Gene gain/loss analysis for Bombella and related microbes

Supplementary Table 1 – All sequenced B. apis strains retain the ability to synthesize all amino acids. Table generated from conserved core orthologs across the included strains showing presence/absence of amnio acid biosynthesis genes. ‘oid’ refers to the ortholog ID in our analysis of orthologous genes, ‘Name’ refers to the amino acid biosynthesis gene annotation, ‘Pathways/steps/scores’ refers to the biosynthetic pathway in which each gene is found, the enzymatic step in the pathway, and the GapMind score. GapMind score is either 2 (high confidence), 1 (medium confidence), or 0 (low confidence). In the columns below each sequenced strain, ‘1’ means that a given gene was identified in the corresponding genome and ‘0’ means that it was not identified. Supplementary Table 2- All B. apis genomes contain multiple cationic amino acid transporter orthologs. Gene gain/loss analysis showing all the gains and losses across the phylogeny of all sequenced B. apis strains and related microbes in Figure 3. ‘oid’ refers to the ortholog ID in our analysis of orthologous genes, ‘Name’ refers to proteins identified across all genomes analyzed. In the columns below each sequenced strain, ‘g’ means that a given gene was gained by that strain and ‘l’ means that it was lost. Supplementary Table 3 – Accession numbers for all sequenced strains used in this work.补充表1——所有测序的蜜蜂芽孢杆菌（B. apis）菌株均具备合成全部氨基酸的能力。该表格基于纳入研究的菌株的保守核心直系同源基因（ortholog）生成，用于展示各氨基酸生物合成基因的存在与缺失情况。其中，"oid"指代本研究直系同源基因分析中的直系同源基因标识，"Name"指代氨基酸生物合成基因的注释信息，"Pathways/steps/scores"指代该基因所属的生物合成途径、该基因在途径中对应的酶促反应步骤，以及GapMind评分。GapMind评分分为三档：2分为高置信度，1分为中置信度，0分为低置信度。在各测序菌株对应的列中，"1"表示在对应基因组中检出了该基因，"0"表示未检出该基因。 补充表2——所有蜜蜂芽孢杆菌（B. apis）基因组均携带多组阳离子氨基酸转运蛋白直系同源基因。本表格基于基因获得/丢失分析构建，展示了所有测序的蜜蜂芽孢杆菌菌株及图3中相关微生物在系统发育（phylogeny）过程中的全部基因获得与丢失事件。其中，"oid"指代本研究直系同源基因分析中的直系同源基因标识，"Name"指代所有分析基因组中鉴定得到的蛋白名称。在各测序菌株对应的列中，"g"表示该菌株获得了对应基因，"l"表示该菌株丢失了对应基因。 补充表3——本研究使用的全部测序菌株的登录号。