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. 2016 Sep;85:199-213.
doi: 10.1016/j.simyco.2016.11.006. Epub 2016 Nov 29.

Aspergillus Is Monophyletic: Evidence From Multiple Gene Phylogenies and Extrolites Profiles

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Free PMC article

Aspergillus Is Monophyletic: Evidence From Multiple Gene Phylogenies and Extrolites Profiles

S Kocsubé et al. Stud Mycol. .
Free PMC article

Abstract

Aspergillus is one of the economically most important fungal genera. Recently, the ICN adopted the single name nomenclature which has forced mycologists to choose one name for fungi (e.g. Aspergillus, Fusarium, Penicillium, etc.). Previously two proposals for the single name nomenclature in Aspergillus were presented: one attributes the name "Aspergillus" to clades comprising seven different teleomorphic names, by supporting the monophyly of this genus; the other proposes that Aspergillus is a non-monophyletic genus, by preserving the Aspergillus name only to species belonging to subgenus Circumdati and maintaining the sexual names in the other clades. The aim of our study was to test the monophyly of Aspergilli by two independent phylogenetic analyses using a multilocus phylogenetic approach. One test was run on the publicly available coding regions of six genes (RPB1, RPB2, Tsr1, Cct8, BenA, CaM), using 96 species of Penicillium, Aspergillus and related taxa. Bayesian (MrBayes) and Ultrafast Maximum Likelihood (IQ-Tree) and Rapid Maximum Likelihood (RaxML) analyses gave the same conclusion highly supporting the monophyly of Aspergillus. The other analyses were also performed by using publicly available data of the coding sequences of nine loci (18S rRNA, 5,8S rRNA, 28S rRNA (D1-D2), RPB1, RPB2, CaM, BenA, Tsr1, Cct8) of 204 different species. Both Bayesian (MrBayes) and Maximum Likelihood (RAxML) trees obtained by this second round of independent analyses strongly supported the monophyly of the genus Aspergillus. The stability test also confirmed the robustness of the results obtained. In conclusion, statistical analyses have rejected the hypothesis that the Aspergilli are non-monophyletic, and provided robust arguments that the genus is monophyletic and clearly separated from the monophyletic genus Penicillium. There is no phylogenetic evidence to split Aspergillus into several genera and the name Aspergillus can be used for all the species belonging to Aspergillus i.e. the clade comprising the subgenera Aspergillus, Circumdati, Fumigati, Nidulantes, section Cremei and certain species which were formerly part of the genera Phialosimplex and Polypaecilum. Section Cremei and the clade containing Polypaecilum and Phialosimplex are proposed as new subgenera of Aspergillus. The phylogenetic analysis also clearly shows that Aspergillus clavatoflavus and A. zonatus do not belong to the genus Aspergillus. Aspergillus clavatoflavus is therefore transferred to a new genus Aspergillago as Aspergillago clavatoflavus and A. zonatus was transferred to Penicilliopsis as P. zonata. The subgenera of Aspergillus share similar extrolite profiles indicating that the genus is one large genus from a chemotaxonomical point of view. Morphological and ecophysiological characteristics of the species also strongly indicate that Aspergillus is a polythetic class in phenotypic characters.

Keywords: Aspergillago Samson, Houbraken & Frisvad, gen. nov.; Aspergillago clavatoflava (Raper & Fennell) Samson, Houbraken & Frisvad, comb. nov.; Aspergillus; Aspergillus subgenus Cremei, subgen. nov.; Aspergillus subgenus Polypaecilum, subgen. nov.; Monophyly; Multigene phylogeny; Nomenclature; Penicilliopsis zonatus (Kwon-Chung & Fennell) Samson, Houbraken & Frisvad, comb. nov.; Teleomorphs.

Figures

Fig. 1
Fig. 1
Tree based on six genes. The tree shown is a rooted consensus tree inferred by maximum likelihood with partitioned dataset (IQ-TREE) and 10 000 bootstrap replicates, branch support values are given for two maximum-likelihood implementations and one Bayesian inference method (from left to right: RaxML bootstrap support; MrBayes posterior probabilities; IQ-TREE bootstrap support; respectively).
Fig. 1
Fig. 1
Tree based on six genes. The tree shown is a rooted consensus tree inferred by maximum likelihood with partitioned dataset (IQ-TREE) and 10 000 bootstrap replicates, branch support values are given for two maximum-likelihood implementations and one Bayesian inference method (from left to right: RaxML bootstrap support; MrBayes posterior probabilities; IQ-TREE bootstrap support; respectively).
Fig. 2
Fig. 2
Phylograms obtained by Maximum Likelihood (ML) and Bayesian analysis inferred from nine loci (18S rDNA, 5.8S rDNA, 28S rDNA (D1-D2), RPB1, RPB2, CaM, BenA, Tsr1, Cct8). Monophyletic groups are collapsed and shown as triangles. A. Best-scoring ML tree obtained by RAxML. B. 50 % majority rule phylogram of Bayesian analysis. Numbers above or below branches are bootstrap values (A) and posterior probabilities (B). Only support values greater than 60 % and 0.95 are shown.
Fig. 3
Fig. 3
Visualization of 1 000–1 000 bootstrap replicates obtained by using nine (NG) and four (FG) loci. Best-scoring ML tree using nine (A) and four loci (B) are shown with bootstrap support above branches higher than 60 %. Monophyletic groups are collapsed and shown as triangles. (C) Orange dots represent bootstrap replicates from the analysis encompassing nine genes, while purple dots are trees obtained with four genes. (D) Visualization of those replicates which support the monophyly of Aspergilli. Orange and purple dot are replicates from the nine-gene and the four-gene analysis respectively. Yellow dots represent the tree space occupied by all replicates from both runs.
Fig. 4
Fig. 4
Post-burnin tree space plots of 1 000 trees of Bayesian analysis with four (A) and nine (B) loci. Lines represent the connections between the subsequent generations while dots represent the two-dimensional place of the trees in the space. The colour of the lines and dots represents the generations. On the heat map green coloured areas represent the space occupied by larger number of trees.
Fig. 5
Fig. 5
Collapsed phylograms showing the support values of the principal nodes involved in the monophyly of Aspergillus based on six (A) and nine (B) genes. The tables are summarizing the values of these nodes obtained by different methods (Bpp – Bayesian posterior probabilities, Rbs – RAxML bootstrap support, Ibs – IQ-Tree UFBoot support). Single branch tests (aBayes, SH-aLRT and aLRT-Chi2) were conducted with PhyML and IQ-Tree. The use of partitioned data set is indicated by -p in the tables.

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References

    1. Aberer A.J., Krompass D., Stamatakis A. Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice. Systematic Biology. 2013;62:162–166. - PMC - PubMed
    1. Anisimova M., Gil M., Dufayard J.F. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Systematic Biology. 2011;60:685–699. - PMC - PubMed
    1. Bhat B., Harrison S.M., Lamont H.M. The biosynthesis of the mould metabolites roquefortine and aszonalenin from L-[2,4,5,6,7-2H5]tryptophan. Tetrahedron. 1993;49:10663–10668.
    1. Borchsenius F. FastGap 1.2. Department of Biosciences, Aarhus University, Denmark. 2009. http://www.aubot.dk/FastGap_home.htm Published online at:
    1. Borg I., Groenen P. Springer-Verlag; Heidelberg: 1997. Modern multidimensional scaling.

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