Complete Plastid Genome Sequencing of Trochodendraceae Reveals a Significant Expansion of the Inverted Repeat and Suggests a Paleogene Divergence between the Two Extant Species

Yan-xia Sun,Michael J. Moore,Pamela S. Soltis,Jian-qiang Li,Ai-ping Meng,Douglas E. Soltis,Heng-chang Wang,Jonathan H. Badger

doi:10.1371/journal.pone.0060429

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.

Highlights

The eudicot order Trochodendrales [1] contains only two extant genera, both of which are monotypic: Trochodendron Sieb. & Zucc. and Tetracentron Oliver
Earlier researchers reported that wood of Trochodendrales wood lacked vessels and suggested that Trochodendrales were among the earliest-diverging angiosperms, recent research has documented the presence of vessels in the wood of both genera [2,7,19]
We report the complete plastid genome sequences of Tetracentron sinense and Trochodendron aralioides, as well as the results of new phylogenetic analyses based on adding Tetracentron and Megaleranthis genomes [52] to the 83-gene data set of Moore et al [26]

Summary

Introduction

The eudicot order Trochodendrales [1] contains only two extant genera, both of which are monotypic: Trochodendron Sieb. & Zucc. and Tetracentron Oliver. Is a large, evergreen shrub or small tree native to the mountains of Japan to South Korea and Taiwan, and the Ryukyu Islands [2,17], whereas Tetracentron sinense Oliver is a deciduous tree occurring in southwestern and central China and the eastern Himalayan regions. Both species are characterized by apetalous flowers arranged in cymose inflorescences and by loculicidal capsules that dehisce to release winged seeds [2,5,7,18]. Earlier researchers reported that wood of Trochodendrales wood lacked vessels and suggested that Trochodendrales were among the earliest-diverging angiosperms, recent research has documented the presence of vessels in the wood of both genera [2,7,19]

Methods

Results

Conclusion