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.序列比对集： 1. 系统发育矩阵：由肠杆菌目（Enterobacteriales）各主要类群的可用代表性蛋白质组中提取的14条直系同源氨基酸（Amino Acid, AA）序列拼接而成的矩阵，采用fasta格式存储；相关分析通过PhyML、MrBayes及PhyloBayes完成。 2. 共进化矩阵（5个蛋白）：由12组新血虱杆菌（L. neohaematopini）组装基因组中提取的5条直系同源氨基酸序列拼接而成的矩阵，采用fasta格式存储；相关分析通过PhyML与MrBayes完成。 3. 共进化矩阵（50个蛋白）：由11组新血虱杆菌（L. neohaematopini）组装基因组中提取的50条直系同源氨基酸序列拼接而成的矩阵，采用fasta格式存储；相关分析通过PhyML完成。 4. 奈瑟菌目（Neisseriales）矩阵：由奈瑟菌目可用代表性蛋白质组中提取的30条直系同源氨基酸序列拼接而成的矩阵，采用fasta格式存储；相关分析通过PhyML与MrBayes完成。 5. 宿主矩阵：来自Bell等人2021年研究的1107个核基因座的独立矩阵，采用fasta格式存储；相关分析通过IQ-TREE完成。 系统发育树文件夹： 包含由PhyML、MrBayes及PhyloBayes生成的newick格式系统发育树文件。 KO编号文件夹： 包含通过BLAST KOALA服务器为对应基因组生成的KO编号信息。 注释文件文件夹： 包含5个最优组装基因组草图的gbk格式注释文件。 所用方法的详细说明可参见材料与方法（Materials and Methods）章节。