Snake's head fritillary at Kew Gardens
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Uncovering the genomic diversity of plants

To understand how plants have diversified, the underlying mechanisms that promote genomic-level changes and the evolutionary and ecological consequences of this over time.

Project details

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Objectives and outputs

The immense diversity of genomes in eukaryotes has long fascinated scientists, who have tried to understand how such diversity evolved as well as its biological significance. From this standpoint, land plants are remarkably diverse. However, despite our realisation of the substantial implications of this genomic diversity for the biology of the plants, little is known about the underlying mechanisms that promote changes at the genomic levels and the evolutionary and ecological consequences over time.

Background

Plants are remarkable in the diverse ways in which they organise, accumulate and express the DNA comprising their genomes. This diversity is seen at many levels including:

  • the DNA sequence
  • how the DNA is expressed (including epigenetic regulation)
  • the number, size and organisation of chromosomes (range 2n = 4 – c. 1440)
  • the number and origin of genomes (ploidy level; range 2x – 96x)
  • the amount of DNA within the nucleus (genome size, range 1C = 63 – 148 ,000 Mbp).

Overall aim

This project aims to document and understand the origin, consequence and evolutionary significance of this striking genome diversity across land plants, and its impact in determining how, where and when a plant lives and responds to environmental change.

A particular research focus of the project is genome size diversity, which varies more than 2,400-fold across plants.The largest genome so far reported for any organism is that of the Japanese canopy plant (Paris japonica; Melanthiaceae); its genome size is about 50 times larger than the human genome, and if its DNA was unravelled, would extend over 100 m. In contrast, the smallest plant genome size is found in a tiny carnivorous plant called Genlisea aurea. Its genome is 1/50th the size of our own and its DNA would extend just 2 cm!

Ongoing Kew projects in the field of plant genome size research

  • Extending knowledge of genome size diversity using flow cytometry to generate new data (currently data are available for just 2% of land plants).
  • Collating new data into the Plant DNA C-Values Database. This database is maintained by Kew to provide a one-stop, user friendly database where plant genome sizes can be readily accessed and compared.
  • Investigating the origin and evolution of genome size diversity in key land plant groups using the latest phylogenetic data available. Recent projects have focused on Nymphaeaceae (one of the first angiosperm families to appear in the fossil record); Melanthiaceae (the angiosperm family with the largest range of genome sizes so far encountered, including the largest genome size); Fritillaria (genus with the largest range of genome sizes in terms of absolute amounts of DNA, and the largest diploid genomes of any plant); and ferns.
  • Probing the types and regulation of DNA sequences which make up genomes of different sizes. Of particular interest are species with giant genomes (including Fritillaria and Paris) to understand how and why such obese genomes evolve.
  • Exploring the consequences of genome size diversity at the ecological level and how this interacts and shapes plant community composition, and ecosystem dynamics and resilience.

Objectives

  • To gain greater insight into the principles, processes and phenomena operating at different genomic levels which contribute to the evolution and persistence of plant biodiversity.
  • To uncover the full extent of genome size and chromosome diversity across different groups of land plants.
  • To understand the role that genomic diversity plays in contributing to a species’ resilience in the face of environmental change.

Outputs

  • Update of the Plant DNA C-values database (release 7.0).
  • Discovery: largest genome size discovered for any plant (Paris japonica), and possibly any eukaryote (Pellicer et al. 2010).
  • Largest survey to date on genome size diversity and evolution in ferns published (Clark, Hidalgo et al. 2016).
  • First insights into the DNA sequences comprising the giant genomes of angiosperms published, using Fritillaria as a model group (Kelly et al. 2016).

Partners and collaborators

International

UK

Further information

Publications

Garcia, S., Leitch, I. J., Anadon-Rosell, A., Canela, M. Á., Gálvez, F., Garnatje, T., Gras, A., Hidalgo, O., Johnston, E., Mas de Xaxars, G., Pellicer, J., Siljak-Yakovlev, S., Vallès, J., Vitales, D. & Bennett, M. D. (2014). Recent updates and developments to plant genome size databases. Nucleic Acids Research 42: D1159-D1166.

Clark, J., Hidalgo, O., Pellicer, J., Liu, H., Marquardt, J., Robert, Y., Christenhusz, M., Zhang, S., Gibby, M., Leitch, I. J. & Schneider, H. (2016). Genome evolution of ferns: evidence for relative stasis of genome size across the fern phylogeny. New Phytologist: DOI: 10.1111/nph.13833.

Pellicer, J., Kelly, L. J., Leitch, I. J., Zomlefer, W. B. & Fay, M. F. (2014). A universe of dwarfs and giants: genome size and chromosome evolution in the monocot family Melanthiaceae. New Phytologist 201: 1484-1497.

Kelly, L. J., Renny-Byfield, S., Pellicer, J., Macas, J., Novák, P., Neumann, P., Lysak, M. A., Day, P. D., Berger, M., Fay, M. F., Nichols, R. A., Leitch, A. R. & Leitch, I, J. (2015). Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size. New Phytologist 208: 596-607.

Ma, L., Hatlen, A., Kelly, L. J., Becher, H., Wang, W., Kovarik, A., Leitch, I. J. & Leitch, A. R. (2015). Angiosperms are unique among land plant lineages in the occurrence of key genes in the RNA-Directed DNA Methylation (RdDM) pathway. Genome Biology and Evolution 7: 2648-2662.