Supplementary Material for: The mitochondrial genome of Isognomon nucleus and mitophylogenomics (Bivalvia: Autobranchia)

Appendix S1: Expanded Materials and Methods Appendix S2: Sequencing depth analysis Appendix S3: Lack of a convincing ATP8 gene Appendix S4: Potential long novel transmembrane domain containing ORFs in I. nucleus and P. fucata martensii Fig. S1. Length versus base quality plot of ONT reads (within Appendix S1) Fig. S2. Evidence for a small gap in the I. nucleus mitogenome from ONT-only assembly (within Appendix S1) Fig. S3. Distribution of observed and theoretical protein sizes from ORFs found in the unannotated portion of the I. nucleus mitogenome (within Appendix S4) Table S1: Structural features of the standard mitochondrial genes in the Isognomon nucleus mitogenome Table S2: Summary statistics for ONT reads via NanoStat (within Appendix S1) Table S3: List of species, accession numbers and mitogenome sizes used in this study (within Appendix S1) Data S1. Sequences of the 4 long Isognomon nucleus proteins with multiple predicted transmembrane domains (these were included in the official annotation of the mitogenome) Data S2. Transmembrane domain identification for the I. nucleus predicted proteins by DeepTMHMM (gff output format) Data S3. Sequences of the 5 long Pinctada fucata martensii proteins with multiple predicted transmembrane domains Data S4. Transmembrane domain identification for the P. fucata martensii predicted proteins by DeepTMHMM (gff output format) Sup. Data 5. (Not in this file; available at Figshare) Contains the curated, GBLOCKS-alignment, all files from the IQTREE run and pdf exports of the estimated ML tree from FigTree. [https://figshare.com/projects/Isognomon_mitogenomes_Supplementary_Data_Files_tables/129485] Sup. Data 6. Sequences of the 3 additional long Isognomon nucleus proteins with multiple predicted transmembrane domains (these were not included in the official mitogenome annotation)

附录S1：扩展材料与方法
附录S2：测序深度分析
附录S3：缺乏可信的ATP8基因
附录S4：伊氏江珧（Isognomon nucleus）与马氏珠母贝（Pinctada fucata martensii）中潜在的长新型跨膜结构域编码开放阅读框（Open Reading Frames, ORFs）
图S1：附录S1内的ONT（Oxford Nanopore Technologies）读长的长度-碱基质量散点图
图S2：附录S1内仅基于ONT组装得到的伊氏江珧线粒体基因组（mitogenome）存在小缺口的证据
图S3：附录S4内伊氏江珧线粒体基因组未注释区域中开放阅读框所编码蛋白的观测与理论蛋白大小分布
表S1：伊氏江珧线粒体基因组标准线粒体基因的结构特征
表S2：附录S1内通过NanoStat统计得到的ONT读长汇总统计量
表S3：本研究所用物种、登录号（accession numbers）与线粒体基因组大小列表
数据S1：4个带有多个预测跨膜结构域的长伊氏江珧蛋白序列（该序列已纳入线粒体基因组官方注释）
数据S2：通过DeepTMHMM对伊氏江珧预测蛋白的跨膜结构域识别结果（gff输出格式）
数据S3：5个带有多个预测跨膜结构域的长马氏珠母贝蛋白序列
数据S4：通过DeepTMHMM对马氏珠母贝预测蛋白的跨膜结构域识别结果（gff输出格式）
补充数据5：（本文件未收录；可于Figshare获取）包含经手工校正的GBLOCKS比对文件、IQTREE运行所得全部文件与通过FigTree导出的最大似然（Maximum Likelihood, ML）树PDF文件。[https://figshare.com/projects/Isognomon_mitogenomes_Supplementary_Data_Files_tables/129485]
补充数据6：3个额外的长伊氏江珧蛋白序列，这些蛋白带有多个预测跨膜结构域（未纳入线粒体基因组官方注释）