Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders ‘Frankiales’ and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov.

• DOI: 10.1099/ijs.0.063966-0
• Publication Date: 2014-08-29T04:16:53Z
• Authors: Arnab Sen; Vincent Daubin; Danis Abrouk; Isaac Gifford; Alison M. Berry; Philippe Normand
• Keywords: Concatenation (mathematics); Tree (set theory)

The phylogeny of the class Actinobacteria remains controversial, essentially because it is very sensitive to choice dataset and phylogenetic methods. We used a test proposed recently, based on complete genome data, which chooses among candidate species phylogenies number lateral gene transfers (LGT) needed explain diversity histories trees for set genomes. 100 completely sequenced genomes representing 35 families 17 orders evaluated eight different hypotheses their phylogeny, including one concatenate 54 conserved proteins present in single copy all these genomes, 16S 23S rRNA sequences or concatenation, tree concatenation MLSA genes (encoding AtpI, GyrA, FtsZ, SecA DnaK). Prunier infer LGT 579 (different from those build concatenated tree) at least 70 species, using hypothetical as references. best tree, with lowest transfers, was proteins. In that Bifidobacteriales, Coriobacteriales, 'Corynebacteriales', 'Micromonosporales', 'Propionibacteriales', 'Pseudonocardiales', Streptomycetales 'Streptosporangiales' were recovered while 'Frankiales' Micrococcales not. It thus order 'Frankiales', has an effectively but not validly published name, be split into Frankiales ord. nov. (type family Frankiaceae), Geodermatophilales (Geodermatophilaceae), Acidothermales (Acidothermaceae) Nakamurellales (Nakamurellaceae). should also (genera Kocuria, Rothia, Micrococcus, Arthrobacter, Tropheryma, Microbacterium, Leifsonia Clavibacter), Cellulomonales (Beutenbergia, Cellulomonas, Xylanimonas, Jonesia Sanguibacter) Brachybacteriales (Brachybacterium) formal proposal this will have wait until more become available significant proportion strains order.