De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms

Area of Science:

• Genomics and Bioinformatics
• Molecular Biology
• Next-Generation Sequencing (NGS)

Background:

• Long-read sequencing platforms, including Pacific Biosciences (PacBio) and Oxford Nanopore MinION, generate reads exceeding 10,000 base pairs.
• These long reads significantly improve genome assembly contiguity and completeness compared to short-read technologies.
• PacBio has demonstrated success across various genome sizes, while MinION gains attention for its portability and cost-effectiveness.

Purpose of the Study:

• To comprehensively compare genome assembly metrics from PacBio, MinION, and Illumina MiSeq platforms.
• To evaluate the impact of platform-specific data characteristics on assembly quality.
• To assess the performance of long-read technologies in assembling nuclear and mitochondrial genomes.

Main Methods:

• Re-sequencing of the Saccharomyces cerevisiae S288C strain using PacBio, MinION, and Illumina MiSeq platforms.
• Generation of genome assemblies using various bioinformatics pipelines.
• Comprehensive metric-based comparison of the resulting assemblies.

Main Results:

• Assemblies from both PacBio and MinION (at 31X read depth) demonstrated excellent continuity and completeness for the 16 nuclear chromosomes.
• Short-read sequencing (MiSeq) was not explicitly detailed but implied as a comparison point.
• Reconstruction of the mitochondrial genome proved challenging across all tested platforms, highlighting persistent difficulties in assembling highly variable or repetitive regions.

Conclusions:

• Long-read sequencing technologies (PacBio and MinION) provide high-quality genome assemblies for nuclear chromosomes.
• The choice of sequencing platform and associated data characteristics significantly influence assembly outcomes.
• Mitochondrial genome assembly remains a significant challenge, even with advanced long-read sequencing capabilities.