Generating high quality reference genomes from field collected specimens by optimizing preservation

Sample preservation challenges efforts to generate high-quality reference genomes or pangenomes for all 2 million+ plant and animal species. Here we compare the impacts of storage methods including solutions, temperature, and time on DNA quality and long-read sequencing quality in 10 fish and 4 plant species. We show 95 percent ethanol protects against sample degradation for fish blood (22 C, less than or equal to 6 weeks) and plant tissue (4 C, less than or equal to 3 weeks). Using Nanopore, we assemble high quality reference genomes from three fish and two plant species (contig N50: 6.5-13.8Mb; BUSCO completeness: 94.4-99.2 percent; QV: 43.8 for M. esculenta).

样本保存问题，为构建覆盖全球200余万种动植物的高质量参考基因组或泛基因组的工作带来了挑战。本研究针对10种鱼类与4种植物物种，对比了保存液类型、保存温度及保存时长对DNA质量与长读长测序质量的影响。研究结果表明，95%乙醇可有效抑制鱼类血液（22℃，保存时长≤6周）与植物组织（4℃，保存时长≤3周）的样本降解。借助纳米孔（Nanopore）测序技术，本研究从3种鱼类与2种植物物种中组装得到高质量参考基因组，其组装指标如下：重叠群N50为6.5~13.8Mb；BUSCO完整度为94.4%~99.2%；木薯（M. esculenta）的QV值为43.8。