The order Chlamydiales includes obligate intracellular pathogens capable of infecting mammals, fishes and amoeba. Unlike other intracellular bacteria for which intracellular adaptation led to the loss of glycogen metabolism pathway, all chlamydial families maintained the nucleotide-sugar dependent glycogen metabolism pathway i.e. the GlgC-pathway with the notable exception of both Criblamydiaceae and Waddliaceae families. Through detailed genome analysis and biochemical investigations, we have shown that genome rearrangement events have resulted in a defective GlgC-pathway and more importantly we have evidenced a distinct trehalose-dependent GlgE-pathway in both Criblamydiaceae and Waddliaceae families. Altogether, this study strongly indicates that the glycogen metabolism is retained in all Chlamydiales without exception, highlighting the pivotal function of storage polysaccharides, which has been underestimated to date. We propose that glycogen degradation is a mandatory process for fueling essential metabolic pathways that ensure the survival and virulence of extracellular forms i.e. elementary bodies of Chlamydiales.

Homologous sequences of TreS-Mak and GlgE were carried out by BLAST against the nr databasefrom NCBI with, respectively, WP_098038072.1 and WP_098038073.1 sequences of Estrellalausannensis. We retrieved the top 2000 homologs with an E-value cut off ≤ 10 -5 and aligned themusing MAFFT with the fast alignment settings. Block selection was then performed using BMGE61 with a block size of four and the BLOSUM30 similarity matrix. Preliminary trees were generatedusing Fasttree and ‘dereplication’ was applied to robustly supported monophyletic clades usingTreeTrimmer in order to reduce sequence redundancy. For each protein, the final set of sequenceswas selected manually. Proteins were realigned with MUSCLE and block selection was carriedout using BMGE with a block size of four and the matrix BLOSUM30. Phylogenetic trees wereinferred using Phylobayes under the catfix C20 + Poisson model with the two chains stoppedwhen convergence was reached (maxdiff<0.1) after at least 500 cycles, discarding 100 burn-intrees. Bootstrap support values were estimated from 100 replicates using IQ-TREE under theLG4X model and mapped onto the Bayesian tree.

This data file is composed of sequence data used for phylogenies of both GlgE and TreS-MAK proteins. Inside, you will find the raw sequences, the aligned sequences as well as blocks selected to perform phylogenies. Finally, the raw tree found in the publication for each one is provided. In addition, for GlgE the tree performed with the same dataset under LG model with 1000 ultrafastbootstraps is provided as a raw tree and with a pdf version, too.