Herzog Kaylee S, Wu Rachel, Hawdon John M, Nejsum Peter, Fauver Joseph R
Department of Epidemiology, University of Nebraska Medical Center, Omaha, NE 68198, USA.
Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington, DC 20037, USA.
iScience. 2024 Jul 30;27(9):110614. doi: 10.1016/j.isci.2024.110614. eCollection 2024 Sep 20.
In this study, we assessed the quality of genome assemblies for three species of parasitic nematodes (, , and ) generated using only Oxford Nanopore Technologies MinION data. Assemblies were compared to current reference genomes and against additional assemblies that were supplemented with short-read Illumina data through polishing or hybrid assembly approaches. For each species, assemblies generated using only MinION data had similar or superior measures of contiguity, completeness, and gene content. In terms of gene composition, depending on the species, between 88.9 and 97.6% of complete coding sequences predicted in MinION data only assemblies were identical to those predicted in assemblies polished with Illumina data. Polishing MinION data only assemblies with Illumina data therefore improved gene-level accuracy to a degree. Furthermore, modified DNA extraction and library preparation protocols produced sufficient genomic DNA from and to generate assemblies from individual specimens.
在本研究中，我们评估了仅使用牛津纳米孔技术MinION数据生成的三种寄生线虫（、和）的基因组组装质量。将这些组装结果与当前的参考基因组以及通过抛光或混合组装方法补充了短读长Illumina数据的其他组装结果进行了比较。对于每个物种，仅使用MinION数据生成的组装在连续性、完整性和基因含量方面具有相似或更优的指标。在基因组成方面，根据物种不同，仅在MinION数据组装中预测的完整编码序列中有88.9%至97.6%与用Illumina数据抛光的组装中预测的序列相同。因此，仅用Illumina数据对MinION数据组装进行抛光在一定程度上提高了基因水平的准确性。此外，改进的DNA提取和文库制备方案从和中产生了足够的基因组DNA，以从单个标本中生成组装。
