A new window into flowering plant origins
There is now an excellent candidate plant to develop as a new model plant system for early angiosperms, the genus Trithuria (family Hydatellaceae). Dr Graham and his students recently demonstrated that this family originated very close to the origin of flowering-plant phylogeny (13). It is an attractive prospect for development as a new model-plant system  because its stem lineage pre-dates the origin of monocots and eudicots (10,13), and the plants are small and easily cultivatable; other early flowering plants are mostly long-lived trees.
The new phylogenetic placement of Hydatellaceae near the origin of all flowering plants (13) re-opens debates on early angiosperm evolution, including the origin of their basic reproductive biology and ecology due to the following characteristics:
- Trithuria possesses combined characteristics of flowers and inflorescences in a possibly primitive structure that has been called a “nonflower” (14,15). This structure has an inside-out floral morphology, with pistils surrounding stamens.
- The entire reproductive unit develops centrifugally, in contrast to centripetal or simultaneous development in typical flowers.
- All Trithuria species exhibit a pre-fertilization maternal resource allocation to ovules/seeds in contrast to the remaining flowering plants. Post-fertilization allocation has been hypothesized to be a key reproductive innovation associated with the origin and subsequent evolutionary radiation of flowering plants (16).
However, knowledge of species boundaries in Trithuria remains unexplored, therefore constraining its use as a new model plant and ultimately the development of genomic tools for detecting orthologs and paralogs genes.
The main objective of ORIGIN is to unravel the evolutionary history of this plant, by defining its species boundaries and by facilitating its use as an “early angiosperm” model plant to root studies of multigene family diversification and gene function. To reach this objective, three main goals have been defined.
Goal 1: Define species boundaries and uncover phylogenetic relationships in Trithuria (Hydatellaceae).
Under this first goal, ORIGIN will address the following questions:
- What are the genetic limits of T. submersa as a species (its taxonomic definition)?
- How is it related to its close relatives (its local phylogenetic relationships)?
The family Hydatellaceae was recently re-classified to comprise only a single genus, Trithuria, with 12 distinct species that are found primarily in Australia (17). Several species are currently being investigated for their suitability for cultivation and potential as a model organism, by Dr. Paula Rudall and colleagues at Royal Botanical Gardens, Kew, UK. The most promising of these is Trithuria submersa, a southern Australian species that can be grown rapidly from seeds on growth medium. This species is short-lived, very small, tractable to handle in culture, and is primarily self-fertilizing (18). Although its genome size is currently unknown, it is likely to be small given its rapid generation time and extremely small chromosomes (19). These are all attractive features in any model plant system (20).
Trithuria submersa has a large geographic range across much of southern Australia, whereas the two closest relatives, T. bibracteata and T. occidentalis, occur in localized areas in Western Australia. Trithuria occidentalis was previously taxonomically lumped with T. submersa based on its overall morphology (21), but a recent morphological study showed that these two species are morphologically distinct from each other (17,22). A preliminary phylogenetic survey based on chloroplast (plastid) genes raises the strong possibility that T. submersa is a species that is “nested” phylogenetically inside another species (T. bibracteata) and that a third species (T. occidentalis) may also be part of this rather poorly-delimited species complex. Thus, it is unclear whether current species delimitation (ie taxonomy) accurately reflects ancestor-descendent relationships (ie, genetic history). Genetic boundaries are arguably at least as important for clarifying species limits as morphology (25). The boundaries of T. submersa in the context of its close relatives need to be clarified if it is to be used as a model plant for genetic and evolutionary research. Thus, ORIGIN, in a first goal, aims to define what are the genetic limits of T. submersa as a species (its taxonomic definition), and how it is related to its close relatives (its local phylogenetic relationships).
Goal 2: Resolve a key ambiguity in early plant evolution.
Under this second goal, ORIGIN will address the following question:
- Where does the root of flowering-plant phylogeny belong?
