AI Article Synopsis
- Strategies for sequencing fungal genomes depend on genome characteristics, DNA quality, and cost.
- Illumina's sequencing by synthesis (SBS) offers fast, cost-effective short reads (~300 bp) but struggles with repetitive areas, while PacBio's single molecule, real-time (SMRT) sequencing provides longer reads (~12,500 bp) that help with complex genomes, albeit at a higher cost.
- Illumina can work with lower quality DNA, whereas PacBio needs intact, long DNA fragments for optimal data quality.
Article Abstract
Strategies for sequencing fungal genomes on next-generation sequencing (NGS) platforms depend on the characteristics of the genome of the targeted species, quantity and quality of the genomic DNA, and cost considerations. Massively parallel sequencing with sequencing by synthesis (SBS) approach by Illumina produces terabases of short read sequences (i.e., ~300 bp) in a time and cost-effective manner, though the read length can limit the assembly particularly in repetitive regions. The single molecule, real-time (SMRT) sequencing approach by Pacific Biosciences (PacBio) produces longer reads (i.e., ~12,500 bp) which can facilitate de novo assembly of genomes that contain long repetitive sequences, though due to the lower-throughput of this platform achieving the coverage needed for assembly is more expensive than by SBS. Additionally, the Illumina SBS platforms can handle low quantity/quality of genomic DNA materials, while the SMRT system requires undamaged long DNA fragments as input to ensure that high-quality data is produced. Both platforms are discussed in this chapter including key decision-making points.
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| http://dx.doi.org/10.1007/978-1-4939-7804-5_4 | DOI Listing |
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