Phylogenetic trees

<br><b>Fig. S1. </b>Phylogenetic tree of the taxa used for comparative genomics analysis, including the 15 uncultured MAST species, using the 18S rDNA gene. The tree was generated with IQTREE using 1000 trees for topology and 1000 trees for bootstrapping. Five non-stramenopile taxa were used as outgroup. Eukaryotic species were assigned to a trophic lifestyle. <br><br><b>Fig. 5. </b>Phylogenetic tree of microbial type I rhodopsins based on 207 protein sequences, including the new MASTs, showing the recognized groups and their prevalent function. Black dots indicate bootstrap support &gt;80% over 1000 replicates. Stars highlight sequences recovered from co-assemblies.<br><b>Fig. S6. </b>Phylogenetic tree of V-ATPases and the related F-ATPases genes constructed from recent bibliographical references (see Material and Methods). MASTs lineages are represented in orange. Values at nodes correspond to bootstraps &gt; 80%.<br><br><b>Fig. S7. </b>Phylogenetic tree of V-PPases genes constructed from recent bibliographical references (see Material and Methods). MASTs lineages are represented in orange. Values at nodes correspond to bootstraps &gt; 80%.<br>

<b>补充图S1</b>：基于18S核糖体DNA（18S rDNA）基因构建的比较基因组学分析用类群系统发育树，包含15株未培养的MAST（MAST）物种。该系统发育树由IQTREE软件生成，拓扑结构推断采用1000次重复采样，自展检验（bootstrapping）同样设置为1000次重复。以5个非不等鞭毛类（stramenopile）类群作为外类群。所有真核生物类群均被赋予了对应的营养生活方式类型。<br><br><b>图5</b>：基于207条蛋白质序列构建的微生物I型视紫红质（type I rhodopsins）系统发育树，涵盖新发现的MAST类群，展示了已确认的类群及其主流功能。黑色圆点代表1000次重复检验下自展支持率大于80%的分支。星号标记了从共组装（co-assemblies）实验中获得的目标序列。<br><br><b>补充图S6</b>：基于近期参考文献构建的V型ATP酶（V-ATPases）及相关F型ATP酶（F-ATPases）基因系统发育树（详见材料与方法部分）。MAST类群谱系以橙色标注。节点旁的数值代表自展支持率大于80%。<br><br><b>补充图S7</b>：基于近期参考文献构建的V型焦磷酸酶（V-PPases）基因系统发育树（详见材料与方法部分）。MAST类群谱系以橙色标注。节点旁的数值代表自展支持率大于80%。