The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA, 92037, USA.
Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA, 92093, USA.
Commun Biol. 2023 Dec 9;6(1):1246. doi: 10.1038/s42003-023-05615-2.
Sample preservation often impedes efforts to generate high-quality reference genomes or pangenomes for Earth's more than 2 million plant and animal species due to nucleotide degradation. Here we compare the impacts of storage methods including solution type, temperature, and time on DNA quality and Oxford Nanopore long-read sequencing quality in 9 fish and 4 plant species. We show 95% ethanol largely protects against degradation for fish blood (22 °C, ≤6 weeks) and plant tissue (4 °C, ≤3 weeks). From this furthest storage timepoint, we assemble high-quality reference genomes of 3 fish and 2 plant species with contiguity (contig N50) and completeness (BUSCO) that achieve the Vertebrate Genome Project benchmarking standards. For epigenetic applications, we also report methylation frequency compared to liquid nitrogen control. The results presented here remove the necessity for cryogenic storage in many long read applications and provide a framework for future studies focused on sampling in remote locations, which may represent a large portion of the future sequencing of novel organisms.
由于核苷酸降解，样本保存常常会阻碍为地球上 200 多万种动植物生成高质量参考基因组或泛基因组的工作。在这里，我们比较了包括溶液类型、温度和时间在内的存储方法对 9 种鱼类和 4 种植物的 DNA 质量和 Oxford Nanopore 长读测序质量的影响。我们发现 95%乙醇在 22°C 下可使鱼类血液（≤6 周）和植物组织（4°C，≤3 周）的样本得到最大程度的保护，防止其降解。从最远的存储时间点开始，我们可以组装出 3 种鱼类和 2 种植物的高质量参考基因组，这些基因组的连续性（contig N50）和完整性（BUSCO）达到了脊椎动物基因组计划的基准标准。对于表观遗传学应用，我们还报告了与液氮对照相比的甲基化频率。本研究结果在许多长读测序应用中消除了低温储存的必要性，并为未来的研究提供了一个框架，这些研究将侧重于在偏远地区进行采样，这可能代表了未来对新型生物进行测序的大部分工作。
