Supplementary data for the article: Lightella neohaematopini: A new lineage of highly reduced endosymbionts coevolving with chipmunk lice of the genus Neohaematopinus

Alignments:

1. Phylogenetic matrix - concatenated matrix of 14 ortholog sequences (AA) extracted from representative set of available proteomes for each major lineage of Enterobacteriales (analyzed by PhyML, MrBayes and PhyloBayes) in a fasta format
2. Coevolutionary matrix (5 proteins) - concatenated matrix of 5 ortholog sequences (AA) extracted from 12 assemblies of L. neohaematopini (analyzed by PhyML and MrBayes) in a fasta format
3. Coevolutionary matrix (50 proteins) - concatenated matrix of 50 ortholog sequences (AA) extracted from 11 assemblies of L. neohaematopini (analyzed by PhyML) in a fasta format
4. Neisseriales matrix - concatenated matrix of 30 ortholog sequences (AA) extracted from representative set of available proteomes for Neisseriales (analyzed by PhyML and MrBayes) in a fasta format
5. Host matrices - individual matrices for 1,107 nuclear loci from Bell et al. 2021 (analyzed by IQ-TREE) in a fasta format

Phylogenetic trees folder:
Phylogenetic trees generated by PhyML, MrBayes and PhyloBayes in a newick format.

KO numbers folder:
KO numbers generated by BLAST KOALA server for corresponding genomes.

Annotations folder:
Annotations of the genome drafts for the five best assemblies in gbk format.

Detailed description of used methods can be found in the Materials and Methods section.