DOI: 10.5061/dryad.td742
title: Data from: Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria

description: Background: Distribution and evolutionary history of resistance genes in
 environmental actinobacteria provide information on intensity of
 antibiosis and evolution of specific secondary metabolic pathways at a
 given site. To this day, actinobacteria producing biologically active
 compounds were isolated mostly from soil but only a limited range of soil
 environments were commonly sampled. Consequently, soil remains an
 unexplored environment in search for novel producers and related
 evolutionary questions. Results: Ninety actinobacteria strains isolated at
 contrasting soil sites were characterized phylogenetically by 16S rRNA
 gene, for presence of erm and ABC transporter resistance genes and
 antibiotic production. An analogous analysis was performed in silico with
 246 and 31 strains from Integrated Microbial Genomes (JGI_IMG) database
 selected by the presence of ABC transporter genes and erm genes,
 respectively. In the isolates, distances of erm gene sequences were
 significantly correlated to phylogenetic distances based on 16S rRNA
 genes, while ABC transporter gene distances were not. The phylogenetic
 distance of isolates was significantly correlated to soil pH and organic
 matter content of isolation sites. In the analysis of JGI_IMG datasets the
 correlation between phylogeny of resistance genes and the strain phylogeny
 based on 16S rRNA genes or five housekeeping genes was observed for both
 the erm genes and ABC transporter genes in both actinobacteria and
 streptomycetes. However, in the analysis of sequences from genomes where
 both resistance genes occurred together the correlation was observed for
 both ABC transporter and erm genes in actinobacteria but in streptomycetes
 only in the erm gene. Conclusions: The type of erm resistance gene
 sequences was influenced by linkage to 16S rRNA gene sequences and site
 characteristics. The phylogeny of ABC transporter gene was correlated to
 16S rRNA genes mainly above the genus level. The results support the
 concept of new specific secondary metabolite scaffolds occurring more
 likely in taxonomically distant producers but suggest that the antibiotic
 selection of gene pools is also influenced by site conditions.
description: Supporting information
 to the Figure 1An alignment of partial
 16S rRNA gene sequences of the isolated strains examined in the study.
 Phylograms constructed by neighbor-joining method based on Jukes-Cantor
 distance matrices calculated from the initial alignment, and from its 1000
 bootstrap replicates.Fig_1.zipSupporting infomation to the Figure 2.Phylogenetic analysis of 17 putative ABC transporters from the isolated strains with 23 reference sequences of ABC transporters described in actinobacteria. An alignment of amino-acid ABC transporter sequences. The phylogenies inferred by Bayesian analysis, maximum-likelihood and neighbor-joining methods.Fig_2.zipSupporting information to the Figure 3Phylogenetic analysis of 7 putative erm genes from the isolated strains obtained in the study with 50 actinobacterial described or putative erm genes. An alignment of the Erm protein sequences. The phylogenies inferred by Bayesian analysis, maximum-likelihood and neighbor-joining methods.Fig_3.zipSupporting information to the Figure 4Phylogenetic relationships of 47 collection strains harboring erm resistance genes. An alignment of 16S rRNA gene sequences. A phylogram constructed by neighbor-joining method based on Jukes-Cantor distance matrices calculated from 1000 bootstrap replicates of the alignment.Fig_4.zip