DOI: 10.6084/m9.figshare.22800263
title: Wolbachia supergroups.;Primers and PCR conditions.;Accession number list of the sequences of Wolbachia used in the phylogenies.;Wolbachia topologies containing at least the supergroups E, M or L;Phylogenetic tree of Wolbachia on 6 markers by Maximum Likelihood with Rickettsiaceae as outgroup. from <i>Wolbachia</i> springs eternal: symbiosis in Collembola is associated with host ecology

description: The first column indicates valids and discarded supergoups. The second column “Authority name”, the third column “Authority year” and the fourth column “Reference” correspond to the first description, the year of the publication and the associated reference number in the bibliography where each supergroup has been described. The fifth, sixth and seventh column indicate the phylum, class and order of the hosts infected by each supergroups. The eigth column indicates supergroups validity: either “Yes”, “No” (with the correcting reference in last column), or “?” due to a lack of information.;The primers in blue are used for the amplification of the first phase of the nested PCR. The primers in green indicate they correspond to the second phase of the nested PCR. Abbreviations: 1: denaturation; 2: annealing; 3: elongation; n: number of amplification cycles; T: Temperature in °C; D: Duration in seconds; BSA: Bovine Serum Albumin.;The name of the genotypes are given in the first column. Columns 2 to 7 present accession numbers for each analysed gene: 16S rDNA; cytochrome c oxidase subunit I (coxA) gene; dnaA gene for chromosomal replication initiator protein; putative fructose-bisphosphate aldolase (fbpA) gene; ftsZ gene for cell division protein; and glutamyl-tRNA(Gln) amidotransferase subunit B (gatB) gene. The sequences produced in this study are in bold. The unavaible sequences are represented by “-”.;The first three columns correspond to the author names, the year of the publication and the associated reference number in the bibliograpahy for each topology. The fourth column “Number of genes” is the number of genetic markers used for each phylogeny. The fifth column “Genom” indicates the markers originate from genomic data. The sixth column “Genes” corresponds to the genetic markers used to infer each phylogeny. The seventh column “Supergroups” indicates the supergroups of Wolbachia represented in each phylogeny, some supergroups have been assigned a posteriori (e.g. the supergroup I in Lo et al. 2007 [26] due to the presence of Wolbachia infecting Ctenocephalides felis, while the supergroup I has been created in 2009 by Ros et al. [88]). The eigth column “Number of genotypes” is the number of Wolbachia genotypes present in each phylogeny. The ninth column “Number of AB” is the number of Wolbachia belonging to the supergroups A and B present in each phylogeny. The tenth column "Number of WbColl” indicates the number of Wolbachia genotypes infecting Collembola in each phylogeny. The eleventh column “Number of E” is the number of Wolbachia belonging to the supergroups E present in each phylogeny. The twelfth column "WbFil status” indicates the phylogenetic status of the Wolbachia clades infecting filariae, the supergroups between parenthesis are those making the Wolbachia clades infecting filariae non-monophyletic. The thirteenth column “Algorithm” shows the algorithm used to infer the phylogeny: “NJ”, Neighbour-joining; “ML”, Maximum Likelihood; “DM”, Distance Method; “BI”, Bayesian Inference; “MP”, Maximum Parsimony; “CAT”, site-heterogenous CAT mixture model; “CAT Composition”, CAT model with removal of compositionally deviant taxa; “MET”, Minimum Evolution Tree. The fourteenth column “Rooted?” indicates if the topology is rooted with an outgroup and the fifteenth column “Outgroup” indicates the taxonomy of the outgroups used, wFcan: Wolbachia infecting Folsomia candida, wCfeT : Wolbachia infecting C. felis. The last column “Basal supergroup” indicates the most basal supergroup in the Wolbachia phylogenies.;Analysis based on partitioned concatenation of 16S rDNA, dnaA, ftsZ, coxA, fbpA and gatB sequences. The total length of datasets is approximately 0 bp. Wolbachia strains were analysed. The topology was inferred using Maximum Likelihood (ML) inference using RaxML v8.2.12. Nodes are associated with Bootstrap values based on 0 replicates. Bootstraps with values inferior to 75 are not displayed. The scale bar indicates the distance in substitutions per nucleotide. Abbreviation: wb, Wolbachia.