**In-Su Choi 1,\*, Tracey A. Ruhlman <sup>1</sup> and Robert K. Jansen 1,2**


Received: 11 January 2020; Accepted: 17 February 2020; Published: 13 March 2020

**Abstract:** The genus *Trifolium* is the largest of the tribe Trifolieae in the subfamily Papilionoideae (Fabaceae). The paucity of mitochondrial genome (mitogenome) sequences has hindered comparative analyses among the three genomic compartments of the plant cell (nucleus, mitochondrion and plastid). We assembled four mitogenomes from the two subgenera (*Chronosemium* and *Trifolium*) of the genus. The four *Trifolium* mitogenomes were compact (294,911–348,724 bp in length) and contained limited repetitive (6.6–8.6%) DNA. Comparison of organelle repeat content highlighted the distinct evolutionary trajectory of plastid genomes in a subset of *Trifolium* species. Intracellular gene transfer (IGT) was analyzed among the three genomic compartments revealing functional transfer of mitochondrial *rps1* to nuclear genome along with other IGT events. Phylogenetic analysis based on mitochondrial and nuclear *rps1* sequences revealed that the functional transfer in Trifolieae was independent from the event that occurred in robinioid clade that includes genus *Lotus*. A novel, independent fission event of *ccmFn* in *Trifolium* was identified, caused by a 59 bp deletion. Fissions of this gene reported previously in land plants were reassessed and compared with *Trifolium*.

**Keywords:** legumes; clover; organelle genetics; mitochondria; endosymbiotic gene transfer; gene fission