Charles Darwin famously observed that the origin and rapid diversification of flowering plants in recent geological time is an “abominable mystery” (26). One major mystery concerning angiosperm origins was partly resolved with the recognition that the root of flowering-plant phylogeny is at or close to a branch leading to the New Caledonian shrub, Amborella trichopoda, and the two water-lily families, Cabombaceae and Nymphaeaceae (27-30). However a persistent and unresolved question concerns the precise placement of the angiosperm root: Is it on the branch leading to Amborella alone, or to Amborella+water lilies?
Amborella is a woody shrub, similar to other early lines of angiosperms (the ‘ANITA’ grade) while the water lilies are aquatic herbs, recently recognized to include Hydatellaceae (31). The new phylogenetic placement of Hydatellaceae near the origin of all flowering plants re-opens debates on the origin of flowering plants (32,33) and also on the possibility that adaptation to aquatic habitats played a role in early angiosperm radiation (34,35). The aquatic reversion has occurred independently at least 50 times during plant evolution (36), but so far, a model plant system has been lacking to test this hypothesis.
Pinpointing the root of angiosperm phylogeny is crucial for clarifying some of the remaining mysteries concerning flowering-plant origins. It is also critical for understanding the origin and subsequent radiation of gene families that arose close to the origin of flowering plants, and that have since then subsequently diversified spectacularly in major plant groups like the monocots and eudicots. The latter groups include almost all of our major crop plants—eg rice, Oryza—and the model plant Arabidopsis. In summary, through this second defined goal, ORIGIN aims to clarify the root of flowering-plant phylogeny by examining large-scale genomic evidence from the nuclear genome.
Goal 3: Determine the origin of orthologs and paralogs genes on a large evolutionary scale
Under this third goal, ORIGIN will address the following questions:
- What is the origin of the genes that control floral development?
Having solved the genetic boundaries of the early-flowering plant Trithuria (Goal 1) and clarified the overall root of the angiosperm tree (Goal 2), ORIGIN will facilitate a clearer determination of orthologs vs. paralogs in other plant groups, such as the monocot model plant Brachypodium. Ecologically important genes such as the ones that control floral development have been well studied in the current model plant systems (37,38). However, the origin of these genes and therefore the prediction of their function relative to environmental change remain unknown. Therefore, in this third goal, ORIGIN aims to identify the origin of gene families that control flowering in the model plant Brachypodium and trace back their evolutionary history relative to Trithuria and other angiosperms, identifying the origin of new functionality (i.e., orthologs vs. paralogs) in this model grass and facilitating functional prediction in other cereal crops.
Journal and book articles:
1. Judd WS, et al. 2008. Sinauer Associates, Inc. Sunderland, Massachusetts, USA. 2. Meinke DW, et al. 1998. Science 282: 662–682. 3. IBI (International Brachypodium Initiative) 2010. Nature, 463: 763-8. 4. Kellogg EA, Bennetzen JL. 2004. American Journal of Botany 91:1709-1725. 5. Adams KL, Wendel JF. 2005. Current Opinion in Plant Biology 8:135–141. 6. Bento et al. 2008. PLoS ONE 3:e1402. 7. Wood TE. 2009. Proceedings of the National Academy of Sciences, USA 106:13875-13879. 8. Ohno S. 1970. Springer-Verlag, Heidelberg, Germany. 9. Lynch M, Connery JS. 2000. Science 290:1151-1155. 10. Bell CD et al. 2010. American Journal of Botany 97: 1296-1303. 11. He X, Zhang J. 2005. Genetics 169:1157-1164. 12. Wall PK, et al. 2008. Nucleic Acids Research 36:D971. 13. Saarela JM et al. 2007. Nature 446:312-315. 14. Rudall PJ et al. 2007. American Journal of Botany 94:1073-1092. 15. Rudall PJ et al. 2009. American Journal of Botany 96:67-82. 16. Friedman WE. 2008. Nature 453:94-97. 17. Sokoloff DD, et al. 2008. Taxon 57:179–200. 18. Taylor, M, et al. 2010. Annals of Botany 106:909-920. 19. De Lange et al. 2004. New Zealand Journal of Botany 42:873-904. 20. Somerville C, Koorrneef M. (2002). Nature Reviews Genetics 3:833-889. 21. Cooke DA. 1987. Australian Government Publishing Service, Canberra. 