title: Phylogenetic analyses of phylum Actinobacteria based on whole genome sequences.
abstract: Actinobacteria constitute one of the largest and ancient taxonomic phylum within the domain bacteria and are well known for their secondary metabolites. Considerable variation in the metabolic properties, genome size and GC content of the members of this phylum has been observed. Therefore, the placement of new or existing species based on 16S rRNA gene sometimes becomes problematic due to the low congruence level. In the present study, phylogeny of ninety actinobacterial genomes was reconstructed using single gene and whole genome based data. Where alignment-free phylogenetic method was found to be more robust, the concatenation of 94 proteins improved the resolution which all single gene based phylogenies failed to resolve. The comprehensive analysis of 94 conserved proteins resulted in a total of 42,447 informative sites, which is so far the largest meta-alignment obtained for this phylum. But the ultimate resolved phylogeny was obtained by generating a consensus tree by combining the information from single gene and genome based phylogenies. The present investigation clearly revealed that the consensus approach is a useful tool for phylogenetic inference and the taxonomic affiliations must be based on this approach. The consensus approach suggested that there is a need for taxonomic amendments of the orders Frankiales and Micrococcales.
authors.affiliation: Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110 007, India. mansiverma20@gmail.com
authors.forename: Mansi
authors.initials: M
authors.lastname: Verma
authors.forename: Devi
authors.initials: D
authors.lastname: Lal
authors.forename: Jaspreet
authors.initials: J
authors.lastname: Kaur
authors.forename: Anjali
authors.initials: A
authors.lastname: Saxena
authors.forename: Jasvinder
authors.initials: J
authors.lastname: Kaur
authors.forename: Shailly
authors.initials: S
authors.lastname: Anand
authors.forename: Rup
authors.initials: R
authors.lastname: Lal
mesh_terms: D039903:Actinobacteria / Q000145:classification* / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics; D020459:Genes, rRNA; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D010802:Phylogeny
chemical_list: D001426:Bacterial Proteins
keywords: Actinobacteria; Concatenated tree; Consensus tree; Genome based phylogeny