The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements

Background

Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and resequencing of the T. sinense genome will help us understand eudicot evolution, the genetic basis of tracheary element development, and the genetic diversity of this relict species.

Results

Here, we report a chromosome-scale assembly of the T. sinense genome. We assemble the 1.07 Gb genome sequence into 24 chromosomes and annotate 32,690 protein-coding genes. Phylogenomic analyses verify that the Trochodendrales and core eudicots are sister lineages and showed that two whole-genome duplications occurred in the Trochodendrales approximately 82 and 59 million years ago. Synteny analyses suggest that the γ event, resulting in paleohexaploidy, may have only happened in core eudicots. Interestingly, we find that vessel elements are present in T. sinense, which has two orthologs of AtVND7, the master regulator of vessel formation. T. sinense also has several key genes regulated by or regulating TsVND7.2 and their regulatory relationship resembles that in Arabidopsis thaliana. Resequencing and population genomics reveals high levels of genetic diversity of T. sinense and identifies four refugia in China.

Conclusions

The T. sinense genome provides a unique reference for inferring the early evolution of eudicots and the mechanisms underlying vessel element formation. Population genomics analysis of T. sinense reveals its genetic diversity and geographic structure with implications for conservation.

Supplementary information

The online version contains supplementary material available at 10.1186/s13059-020-02198-7.

Two early eudicot fossil flowers from the Kamikitaba assemblage (Coniacian, Late Cretaceous) in northeastern Japan

Two new fossil taxa referable to the basal eudicot grade are described from the Kamikitaba locality (ca. 89 MYBP, early Coniacian: Late Cretaceous) of the Futaba Group in Japan. These charcoalified mesofossils exhibit well-preserved three-dimensional structure and were analyzed using synchrotron-radiation X-ray microtomography to document their composition and internal structure. Cathiaria japonica sp. nov. is represented by infructescence segments that consist of an axis bearing three to four fruits. The capsular fruits are sessile and dehiscent and consist of a gynoecium subtended by a bract. No perianth parts are present. The gynoecium is monocarpellate containing two pendulous seeds. The carpel is ascidiate in the lower half and conduplicate in the upper part, and the style is deflected abaxially with a large, obliquely decurrent stigma. Pollen grains are tricolpate with a reticulate exine. The morphological features of Cathiaria are consistent with an assignment to the Buxaceae s. l. (including Didymelaceae). Archaestella verticillatus gen. et sp. nov. is represented by flowers that are small, actinomorphic, pedicellate, bisexual, semi-inferior, and multicarpellate. The floral receptacle is cup shaped with a perigynous perianth consisting of several tepals inserted around the rim. The gynoecium consists of a whorl of ten conduplicate, laterally connate but distally distinct carpels with a conspicuous dorsal bulge, including a central cavity. The styles are short, becoming recurved with a ventrally decurrent stigma. Seeds are ca. 10 per carpel, marginal, pendulous from the broad, oblique summit of the locule. Pollen grains are tricolpate with a reticulate exine pattern, suggesting a relationship to eudicots. The morphological features of Archaestella indicate a possible relationship to Trochodendraceae in the basal grade of eudicots. The fossil currently provides the earliest record of the family and documents the presence of Trochodendraceae in eastern Eurasia during the middle part of the Late Cretaceous.

Ozakia, a new genus of winged fruit shared between the Miocene of Japan and western North America

A new genus is recognized based on winged fruits with a single species shared between the Miocene of southwestern Honshu, Japan, and the Miocene of Oregon and Idaho, USA. Calyces of Ozakia emryi gen. et sp. n. were formerly attributed to Heptacodium (Caprifoliaceae) and Amelanchier (Rosaceae); however, newly recovered specimens reveal additional characters that contradict these assignments. The pedicellate fruits are obovate, tapering basally and truncate apically, with about 10 longitudinal ribs, a prominent epigynous synsepalous calyx of five lobes, each with a midvein and a pair of weaker, ascending intramarginal primary veins. The single style has a capitate stigma. Ozakia is considered to represent an extinct eudicot genus, the familial affinities of which remain uncertain. The eastern Asian-western North American disjunction of Ozakia occurrences suggests that this plant traversed the Beringia land bridge during or prior to the Middle Miocene. Relatively few extinct angiosperm genera are known as late as the Miocene.

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

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.

