Circular DNA is ubiquitous in nature in the form of plasmids, circular DNA viruses, and extrachromosomal circular DNA (eccDNA) in eukaryotes. Sequencing of such molecules is essential to profiling virus distributions, discovering new viruses and understanding the roles of eccDNAs in eukaryotic cells. Circular DNA enrichment sequencing (CIDER-Seq) is a technique to enrich and accurately sequence circular DNA without the need for polymerase chain reaction amplification, cloning, and computational sequence assembly. The approach is based on randomly primed circular DNA amplification, which is followed by several enzymatic DNA repair steps and then by long-read sequencing. CIDER-Seq includes a custom data analysis package (CIDER-Seq Data Analysis Software 2) that implements the DeConcat algorithm to deconcatenate the long sequencing products of random circular DNA amplification into the intact sequences of the input circular DNA. The CIDER-Seq data analysis package can generate full-length annotated virus genomes, as well as circular DNA sequences of novel viruses. Applications of CIDER-Seq also include profiling of eccDNA molecules such as transposable elements (TEs) from biological samples. The method takes ~2 weeks to complete, depending on the computational resources available. Owing to the present constraints of long-read single-molecule sequencing, the accuracy of circular virus and eccDNA sequences generated by the CIDER-Seq method scales with sequence length, and the greatest accuracy is obtained for molecules <10 kb long.

中文翻译：

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使用 CIDER-Seq 对环状 DNA 病毒和染色体外环状 DNA 进行全长测序。

环状 DNA 在自然界中以质粒、环状 DNA 病毒和染色体外环状 DNA (eccDNA) 的形式在真核生物中普遍存在。对这些分子进行测序对于分析病毒分布、发现新病毒和了解 eccDNA 在真核细胞中的作用至关重要。环状 DNA 富集测序 (CIDER-Seq) 是一种无需聚合酶链式反应扩增、克隆和计算序列组装即可富集和准确测序环状 DNA 的技术。该方法基于随机引发的环状 DNA 扩增，随后是几个酶促 DNA 修复步骤，然后是长读长测序。CIDER-Seq 包括一个自定义数据分析包（CIDER-Seq 数据分析软件 2），它实施 DeConcat 算法，将随机环状 DNA 扩增的长测序产物分离成输入环状 DNA 的完整序列。CIDER-Seq 数据分析包可以生成带注释的全长病毒基因组，以及新型病毒的环状 DNA 序列。CIDER-Seq 的应用还包括分析 eccDNA 分子，例如来自生物样品的转座因子 (TE)。该方法需要大约 2 周才能完成，具体取决于可用的计算资源。由于目前长读长单分子测序的限制，由 CIDER-Seq 方法生成的环状病毒和 eccDNA 序列的准确性与序列长度成比例，