Supporting data for "Fully resolved assembly of <i>Cryptosporidium parvum</i>"

<i>Cryptosporidium parvum</i> is an apicomplexan parasite commonly found across many species with a global infection prevalence of 7.6%. As such, it is important to understand the diversity and genomic makeup of this prevalent parasite to prohibit further spread and to fight infection. The general basis of every genomic study is a high quality reference genome that has continuity and completeness and is of high quality, thus enabling comprehensive comparative studies. <br>Here, we provide a highly accurate and complete reference genome of <i>Cryptosporidium parvum</i>. The assembly is based on Oxford Nanopore reads and was improved using Illumina reads for error correction. We also outlined how to evaluate and choose from different assembly methods based on two main approaches that can be applied to other <i>Cryptosporidium</i> species. The assembly encompasses 8 chromosomes and includes 13 telomeres that were resolved. Overall, the assembly shows a high completion rate with 98.4% single copy BUSCO genes. The consensus accuracy of the established reference genome was further validated by sequence alignment of established genetic markers for <i>C. parvum. </i> <br>This high quality reference genome of a zoonotic IIaA17G2R1 <i>C. parvum</i> subtype isolate provides the basis for subsequent studies and comparative genomic studies across the <i>Cryptosporidium</i> clade. Thus will enable improved understanding of diversity, functional and thus association studies.

微小隐孢子虫（Cryptosporidium parvum）是一种顶复门寄生虫（apicomplexan parasite），广泛寄生于多种宿主物种，全球感染流行率达7.6%。鉴于其高流行特征，解析该寄生虫的多样性与基因组构成，对于遏制其进一步传播、对抗感染具有重要意义。所有基因组学研究的核心基础，均为具备连续性、完整性与高质量的参考基因组，唯有如此方可开展全面的比较基因组学研究。

本研究针对微小隐孢子虫（Cryptosporidium parvum）提供了一套高精度且完整的参考基因组。该基因组组装基于牛津纳米孔（Oxford Nanopore）测序读段，并通过因美纳（Illumina）测序读段进行错误校正以优化组装效果。本研究还基于两种可推广至其他隐孢子虫（Cryptosporidium）物种的核心策略，阐述了如何评估并筛选不同的基因组组装方法。此次组装覆盖了8条染色体，并成功解析出13个端粒（telomeres）。整体而言，该组装的完整度极高，单拷贝BUSCO基因占比达98.4%。针对该已构建参考基因组的序列一致性准确度，本研究通过比对微小隐孢子虫已报道的遗传标记序列，进一步验证了其准确性。

本研究针对一株人畜共患的IIaA17G2R1亚型微小隐孢子虫分离株构建了该高质量参考基因组，可为后续研究以及隐孢子虫属（Cryptosporidium）演化支（clade）内的比较基因组学研究提供核心支撑。进而助力研究者更深入地理解该寄生虫的多样性与功能机制，并推动相关关联研究的开展。