Abstract
BackgroundSome 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.ResultsThe 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) and Trifolium subg. Trifolium (16.1 MYA).ConclusionsWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-014-0228-6) contains supplementary material, which is available to authorized users.
Highlights
Some clover species, 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
Subterranean clover (Trifolium subterraneum) is known to have an unusual plastid genome structure [7]. It lacks one copy of the inverted repeat, but that is a character shared with a large group of papilionoid legumes [8], designated the inverted repeat lacking clade (IRLC)
It is clear that this plastome contains several repeated regions, similar to T. subterraneum
Summary
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. There are currently 512 plastome sequences listed at NCBI’s Organelle Genome Resource website (http://tinyurl.com/ncbi-plastid-genomes, 17 April 2014) and half of them have been made available since 2012 Their structure, gene order and gene content is generally highly conserved across most flowering plants, where most plastomes have two copies of a highly conserved. The extent to which this is a widespread feature of Trifolium species, or characteristic of a restricted part of the genus Trifolium still needs further investigation To answer this question, we performed a low coverage whole genome shotgun sequencing of nine strategically sampled Trifolium species and were able to assemble eight plastid genomes. We performed a low coverage whole genome shotgun sequencing of nine strategically sampled Trifolium species and were able to assemble eight plastid genomes These plastomes were analysed to elucidate the phylogenetic distribution of plastome variation in the genus
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