22. Sokoloff DD, et al. 2010. Australian Systematic Botany 23:217-228. 23. Iles WJD, et al. 2008. Vancouver July 2008. 24. Iles WJD, et al. 2010. Providence, Rhode Island, August 2008. 25. Fujita MK, Leaché AD. 2010. Proceedings of the Royal Society B 278:493-495. 26. Friedman WE. 2009. American Journal of Botany 96:5-21. 27. Mathews S, Donoghue MJ. 1999. Science 286:947-950. 28. Soltis PS, et al. 1999. Nature 402:402-404. 29. Qiu Y-L, et al. 1999. Nature 402:404-407. 30. Graham SW, Olmstead RG. 2000. American Journal of Botany 87:1712-1730. 31. Graham SW, Iles WJD. 2009. American Journal of Botany 96:216-227. 32. Leebens-Mack J, et al. 2005. Molecular Biology and Evolution 22:1948-1963. 33. Moore MJ, et al. 2007. Proceedings of the National Academy of Sciences, USA 104:19363-19368. 34. Doyle JA, Hickey LJ. 1976. Columbia University Press, New York, USA. 35. Feild TS, et al. 2004. Paleobiology 30:82-107. 36. Cook CDK. 1996. SPB Academic Publishing, Amsterdam, Netherlands. 37. Malcomber ST, Kellogg EA. 2006. New Phytologist 170: 885-899. 38. Whipple CJ, Zanis MJ, Kellogg EA, Schmidt RJ. 2007. Proceedings of the National Academy of Sciences, USA 104: 1081–1086.
Originality and Innovative nature of the project, and relationship to the ‘state of the art’ of research in the field
To date, inferring the phylogeny of genes and their functions is based on model-derived organisms such as Arabidopsis, which often do not allow us to fully distinguish gene copies inherited in different plants through speciation events (“orthologs”) from gene copies derived from genome duplication events (“paralogs”). ORIGIN’s main innovative aspect is the prediction of gene function using an early model plant (Trithuria) that evolved before the origin of current model angiosperms. ORIGIN will be a pioneering project, uncovering the most ancient patterns of gene and species diversification in angiosperm phylogeny. The use of an early flowering-plant lineage facilitates our ability to distinguish which gene copies are orthologs versus paralogs in other model plants by using tree reconciliation methods that consider (or co-predict) species phylogeny. Hence, information from a phylogenetic split that slightly predates other model plants (Hydatellaceae) will help to correctly orient this angiosperm-wide prediction process.
Another original aspect of ORIGIN is the use of large-scale multi-gene phylogenies in order to assess the origin of flowering plants, the plant group on which human civilization depends. Unrooted chloroplast trees are often used to summarize gene relationships in studies of Arabidopsis, grasses (e.g., Brachypodium-wheat-rice) and similar model plants, defining rough clusters of functionally related genes. ORIGIN will predict and use rooted gene phylogenies of single-copy vs. multigene family loci, facilitating more accurate prediction of gene function, providing an arrow of time for subsequent functional predications, by indicating which diversifications happened first. Furthermore, ORIGIN is also innovative in its multidisciplinary approach by using a combination of bioinformatic/genomic/evolutionary methods to solve the origin of flowering plants and one of its first evolutionary radiations (water lilies and relatives), considered some of the most important questions in plant evolution.
In summary, ORIGIN will contribute to the advancement of the current state of the art in the following topics:
- Definition of species limits in submersa (Goal 1), which will supply a key piece of information for the future development of this species as a model plant system. It will also have significance for developing future management strategies for conserving members of this family in the wild.
- Accurate rooting of flowering-plant phylogeny (Goal 2), which will facilitate attempts to reconstruct early evolutionary transitions and the origin of new adaptations in plants.
- New inferences on the timing of the first splits in angiosperm evolution (Goal 1 and 2) are relevant to other phylogenetic and biogeographical plant studies like those using molecular dating methods.
- Contribution to the detection of which genes predate vs. postdate the origin of monocot and eudicot plants (Goal 3) is a crucial aspect for the European and global economy since these two groups include almost all of the crop plants that we rely on for our food and other natural resources.