Abstract
We sequenced the Paenibacillus sp. R4 using Oxford Nanopore Technology (ONT), single molecule real-time (SMRT) technology from Pacific Biosciences (PacBio), and Illumina technologies to investigate the application of nanopore reads in de novo sequencing of bacterial genomes. We compared the differences in both genome sequences between genome assemblies using nanopore and PacBio reads and focused on the difference in the prediction of coding sequences. The results indicated that for more accurate predictions of open reading frames, contigs in the assemblies using only PacBio reads also needed to be corrected using short reads with high-quality bases, and repeat regions in genomes did not affect the increase of mispredicted coding sequences via genome polishing significantly. In assemblies using only nanopore reads, genome polishing was essential, but many repeat regions in genomes might increase the number of mispredicted coding sequences via genome polishing. The hybrid assembly combining the long reads and short reads represents the best result for coding sequence predictions in genome assemblies using nanopore reads.
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Availability of data and material
The raw data have been deposited at the National Center for Biotechnology Information (NCBI) BioProject repository PRJNA564035 (SRX6807868-SRX6807870). This strain is available from the Polar and Alpine Microbial Collection (PAMC) of Korea Polar Research Institute with the accession number PAMC 29622.
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Funding
This research was supported by a National Research Foundation of Korea Grant from the Korean Government (MSIT; the Ministry of Science and ICT) (NRF-2017M1A5A1013568) (KOPRI-PN20082) (Title: application study on the Arctic cold-active enzyme degrading organic carbon compounds).
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Conceptualization: HWK, JHL, SCS; methodology: HJK, SCS; software: SCS; formal analysis: WC, SCS; investigation: WC; resources: SCS; data curation: SCS; writing—original draft preparation: All authors; writing—review and editing: All authors; visualization: SCS, HWK; supervision: SCS, HWK; project administration: SCS, HWK; funding: HWK.
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Shin, S.C., Choi, W., Lee, J. et al. Evaluation of assembly methods combining long-reads and short-reads to obtain Paenibacillus sp. R4 high-quality complete genome. 3 Biotech 10, 480 (2020). https://doi.org/10.1007/s13205-020-02474-0
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DOI: https://doi.org/10.1007/s13205-020-02474-0