The COX1 Mutation Drives Structural Innovation Despite Silent tRNA Variation in Semiaquatic Bugs

Supplementary Figure 1 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of AA dataset. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with full partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support. Supplementary Figure 2 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of P12R dataset. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with full partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support. Supplementary Figure 3 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of P123R dataset. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with full partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support. Supplementary Figure 4 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of AA dataset. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with merged partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support. Supplementary Figure 5 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of P12R dataset. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with merged partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support. Supplementary Figure 6 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of P123R dataset. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with merged partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support. Supplementary Figure 7 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of AA dataset. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with no partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support. Supplementary Figure 8 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of P12R dataset. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with no partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support. Supplementary Figure 9 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of P123R dataset. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with no partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support. Supplementary Figure 10 Bayesian phylogenetic reconstruction of Gerromorpha using P123R dataset. The topology is based on the CAT-GTR model by PhyloBayes. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the posterior probability support. Supplementary Figure 11 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of P123R dataset containing the mitochondrial data of Potamometra zhengi generated in this study. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with no partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support. Supplementary Figure 12 The proposed transcriptional model for mitochondrial protein-coding genes (PCGs) in Potamometra zhengi. Polycistronic primary transcripts are highlighted with red boxes, while monocistronic processed mRNAs are shown in grey. Supplementary Figure 13 Selection pressure, CAI and amino acid statistics for 13 PCGs in Gerromorpha. The phylogenetic relationships of Gerromorpha are depicted based on the optimal tree derived from the P123R dataset. Species marked with an asterisk (*) indicate those sequenced in this study. The pie chart below the node represents the proportion of selected pressure sites based on the aBSREL results. The first heat map block illustrates the CAI values of the 13 PCGs. The second dot chart block shows the amino acid composition statistics of PCGs. Supplementary Figure 14 Divergence phylogenetic tree of Gerromorpha based on P123R dataset. Green horizontal bars represent 95% credibility intervals. The fossil calibrations employed in this study are depicted as orange nails. The scale axis of the tree is expressed in millions of years. The Quaternary is represented by purple rectangles, the Neogene is denoted by ‘Neo.’, and other periods are not abbreviated. Key nodes were annotated with the estimated divergence times and their confidence intervals. The time unit is Mya. Species marked with an asterisk (*) indicate those sequenced in this study. Supplementary Figure 15 Multiple sequence alignment of mitochondrial COX1 codons in Gerromorpha. Visualization produced with TranslatorX. The GFF file within the Potamometra zhengi full-length transcript archive can be imported into Geneious for visualization of full-length transcripts.补充图1 本研究基于氨基酸（AA）数据集的最优树，构建了黾蝽次目（Gerromorpha）的系统发育关系。带星号（*）的物种为本次研究中完成测序的类群。该系统发育拓扑结构基于完全分区的最大似然法分析结果，节点处的数字代表自举支持值。 补充图2 本研究基于P12R数据集的最优树，构建了黾蝽次目的系统发育关系。带星号（*）的物种为本次研究中完成测序的类群。该系统发育拓扑结构基于完全分区的最大似然法分析结果，节点处的数字代表自举支持值。 补充图3 本研究基于P123R数据集的最优树，构建了黾蝽次目的系统发育关系。带星号（*）的物种为本次研究中完成测序的类群。该系统发育拓扑结构基于完全分区的最大似然法分析结果，节点处的数字代表自举支持值。 补充图4 本研究基于AA数据集的最优树，构建了黾蝽次目的系统发育关系。带星号（*）的物种为本次研究中完成测序的类群。该系统发育拓扑结构基于合并分区的最大似然法分析结果，节点处的数字代表自举支持值。 补充图5 本研究基于P12R数据集的最优树，构建了黾蝽次目的系统发育关系。带星号（*）的物种为本次研究中完成测序的类群。该系统发育拓扑结构基于合并分区的最大似然法分析结果，节点处的数字代表自举支持值。 补充图6 本研究基于P123R数据集的最优树，构建了黾蝽次目的系统发育关系。带星号（*）的物种为本次研究中完成测序的类群。该系统发育拓扑结构基于合并分区的最大似然法分析结果，节点处的数字代表自举支持值。 补充图7 本研究基于AA数据集的最优树，构建了黾蝽次目的系统发育关系。带星号（*）的物种为本次研究中完成测序的类群。该系统发育拓扑结构基于无分区的最大似然法分析结果，节点处的数字代表自举支持值。 补充图8 本研究基于P12R数据集的最优树，构建了黾蝽次目的系统发育关系。带星号（*）的物种为本次研究中完成测序的类群。该系统发育拓扑结构基于无分区的最大似然法分析结果，节点处的数字代表自举支持值。 补充图9 本研究基于P123R数据集的最优树，构建了黾蝽次目的系统发育关系。带星号（*）的物种为本次研究中完成测序的类群。该系统发育拓扑结构基于无分区的最大似然法分析结果，节点处的数字代表自举支持值。 补充图10 本研究采用P123R数据集，通过贝叶斯推断构建黾蝽次目的系统发育关系。该拓扑结构基于PhyloBayes软件实现的CAT-GTR模型。带星号（*）的物种为本次研究中完成测序的类群，节点处的数字代表后验概率支持值。 补充图11 本研究基于纳入本次测序得到的郑氏水黾（Potamometra zhengi）线粒体数据的P123R数据集最优树，构建了黾蝽次目的系统发育关系。带星号（*）的物种为本次研究中完成测序的类群。该系统发育拓扑结构基于无分区的最大似然法分析结果，节点处的数字代表自举支持值。 补充图12 本研究提出的郑氏水黾线粒体蛋白质编码基因（Protein-Coding Genes, PCGs）转录模型。多顺反子初级转录本以红色方框标注，单顺反子加工成熟mRNA以灰色方框展示。 补充图13 黾蝽次目13个线粒体蛋白质编码基因的选择压、密码子适应指数（Codon Adaptation Index, CAI）及氨基酸组成统计。本研究基于P123R数据集的最优树构建黾蝽次目的系统发育关系。带星号（*）的物种为本次研究中完成测序的类群。节点下方的饼图展示基于aBSREL分析结果的选择压位点占比；第一块热图展示13个蛋白质编码基因的密码子适应指数值；第二块散点图展示蛋白质编码基因的氨基酸组成统计结果。 补充图14 基于P123R数据集构建的黾蝽次目分化时间系统发育树。绿色横向条带代表95%置信区间。本研究采用的化石校准点以橙色锚点标注。树的标尺轴以百万年为单位。第四纪以紫色矩形标注，新近纪简写为“Neo.”，其余地质年代不简写。关键节点标注了估计的分化时间及其置信区间，时间单位为百万年前（Mya）。带星号（*）的物种为本次研究中完成测序的类群。 补充图15 黾蝽次目线粒体细胞色素c氧化酶亚基1（Cytochrome c Oxidase Subunit 1, COX1）密码子的多序列比对结果。可视化工作由TranslatorX软件完成。 郑氏水黾全长转录本存档文件中的GFF格式文件可导入Geneious软件，用于可视化展示全长转录本。