*4.3. Completion of the Trifolium Pratense Plastome*

Plastome drafts of *Trifolium pratense* were reported in two different studies [31,34] but these sequences contained a complex repeat structure. Since these previous assemblies were based on short insert size data only (400-800 bp), the *T. pratense* plastome was redone using sequences generated from one of the previous studies [31] as well as mapping data from mate-pair Illumina sequences (ERX946087) with long insert sizes (7 kb) [43]. The newly assembled plastome was annotated as described above but with MPI-MP chloroplast references in GeSeq [64].
