Appendix of the thesis "Acquisition of new genetic knowledge on strains of Mycobacterium bovis, circulating in France, by the whole genome sequencing approach." Ciriac CHARLES

Appendix 1 Table showing the <em>Mycobacterium bovis </em>genome information used in this study in panel 1 The 87 genomes are from previous work (Hauer et al., 2019). The names of the genomes are highlighted with color to distinguish them within a previously defined M. bovis cluster. In Yellow Cluster I/Clonal Complex Eu3. In orange Cluster G/Family F9. In brown Cluster C/Family SB0134. In purple Cluster D/Clonal Complex Eu1. In pink the Cluster A/Family F4. In blue the Cluster F/Clonal Complex Eu2. In grey, the others. Appendix 2 Table showing the <em>Mycobacterium bovis </em>genome information used in this study in panel 3. The 187 genomes are of genotypes F7 and F15 (SB0821 and SB0832 respectively) which are two closely related genotypes. These genomes had already been sequenced before the start of the thesis work. Some were published with the work of Duault and collaborators and others have not yet been published (noted NA) (Duault et al., 2022). Appendix 3 Table showing the <em>Mycobacterium bovis </em>genome information used in this study in panel 4. The 227 genomes are of genotype SB0120-DHV. These genomes had already been sequenced before the start of the thesis work but are currently unpublished (noted NA in the columns "Date of deposit" and "Genbank biosample"). Appendix 4 Position of IS<em>6110</em> insertion sites in the panel of <em>Mycobacterium bovis </em>strains from Pyrénées-Atlantiques (SB0821 and SB0832). The position of the start and end of IS<em>6110</em> are determined with the ISMapper tool and the reference genome AF2122/97. Appendix 5 Position of IS<em>6110</em> insertion sites in the <em>Mycobacterium bovis </em>strain panel of SB0120-DHV. Position of the start and end of IS<em>6110</em> are determined with the ISMapper tool and the Mb3601 reference genome. Appendix 6 This figure from the Modenesi internship report represents a circular consensus phylogenetic tree of 300 strains of SB0120-DHV (Modenesi 2019). The strains in panel 3 are part of these 300 strains and were selected according to their sequencing quality, which explains the smaller number of strains retained (227). This tree is divided into 11 different colored clades. The posterior probability values (which correspond to the probability that these clades are true) determined with Beast (Drummond and Rambaut, 2007) are represented inside the tree.附录1 表格展示了本研究第1组所用的牛分枝杆菌（*Mycobacterium bovis*）基因组信息。该87株基因组来自既往研究（Hauer等，2019）。基因组名称通过色彩标记以区分于此前定义的牛分枝杆菌簇：黄色为簇I/克隆复合体Eu3；橙色为簇G/家族F9；棕色为簇C/家族SB0134；紫色为簇D/克隆复合体Eu1；粉色为簇A/家族F4；蓝色为簇F/克隆复合体Eu2；灰色为其余菌株。 附录2 表格展示了本研究第3组所用的牛分枝杆菌基因组信息。该187株基因组均属于基因型F7与F15（分别对应SB0821与SB0832），二者为亲缘关系紧密的两种基因型。这些基因组在本论文研究启动前已完成测序，其中部分随Duault及其合作者的研究发表，其余尚未发表（标注为NA）（Duault等，2022）。 附录3 表格展示了本研究第4组所用的牛分枝杆菌基因组信息。该227株基因组均属于SB0120-DHV基因型。这些基因组在本论文研究启动前已完成测序，但目前尚未发表（在"提交日期"与"GenBank生物样本"列中标注为NA）。 附录4 大西洋比利牛斯省牛分枝杆菌菌株面板（SB0821与SB0832）中IS6110的插入位点位置。IS6110的起始与终止位点通过ISMapper工具结合参考基因组AF2122/97确定。 附录5 SB0120-DHV型牛分枝杆菌菌株面板中IS6110的插入位点位置。IS6110的起始与终止位点通过ISMapper工具结合参考基因组Mb3601确定。 附录6 该图来自Modenesi的实习报告，展示了300株SB0120-DHV菌株的环状共识系统发育树（Modenesi，2019）。第3组所用菌株属于该300株菌株的子集，系根据测序质量筛选得到，故保留的菌株数量更少（共227株）。该系统发育树被划分为11个不同颜色的进化枝。通过Beast工具确定的后验概率值（即表征该进化枝真实性的概率）标注于树内（Drummond与Rambaut，2007）。