Data from: Evolutionary origin of highly repetitive plastid genomes within the clover genus (Trifolium)

Abstract
Background: Some clover species, particularly Trifolium subterraneum, have previously been reported to have highly unusual plastomes, relative to closely related legumes, enlarged with many duplications, gene losses and the presence of DNA unique to Trifolium, which may represent horizontal transfer. In order to pinpoint the evolutionary origin of this phenomenon within the genus Trifolium, we sequenced and assembled the plastomes of eight additional Trifolium species widely sampled from across the genus. Results: The Trifolium plastomes fell into two groups: those of Trifolium boissieri, T. strictum and T. glanduliferum (representing subgenus Chronosemium and subg. Trifolium section Paramesus) were tractable, assembled readily and were not unusual in the general context of Fabeae plastomes. The other Trifolium species (“core Trifolium”) proved refractory to assembly mainly because of numerous short duplications. These species form a single clade, which we call the “refractory clade” (comprising subg, Trifolium sections Lupinaster, Trifolium, Trichocephalum, Vesicastrum and Trifoliastrum). The characteristics of the refractory clade are the presence of numerous short duplications and 7-15% longer genomes than the tractable species. Molecular dating estimates that the origin of the most recent common ancestor (MRCA) of the refractory clade is approximately 13.1 million years ago (MYA). This is considerably younger than the estimated MRCA ages of Trifolium (c. 18.6 MYA) andTrifolium subg. Trifolium (16.1 MYA). Conclusions: We conclude that the unusual repetitive plastome type previously characterized in Trifolium subterraneum had a single origin within Trifolium and is characteristic of most (but not all) species of subgenus Trifolium. It appears that an ancestral plastome within Trifolium underwent an evolutionary change resulting in plastomes that either actively promoted, were permissive to, or were unable to control, duplications within the genome. The precise mechanism of this important change in the mode and tempo of plastome evolution deserves further investigation. (2020-06-24)

Usage notes
Trifolium_plastid_codingA concatenated matrix of 59 protein coding plastid genes. Only coding regions were used, introns and intergenic regions were excluded in the alignment, due to plastome rearrangements (see manuscript of further description). The alignment was generated using Mafft v7.053b using -auto flag and trimmed using TrimAl with the -automated1 flag. This process was pipelined using Plast2Phy (https://github.com/saemi/plast2phy).Trifolium_plastid_coding_MLML tree generated using GARLI (the config file is the ReadMe file). The model used GTR+G, based on a jModelTest search and an AIC test. 10 starts were prefromed and a 100 bootstrap replicates. Medicago truncatula is the outrgroup. (2020-06-24)