A critical comparison of technologies for a plant genome sequencing project

Paajanen, Pirita, Kettleborough, George, López-Girona, Elena, Giolai, Michael, Heavens, Darren, Baker, David, Lister, Ashleigh, Cugliandolo, Fiorella, Wilde, Gail, Hein, Ingo, MacAulay, Iain, Bryan, Glenn J. and Clark, Matthew D. (2019) A critical comparison of technologies for a plant genome sequencing project. GigaScience, 8 (3). ISSN 2047-217X

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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.

Item Type: Article
Additional Information: Funding Information: This work was funded with BBSRC project grants (BB/K019325/1) and (BB/K019090/1). This work was strategically funded by the BBSRC, Core Strategic Programme Grant (BB/CSP17270/1) at the Earlham Institute. High-throughput sequencing and library construction was delivered via the BBSRC National Capability in Genomics (BB/CCG1720/1) at the Earlham Institute (EI, formerly The Genome Analysis Centre, Norwich), by members of the Platforms and Pipelines Group. This research was supported in part by the NBI Computing infrastructure for Science (CiS) group through the HPC cluster and UV systems. We thank Duke University for providing sequencing costs via Dugsim (https://dugs im.net/). Publisher Copyright: © 2019 The Author(s). Published by Oxford University Press.
Uncontrolled Keywords: 10x genomics,assembly,long reads,optical mapping,pacbio,pacific biosciences,short reads,health informatics,computer science applications ,/dk/atira/pure/subjectarea/asjc/2700/2718
Faculty \ School:
Faculty of Science > School of Biological Sciences
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 01 Nov 2022 16:30
Last Modified: 17 Nov 2022 14:30
URI: https://ueaeprints.uea.ac.uk/id/eprint/89489
DOI: 10.1093/gigascience/giy163

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