Diversification of land plants: insights from a family-level phylogenetic analysis

Background

Some of the evolutionary history of land plants has been documented based on the fossil record and a few broad-scale phylogenetic analyses, especially focusing on angiosperms and ferns. Here, we reconstructed phylogenetic relationships among all 706 families of land plants using molecular data. We dated the phylogeny using multiple fossils and a molecular clock technique. Applying various tests of diversification that take into account topology, branch length, numbers of extant species as well as extinction, we evaluated diversification rates through time. We also compared these diversification profiles against the distribution of the climate modes of the Phanerozoic.

Results

We found evidence for the radiations of ferns and mosses in the shadow of angiosperms coinciding with the rather warm Cretaceous global climate. In contrast, gymnosperms and liverworts show a signature of declining diversification rates during geological time periods of cool global climate.

Conclusions

This broad-scale phylogenetic analysis helps to reveal the successive waves of diversification that made up the diversity of land plants we see today. Both warm temperatures and wet climate may have been necessary for the rise of the diversity under a successive lineage replacement scenario.

Fossils and plant phylogeny

Developing a detailed estimate of plant phylogeny is the key first step toward a more sophisticated and particularized understanding of plant evolution. At many levels in the hierarchy of plant life, it will be impossible to develop an adequate understanding of plant phylogeny without taking into account the additional diversity provided by fossil plants. This is especially the case for relatively deep divergences among extant lineages that have a long evolutionary history and in which much of the relevant diversity has been lost by extinction. In such circumstances, attempts to integrate data and interpretations from extant and fossil plants stand the best chance of success. For this to be possible, what will be required is meticulous and thorough descriptions of fossil material, thoughtful and rigorous analysis of characters, and careful comparison of extant and fossil taxa, as a basis for determining their systematic relationships.

Hardly a relict: freezing and the evolution of vesselless wood in Winteraceae

The Winteraceae are traditionally regarded as the least-specialized descendents of the first flowering plants, based largely on their lack of xylem vessels. Since vessels have been viewed as a key innovation for angiosperm diversification, Winteraceae have been portrayed as declining relicts, limited to wet forest habitats where their tracheid-based wood does not impose a significant hydraulic constraints. In contrast, phylogenetic analyses place Winteraceae among angiosperm clades with vessels, indicating that their vesselless wood is derived rather than primitive, whereas extension of the Winteraceae fossil record into the Early Cretaceous suggests a more complex ecological history than has been deduced from their current distribution. However, the selective regime and ecological events underlying the possible loss of vessels in Winteraceae have remained enigmatic. Here we examine the hypothesis that vessels were lost as an adaptation to freezing-prone environments in Winteraceae by measuring the responses of xylem water transport to freezing for a diverse group of Winteraceae taxa as compared to Canella winterana (Canellaceae, a close relative with vessels) and sympatric conifer taxa. We found that mean percent loss of xylem water transport capacity following freeze-thaw varied from 0% to 6% for Winteraceae species from freezing-prone temperate climates and approximately 20% in those taxa from tropical (nonfreezing) climates. Similarly, conifers exhibit almost no decrease in xylem hydraulic conductivity following freezing. In contrast, water transport in Canella stems is nearly 85% blocked after freeze-thaw. Although vessel-bearing wood of Canella possesses considerably greaterhydraulic capacity than Winteraceae, nearly 20% of xylem hydraulic conductance remains, a value that is comparable to the hydraulic capacity of vesselless Winteraceae xylem, if the proportion of hydraulic flow through vessels (modeled as ideal capillaries) is removed. Thus, the evolutionary removal of vessels may not necessarily require a deleterious shift to an ineffective vascular system. By integrating Winteraceae's phylogenetic relationships and fossil history with physiological and ecological observations, we suggest that, as ancestors of modern Winteraceae passed through temperate conditions present in Southern Gondwana during the Early Cretaceous, they were exposed to selective pressures against vessel-possession and returned to a vascular system relying on tracheids. These results suggest that the vesselless condition is advantageous in freezing-prone areas, which is supported by the strong bias in the ecological abundance of Winteraceae to wet temperate and tropical alpine habitats, rather than a retained feature from the first vesselless angiosperms. We believe that vesselless wood plays an important role in the ecological abundance of Winteraceae in Southern Hemisphere temperate environments by enabling the retention of leaves and photosynthesis in the face of frequent freeze-thaw events.