**5. Conclusions**

The newly sequenced mitogenomes of *Trifolium* allowed comparative analyses of genome evolution for all three cellular compartments—mitochondrion, nucleus and plastid. Unlike many angiosperms, *Trifolium* lacks the highly repetitive genome organization of mitogenome. Some *Trifolium* plastomes has a much more complex organization and has accumulated more repeat contents than the mitogenome. a substantial amount of organellar DNA was detected in nuclear genomes of *Trifolium*, likely resulting from recent and nonfunctional IGT events. In addition, there has been an ancestral, functional transfer of mitochondrial *rps1* to the nuclear genome. a notable finding from the mitogenome of *Trifolium* was a novel gene fission of *ccmFn*. Analyses of *ccmF* genes in selected land plants provided further insights into the fission events. Although the current study is based on limited sampling of the three genomic compartments, our findings expand the understanding of how these genomes evolved in *Trifolium*. The underlying evolutionary and molecular mechanisms should be examined in future comparisons that incorporate broader taxonomic sampling for all three genomic compartments.

**Supplementary Materials:** Supplementary Materials can be found at http://www.mdpi.com/1422-0067/21/6/1959/ s1. Figure S1. Nucleotide alignment showing deletion of mitochondrial *rps1* in *Trifolium* species. Figure S2. Gene and cis-spliced intron content across six Papilionoideae genera. Figure S3. Circoletto map showing similar sequences between mitogenome of *T. meduseum* (left arc) and a continuous region of nuclear genome (right arc) of *T. repens* (chromosome 4; NCBI accession: VCDJ01010667; position: 72,476,623-72,825,180). Figure S4. Sequence variation of *ccmFn* in *Trifolium* species. Figure S5. Alignment of the mitochondrial region containing *ccmFn* and *ccmFc* genes from five species of Marchantiales. Table S1. Information on nuclear genomes, used for comparative study. Table S2. List of taxa for *ccmF* analysis with information about sequence sources and status of the genes.

**Author Contributions:** Conceptualization, I.-S.C. and R.K.J.; Validation, R.K.J. and T.A.R.; Formal Analysis, I.-S.C.; Investigation, I.-S.C.; Resources, R.K.J. and T.A.R.; Data Curation, R.K.J. and T.A.R.; Writing—Original Draft Preparation, I.-S.C.; Writing—Review & Editing, I.-S.C., T.A.R. and R.K.J.; Visualization, I.-S.C.; Supervision, R.K.J.; Funding Acquisition, R.K.J. and T.A.R. All authors have read and agreed to the published version of the manuscript.

**Funding:** This work was supported by a National Science Foundation grant (DEB-1853024) to R.K.J. and T.A.R. and the S. F. Blake Centennial Professorship to R.K.J.

**Conflicts of Interest:** The authors declare no conflict of interest.
