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Exploring giant plant genomes with next-generation sequencing technology

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Abstract

Genome size in plants is characterised by its extraordinary range. Although it appears that the majority of plants have small genomes, in several lineages genome size has reached giant proportions. The recent advent of next-generation sequencing (NGS) methods has for the first time made detailed analysis of even the largest of plant genomes a possibility. In this review, we highlight investigations that have utilised NGS for the study of plants with large genomes, as well as describing ongoing work that aims to harness the power of these technologies to gain insights into their evolution. In addition, we emphasise some areas of research where the use of NGS has the potential to generate significant advances in our current understanding of how plant genomes evolve. Finally, we discuss some of the future developments in sequencing technology that may further improve our ability to explore the content and evolutionary dynamics of the very largest genomes.

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Abbreviations

ChIP-seq:

Chromatin immunoprecipitation followed by sequencing

IR:

Illegitimate recombination

LINE:

Long interspersed nuclear element

LTR:

Long terminal repeat

Mb:

Mega base pairs of DNA

MITE:

Miniature inverted repeat transposable element

NGS:

Next-generation sequencing

SINE:

Short interspersed nuclear element

siRNA:

Small interfering RNA

SMRT sequencing:

Single molecule real-time sequencing

sRNA:

Small RNA

TE:

Transposable element

TGS:

Third-generation sequencing

TIR:

Terminal inverted repeat

UR:

Unequal homologous recombination

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Acknowledgements

We thank James Tosh and Andrew Leitch for helpful comments on an earlier version of this manuscript, and Andrew Leitch, Richard Nichols, Mike Fay, Simon Renny-Byfield, Jiří Macas, Petr Novák and Pavel Neumann for useful discussion on the analysis of NGS data from plants with very large genomes. We also thank two anonymous reviewers and the editors for helpful comments that allowed us to improve this manuscript. Research into the dynamics of genome evolution in Fritillaria is part of a Natural Environment Research Council (NERC)-funded project (‘Evolutionary Dynamics of Genome Obesity’; grant number NE/G01724/1) to the Royal Botanic Gardens, Kew (UK) and Queen Mary, University of London (UK), and is being conducted in collaboration with the Biology Centre ASCR, Institute of Plant Molecular Biology (Czech Republic); 454 sequencing for this project is supported by the NERC Biomolecular Analysis Facility at the University of Liverpool (UK); plant material for this research has been kindly provided from specimens grown by Laurence Hill, Jeremy Broome, Richard Kernick and Kit Strange.

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  1. Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK

    Laura J. Kelly & Ilia J. Leitch

  2. School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS, London, UK

    Laura J. Kelly

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  1. Laura J. Kelly
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Correspondence to Laura J. Kelly.

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Responsible Editor: H. Macgregor and C. Rieder.

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Kelly, L.J., Leitch, I.J. Exploring giant plant genomes with next-generation sequencing technology. Chromosome Res 19, 939–953 (2011). https://doi.org/10.1007/s10577-011-9246-z

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