Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

GENOME SEQUENCING

Size does matter

Nature Plants volume 4, pages 859–860 (2018)Cite this article

Subjects

Chromosome-scale assemblies are quickly becoming the standard for high-quality de novo reference plant genomes. Combining nanopore technology sequencing and optical map information is one way to achieve this.

Almost two decades after the first plant genome, Arabidopsis thaliana, was sequenced and published1, more than 100 complete genome sequences of different plant species have been described, with many more on the way. Notwithstanding this number, the announcement of yet another new plant genome sequence usually still sparks quite an interest; whole genome information often provides novel insights into important aspects of plant biology such as development, metabolism, evolution and adaptation. Furthermore, full genome sequences generally serve a wide community of plant biologists and bioinformaticians. However, not all genome sequences that are published and available to the community are considered to be of equal quality. The ‘quality of a genome’ is repeatedly measured in function of the number of fragments (contigs or scaffolds) the genome consists of. While in this respect the first Arabidopsis genome sequence proved excellent — it was sequenced using the so-called bacterial artificial chromosome (BAC) technique, still the gold standard for sequencing — the investments in labour and costs were huge. This all changed with so-called next-generation sequencing techniques, where massive numbers of short reads of DNA can be generated quickly and at low cost. The downside though is that genome assembly proved to be notoriously difficult, in particular for larger and complex plant genomes. In general, there are a number of factors that affect the contiguity of genome assembly, such as (high levels of) heterozygosity, repetitive sequences and duplicated regions, and plant genomes often suffer from all of these. Algorithms used for assembling short reads, such as de Bruijn2 or string graphs3, have a hard time dealing with highly polymorphic or repeat regions. Allelic sequences in highly heterozygous species are often considered as independent sequences, while repeat regions are collapsed. Luckily, we have now entered the era of next-next, or third generation, sequencing that allows the generation of longer reads and thus higher quality (in terms of less fragmented) genomes. Long-read sequencing removes many of the problems just mentioned and long reads can span entire repeat-containing regions, reconstruct haplotypes (also known as phasing) and resolve structural rearrangements. Ideally, long-read sequencing should lead to chromosome-scale ‘reference’ genomes but, as described by Belser et al.4 in this issue of Nature Plants, long-read sequencing alone will not (yet) do the job.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Get just this article for as long as you need it

$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

References

  1. Arabidopsis Genome Initiative. Nature 408, 796–815 (2000).

    Article  Google Scholar 

  2. Pevzner, P. A., Tang, H. & Waterman, M. S. Proc. Natl Acad. Sci. USA 98, 9748–9753 (2001).

    Article  CAS  Google Scholar 

  3. Myers, E. W. Bioinformatics 21, 79–85 (2005).

    Google Scholar 

  4. Belser et al. Nat. Plants. https://doi.org/10.1038/s41477-018-0289-4 (2018).

    Article  Google Scholar 

  5. Zhang, G. Q. et al. Nature 549, 379–383 (2017).

    Article  CAS  Google Scholar 

  6. Cai, J. et al. Nat. Genet. 47, 65–72 (2015).

    Article  CAS  Google Scholar 

  7. Michael, T. P. et al. Nat. Commun. 9, 541 (2018).

    Article  Google Scholar 

  8. Teh, B. T. et al. Nat. Genet. 49, 1633–1641 (2017).

    Article  CAS  Google Scholar 

  9. Jarvis, D. E. et al. Nature 542, 307–312 (2017).

    Article  CAS  Google Scholar 

  10. Burton, J. N. et al. Nat. Biotechnol. 31, 1119–1125 (2013).

    Article  CAS  Google Scholar 

  11. Dudchenko, O. et al. Science 356, 92–95 (2017).

    Article  CAS  Google Scholar 

  12. Lieberman-Aiden, E. et al. Science 326, 289–293 (2009).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium

    Yves Van de Peer

  2. Center for Plant Systems Biology, VIB, Ghent, Belgium

    Yves Van de Peer

  3. Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa

    Yves Van de Peer

Authors
  1. Yves Van de Peer
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yves Van de Peer.

Ethics declarations

Competing interests

The author declares no competing interests.

Rights and permissions

Reprints and Permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Van de Peer, Y. Size does matter. Nature Plants 4, 859–860 (2018). https://doi.org/10.1038/s41477-018-0293-8

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41477-018-0293-8

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research