureus, and M. sanguineus in the same clade, reflecting high sequence similarity. M. sanguineus, M. purpureus, M. ruber, and M. pilosus differed in one or two nucleotides. The sequence of M. eremophilus ATCC 62925 isolated from a xerophilic environment differed from M. purpureus in only one nucleotide, despite pronounced morphological and ecological differences when compared with the other species. M. lunisporas, M. floridanus, M. pallens, and X. bisporus were each placed in a separate branch, confirming their taxonomic descriptions as individual species.Maximum-likelihood analysis on the same data set generated a single tree and grouped the species of the first clade in the parsimony analysis into a single clade but placed the rest of the Monascus species and Xeromyces bisporus on different branches. The trees inferred from both analyses revealed a monophyletic relationship between Monascus and Xeromyces, when compared with other related cleistothecial or imperfect genera.

Genetic diversity analysis of Monascus strains using SRAP and ISSR markers

“…In regard to control strains, there also were some dissimilarities in cluster position; for instance, M. serorubescens was classified as M. pilosus by Hawskworth and Pitt (1983) Based on dendrograms produced by SRAP and ISSR data, M. aurantiacus (CICC 5015), M. serorubescens (CICC 5016), and M. purpureus were placed into the same subgroup, suggesting that they shared great similarities in genetic background; M. albidus (CICC 5017), M. fuliginosus (CICC5020), M. barkeri (OUT 2012), and M. pilosus (OUT 2137) were grouped in the same clade. However, the phylogenetic relationship inferred from the D1/D2 regions of LSU rRNA genes (Park and Jong 2003) was incongruent in regard to M. albidus, M. serorubescens, and M. fuliginosus. Although there are remarkable differences between M. pilosus and M. ruber, these two species could not be differentiated by molecular markers based on the D1/D2 regions of LSU rRNA genes, the partial b-tubulin gene, and MRT sequence (Park and Jong 2003;Park et al 2004;Chen et al 2007), although the two species were clustered into different clades according to the dendrograms by SRAP and ISSR.…”

“…However, the phylogenetic relationship inferred from the D1/D2 regions of LSU rRNA genes (Park and Jong 2003) was incongruent in regard to M. albidus, M. serorubescens, and M. fuliginosus. Although there are remarkable differences between M. pilosus and M. ruber, these two species could not be differentiated by molecular markers based on the D1/D2 regions of LSU rRNA genes, the partial b-tubulin gene, and MRT sequence (Park and Jong 2003;Park et al 2004;Chen et al 2007), although the two species were clustered into different clades according to the dendrograms by SRAP and ISSR. The incongruent phylogenetic relationships may be caused by these two reasons: (1) the molecular markers are based on different principles, for instance, SRAP and ISSR target the whole genomic DNA sequences, whereas amplification of D1/D2 regions of LSU rRNA genes and partial b-tubulin sequences is based on the comparison of nucleotide sequence; and (2) the strains used in this study were different from those in other studies.…”

“…Currently, various DNA molecular markers have been used to delimit species boundaries and determine the genetic relationships of different Monascus strains, such as random amplified length polymorphic DNA (RAPD) (Lakrod et al 2000;Shinzato et al 2009), amplification of DNA sequences of D1/D2 region of the large subunit (Park and Jong 2003), b-tubulin gene, internal transcribed spacer (ITS) of rDNA (Park et al 2004), and Monascus retrotransposon (MRT) (Chen et al 2007). These methods have their own advantages and disadvantages.…”

Phylogeny and intraspecific variation of the extreme xerophile, Xeromyces bisporus

“…Based on pilot studies and earlier published phylogenies (Park & Jong 2003, Gueidan et al 2008, three sets of taxa were selected in order to investigate various aspects of the phylogenetic position of Xeromyces. To place this genus within Eurotiales, representative taxa of Eurotiales were selected and sequenced for the 28S rDNA marker (incl.…”

“…The taxonomic position of this genus has long been debated, although most place the genus close to Monascus in the family Monascaceae, based on the morphology of the fruiting bodies as well as DNA sequences (e.g. Park & Jong 2003;Stchigel et al 2004;Pitt & Hocking 2009). von Arx (1970) united the genera Monascus and Xeromyces, introducing the new name, Monascus bisporus, a conclusion that Stchigel et al (2004) claimed was supported by their phylogenetic study.…”