The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisjunction during spermatogenesis, paternal X elimination during embryogenesis, intrachromosomal DNA amplification of DNA puff loci during larval development, and germline-limited chromosome elimination from all somatic cells. Paternal chromosome elimination in Sciara was the first observation of imprinting, though the mechanism remains a mystery. Here, we present the first draft genome sequence for Sciara coprophila to take a large step forward in addressing these features. We assembled the Sciara genome using PacBio, Nanopore, and Illumina sequencing. To find an optimal assembly using these datasets, we generated 44 short-read and 50 long-read assemblies. We ranked assemblies using 27 metrics assessing contiguity, gene content, and dataset concordance. The highest-ranking assemblies were scaffolded using BioNano optical maps. RNA-seq datasets from multiple life stages and both sexes facilitated genome annotation. A set of 66 metrics was used to select the first draft assembly for Sciara. Nearly half of the Sciara genome sequence was anchored into chromosomes, and all scaffolds were classified as X-linked or autosomal by coverage. We determined that X-linked genes in Sciara males undergo dosage compensation. An entire bacterial genome from the Rickettsia genus, a group known to be endosymbionts in insects, was co-assembled with the Sciara genome, opening the possibility that Rickettsia may function in sex determination in Sciara. Finally, the signal level of the PacBio and Nanopore data support the presence of cytosine and adenine modifications in the Sciara genome, consistent with a possible role in imprinting.

中文翻译：

---

使用单分子测序对真菌蝇 Sciara coprophila 进行高连续性基因组从头组装和 DNA 修饰分析


低等双翅目真菌蝇 Sciara coprophila 具有许多独特的生物学特征，挑战着基因组 DNA 恒定性的规则。例如，Sciara 在精子发生过程中经历父本染色体消除和母本 X 染色体不分离，在胚胎发生过程中经历父本 X 染色体消除，在幼虫发育过程中经历 DNA 泡状基因座的染色体内 DNA 扩增，以及所有体细胞中种系限制的染色体消除。夏拉的父系染色体消除是首次观察到印记，尽管其机制仍然是个谜。在这里，我们提出了 Sciara coprophila 的第一份基因组序列草案，在解决这些特征方面向前迈出了一大步。我们使用 PacBio、Nanopore 和 Illumina 测序组装了 Sciara 基因组。为了使用这些数据集找到最佳组装，我们生成了 44 个短读组装和 50 个长读组装。我们使用 27 个评估连续性、基因内容和数据集一致性的指标对程序集进行排名。排名最高的组件是使用 BioNano 光学图搭建的。来自多个生命阶段和两性的 RNA-seq 数据集促进了基因组注释。 Sciara 使用了一组 66 个指标来选择第一个程序集草案。 Sciara 基因组序列的近一半被锚定到染色体上，所有支架根据覆盖范围被分类为 X 连锁或常染色体。我们确定 Sciara 雄性中的 X 连锁基因经历了剂量补偿。立克次体属（已知是昆虫内共生体）的完整细菌基因组与 Sciara 基因组共同组装，开启了立克次体可能在 Sciara 性别决定中发挥作用的可能性。 最后，PacBio 和 Nanopore 数据的信号水平支持 Sciara 基因组中存在胞嘧啶和腺嘌呤修饰，这与印记中可能的作用一致。