Generating high-quality plant and fish reference genomes from field-collected specimens by optimizing preservation.

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• DNA degradation during sample preservation hinders high-quality reference genome and pangenome generation for diverse species.
• Current methods often require cryogenic storage, limiting accessibility for fieldwork and large-scale biodiversity studies.

Purpose of the Study:

• To evaluate the impact of different storage solutions, temperatures, and durations on DNA quality and long-read sequencing performance.
• To identify optimal, non-cryogenic preservation methods for generating high-quality genomes from various plant and animal species.

Main Methods:

• Tested DNA preservation methods using 9 fish and 4 plant species.
• Assessed DNA quality and Oxford Nanopore long-read sequencing output after storage in 95% ethanol at different temperatures and time points.
• Assembled reference genomes and evaluated their contiguity (contig N50) and completeness (BUSCO scores).
• Compared DNA methylation frequencies to assess suitability for epigenetic analyses.

Main Results:

• 95% ethanol demonstrated significant protection against DNA degradation in fish blood (stored at 22°C for up to 6 weeks) and plant tissue (stored at 4°C for up to 3 weeks).
• High-quality reference genomes meeting Vertebrate Genome Project standards were assembled from samples stored under these conditions.
• Methylation frequencies were comparable to liquid nitrogen controls, indicating preservation for epigenetic studies.

Conclusions:

• Non-cryogenic storage using 95% ethanol is a viable alternative for preserving DNA quality for long-read sequencing and genome assembly.
• This approach simplifies sample preservation for genomic studies, particularly in remote locations, and broadens the scope for sequencing novel organisms.