*4.7. Investigation of ccmF Fissions in Selected Land Plants*

To investigate previously reported fission events of *ccmF* genes in land plants [22–25], all available sequences from published mitogenome sequences related to *Marchantia*, Brassicaceae, *Allium* (Amaryllidaceae) and Fabaceae were acquired. For *Marchantia*, published mitogenomes [22,73,74] of three species (*M. inflexa*, *M. polymorpha* subsp. *ruderalis* and *M. paleacea*) were examined: two from NCBI [*M. polymorpha* subsp. *ruderalis* (NC\_037508.1) and *M. paleacea* (NC\_001660.1)] and *M. inflexa*, which was downloaded from FigShare (https://figshare.com/ articles/Marchantia\_inflexa\_mitochondrion\_and\_chloroplast\_genomes/6639209/1). Two mitogenomes [*Dumortiera hirsuta* (NC\_042873) and *Riccia fluitans*(NC\_043906)], which are closely related to *Marchantia* in Marchantiales [75,76], were also included. For Amaryllidaceae, a single mitogenome [*Allium cepa* (NC\_030100)] was available.

In addition to previously published and newly assembled mitogenomes, mitochondrial contigs were generated from available NGS reads for Brassicales and Fabaceae (Table S2). Raw sequences were mapped to reference *ccmF* sequences and the mapped reads were assembled in Geneious. The *ccmF* sequences of *Medicago truncatula* and *Batis maritima* were used as references for Fabaceae and Brassicales, respectively. Read depth of assembled *ccmF* genes (*ccmFn* and *ccmFc*) were compared to confirm that sequences originated from mitogenome rather than from other genomic compartments (i.e., nuclear and plastid genome). To search for nuclear copies of *ccmFn1* and *ccmFn2*, subject databases comprising four *Trifolium* nuclear genomes (Table S1) were queried with the mitochondrial *ccmFn* of *T. aureum* using MegaBLAST with default options. All sequences were aligned with MAFFT as described above. The status of *ccmFn* was plotted on cladograms from published phylogenetic studies of *Trifolium* [42] and Brassicaceae [47]. Conserved domains of *ccmFn* were detected using the Motif Scan of MyHits (http://myhits.isb-sib.ch/cgi-bin/motif\_scan) [77,78].
