A critical comparison of technologies for a plant genome sequencing project

  1. Pirita Paajanen
  2. George Kettleborough
  3. Elena López-Girona
  4. Michael Giolai
  5. Darren Heavens
  6. David Baker
  7. Ashleigh Lister
  8. Fiorella Cugliandolo
  9. Gail Wilde
  10. Ingo Hein
  11. Iain Macaulay
  12. Glenn J Bryan
  13. Matthew D Clark

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Abstract

Background

A high-quality genome sequence of any model organism is an essential starting point for genetic and other studies. Older clone-based methods are slow and expensive, whereas faster, cheaper short-read–only assemblies can be incomplete and highly fragmented, which minimizes their usefulness. The last few years have seen the introduction of many new technologies for genome assembly. These new technologies and associated new algorithms are typically benchmarked on microbial genomes or, if they scale appropriately, on larger (e.g., human) genomes. However, plant genomes can be much more repetitive and larger than the human genome, and plant biochemistry often makes obtaining high-quality DNA that is free from contaminants difficult. Reflecting their challenging nature, we observe that plant genome assembly statistics are typically poorer than for vertebrates.

Results

Here, we compare Illumina short read, Pacific Biosciences long read, 10x Genomics linked reads, Dovetail Hi-C, and BioNano Genomics optical maps, singly and combined, in producing high-quality long-range genome assemblies of the potato species Solanum verrucosum. We benchmark the assemblies for completeness and accuracy, as well as DNA compute requirements and sequencing costs.

Conclusions

The field of genome sequencing and assembly is reaching maturity, and the differences we observe between assemblies are surprisingly small. We expect that our results will be helpful to other genome projects, and that these datasets will be used in benchmarking by assembly algorithm developers.

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  1. GigaScience

    Now published in GigaScience doi: 10.1093/gigascience/giy163

    Pirita Paajanen 1Earlham Institute, Norwich, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteGeorge Kettleborough 1Earlham Institute, Norwich, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for George KettleboroughElena López-Girona 2The James Hutton Institute, Invergowrie, Dundee, UK.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichael Giolai 1Earlham Institute, Norwich, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteDarren Heavens 1Earlham Institute, Norwich, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid Baker 1Earlham Institute, Norwich, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteAshleigh Lister 1Earlham Institute, Norwich, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ashleigh ListerGail Wilde 2The James Hutton Institute, Invergowrie, Dundee, UK.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteIngo Hein 2The James Hutton Institute, Invergowrie, Dundee, UK.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteIain Macaulay 1Earlham Institute, Norwich, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Iain MacaulayGlenn J. Bryan 2The James Hutton Institute, Invergowrie, Dundee, UK.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteMatthew D. Clark 1Earlham Institute, Norwich, UK;Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Matthew D. ClarkFor correspondence: matt.clark@earlham.ac.uk

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy163 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101497 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101498

  2. Version published to 10.1093/gigascience/giy163
  3. Version published to 10.1101/201830v1 on bioRxiv