Phylogenetic analysis of Penicillium subgenus Penicillium using partial P-tubulin sequences

Partial β-tubulin sequences were determined for 180 strains representing all accepted species of Penicillium subgenus Penicillium. The overall phylogenetic structure of the subgenus was determined by a parsimony analysis with each species represented by its type (or other reliably identified) strain. Eight subsequent analyses explored the relationships of three or four strains per species for clades identified from the initial analysis. β-tubulin sequences were excellent species markers, correlating well with phenotypic characters. The phylogeny correlated in general terms with the classification into sections and series proposed in the accompanying monograph. There was good strict consensus support for much of the gene tree, and good bootstrap support for some parts. The phylogenetic analyses suggested that sect. Viridicata, the largest section in the subgenus, is divided into three clades. Section Viridicata ser. Viridicata formed a monophyletic group divided into three subclades supported by strict consensus, with strong bootstrap support for P. tricolor (100%), P. melanoconidium (99%), P. polonicum (87%) and P. cyclopium (99%) and moderate support for P. aurantiogriseum (79%). The three strains each of Penicillium freii and P. neoechinulatum had identical sequences. Three strains of P. viridicatum had unique sequences, with two strains differing in two or three positions from the type. Within ser. Camemberti, P. palitans (83%) and P. crustosum (99%) were supported by bootstrap. Penicillium camemberti and P. caseifulvum had identical sequences to each other, and to the type strain of P. commune. Section Viridicata ser. Verrucosa was monophyletic and included two well-supported subclades, one consisting of P. thymicola (87%), and the other of P. verrucosum (88%), derived within the paraphyletic P. nordicum. The phylogeny for sect. Roqueforti (100%) was robust, with excellent bootstrap support for all included species, i.e. P. roqueforti (100%), P. carneum (94%) and P. paneum (100%). In sect. Penicillium, Series Expansa was paraphyletic, with the monophyletic ser. Italica derived within it. The synnematous species in ser. Claviformia were a paraphyletic group with the species of ser. Urticicolae., including P. griseofulvum (99%), derived within. Section Digitata, ser. Digitata comprised a single well-supported species, P. digitatum (100%). The phylogenetic structure of sect. Chrysogena had limited strict consensus and bootstrap support. One clade comprises P. chrysogenum and P. flavigenum (96%), another P. dipodomyis and P. nalgiovense, and a third P. mononematosum and P. confertum. Penicillium persicinum and P. aethiopicum were weakly placed in this section, both emerging from the backbone of the gene tree. Section Coronata (82%) was a well-supported monophyletic group at the base of the phylogram. Penicillium olsonii (100%) was basal in the section, with the sibling species P. bialowiezense (100%) and P. brevicompactum (100%) together forming a well-supported clade (96%).

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