Complete plastid genome sequencing of Trochodendraceae reveals a significant expansion of the inverted repeat and suggests a Paleogene divergence between the two extant species

Abstract

The early-diverging eudicot order Trochodendrales contains only two monospecific genera, Tetracentron and Trochodendron. Although an extensive fossil record indicates that the clade is perhaps 100 million years old and was widespread throughout the Northern Hemisphere during the Paleogene and Neogene, the two extant genera are both narrowly distributed in eastern Asia. Recent phylogenetic analyses strongly support a clade of Trochodendrales, Buxales, and Gunneridae (core eudicots), but complete plastome analyses do not resolve the relationships among these groups with strong support. However, plastid phylogenomic analyses have not included data for Tetracentron. To better resolve basal eudicot relationships and to clarify when the two extant genera of Trochodendrales diverged, we sequenced the complete plastid genome of Tetracentron sinense using Illumina technology. The Tetracentron and Trochodendron plastomes possess the typical gene content and arrangement that characterize most angiosperm plastid genomes, but both genomes have the same unusual ∼4 kb expansion of the inverted repeat region to include five genes (rpl22, rps3, rpl16, rpl14, and rps8) that are normally found in the large single-copy region. Maximum likelihood analyses of an 83-gene, 88 taxon angiosperm data set yield an identical tree topology as previous plastid-based trees, and moderately support the sister relationship between Buxaceae and Gunneridae. Molecular dating analyses suggest that Tetracentron and Trochodendron diverged between 44-30 million years ago, which is congruent with the fossil record of Trochodendrales and with previous estimates of the divergence time of these two taxa. We also characterize 154 simple sequence repeat loci from the Tetracentron sinense and Trochodendron aralioides plastomes that will be useful in future studies of population genetic structure for these relict species, both of which are of conservation concern.

Figure 1. Map of the Tetracentron sinense plastid genome.

Figure 2. Map of the Trochodendron aralioides plastid genome.

Figure 3. Comparison of the IR junctions in Tetracentron and Trochodendron.

Figure 4. Amount of sequence divergence between the protein-coding genes of Tetracentron and Trochodendron.

Figure 5. Sequence identity plot between Trochodendron and Tetracentron.

Figure 6. A maximum likelihood tree determined by GARLI (−ln L = −1095466.026) for the 83-gene, 88-taxon data set.

Numbers associated with branches are ML bootstrap support values. Error bars around nodes correspond to 95% highest posterior distributions of divergence times based on 6 fossils using the program BEAST. Eo = Eocene, Mi = Miocene, Ol. = Oligocene, Pa = Paleocene, Pl = Pliocene.