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Updated: Apr 25, 2026
06:40
G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
Published on: March 22, 2018
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Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes
Mari Miyamoto, Daisuke Motooka, Kazuyoshi Gotoh
1Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan. nshota@gen-info.osaka-u.ac.jp.
BMC Genomics
|August 22, 2014
Summary
Pacific Biosciences RS sequencer (PacBio) achieved a finished-grade genome assembly for Vibrio parahaemolyticus, outperforming other sequencing technologies with its long reads. This demonstrates PacBio
Area of Science:
- Genomics
- Bioinformatics
- Microbial sequencing
Background:
- Diverse second- and third-generation sequencing technologies are available for bacterial genome determination.
- Choosing the optimal technology for finished genomes with multiple chromosomes remains challenging.
Purpose of the Study:
- To evaluate Roche 454 GS Junior (GS Jr), Life Technologies Ion PGM (Ion PGM), Illumina MiSeq (MiSeq), and Pacific Biosciences RS sequencer (PacBio) for bacterial genome sequencing and assembly.
- To determine the most suitable sequencing technology for producing a finished genome with multiple chromosomes.
Main Methods:
- Sequencing of Vibrio parahaemolyticus (5-Mb, two chromosomes) using GS Jr, Ion PGM, MiSeq, and PacBio.
- De novo assembly of sequencing data using various genome assemblers.
Main Results:
- Second-generation sequencers (GS Jr, Ion PGM, MiSeq) produced fragmented assemblies with shorter contigs.
- PacBio generated exceptionally long contigs (3,288,561 bp and 1,875,537 bp) with high accuracy, enabling complete rRNA operon positioning.
- PacBio achieved a "finished grade" assembly, outperforming others in contig length and genome reconstruction.
Conclusions:
- PacBio's long-read sequencing is superior for assembling complex bacterial genomes with multiple chromosomes.
- The technology demonstrates potential for assembling genomes with repetitive sequences.
- PacBio enables high-quality genome assemblies essential for comprehensive genomic analysis.
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