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)