Comparison of long read sequencing technologies in interrogating bacteria and fly genomes
Author
Tvedte, Eric SGasser, Mark
Sparklin, Benjamin C
Michalski, Jane
Hjelmen, Carl E
Johnston, J Spencer
Zhao, Xuechu
Bromley, Robin
Tallon, Luke J
Sadzewicz, Lisa
Rasko, David A
Dunning Hotopp, Julie C
Date
2021-04-19Journal
G3: Genes, Genomes, GeneticsPublisher
Oxford University PressType
Article
Metadata
Show full item recordAbstract
The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined. © The Author(s) 2021.Rights/Terms
© The Author(s) (2021). Published by Oxford University Press on the Genetics Society of America.Identifier to cite or link to this item
http://hdl.handle.net/10713/16343ae974a485f413a2113503eed53cd6c53
10.1093/g3journal/jkab083
Scopus Count
Collections
Related articles
- Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore.
- Authors: Lang D, Zhang S, Ren P, Liang F, Sun Z, Meng G, Tan Y, Li X, Lai Q, Han L, Wang D, Hu F, Wang W, Liu S
- Issue date: 2020 Dec 15
- Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes.
- Authors: De Maio N, Shaw LP, Hubbard A, George S, Sanderson ND, Swann J, Wick R, AbuOun M, Stubberfield E, Hoosdally SJ, Crook DW, Peto TEA, Sheppard AE, Bailey MJ, Read DS, Anjum MF, Walker AS, Stoesser N, On Behalf Of The Rehab Consortium
- Issue date: 2019 Sep
- Completion of draft bacterial genomes by long-read sequencing of synthetic genomic pools.
- Authors: Derakhshani H, Bernier SP, Marko VA, Surette MG
- Issue date: 2020 Jul 29
- Comparison of long-read methods for sequencing and assembly of a plant genome.
- Authors: Murigneux V, Rai SK, Furtado A, Bruxner TJC, Tian W, Harliwong I, Wei H, Yang B, Ye Q, Anderson E, Mao Q, Drmanac R, Wang O, Peters BA, Xu M, Wu P, Topp B, Coin LJM, Henry RJ
- Issue date: 2020 Dec 21
- Comparison of De Novo Assembly Strategies for Bacterial Genomes.
- Authors: Zhang P, Jiang D, Wang Y, Yao X, Luo Y, Yang Z
- Issue date: 2021 Jul 17