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

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