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Abstract

<h3>ABSTRACT</h3> The lower Dipteran fungus fly, <i>Sciara coprophila</i>, has many unique biological features. For example, <i>Sciara</i> 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 <i>Sciara</i> was the first observation of imprinting, though the mechanism remains a mystery. Here, we present the first draft genome sequence for <i>Sciara coprophila</i> to take a large step forward in aiding these studies. We approached assembling the <i>Sciara</i> genome using multiple sequencing technologies: PacBio, Oxford Nanopore MinION, and Illumina. To find an optimal assembly using these datasets, we generated 44 Illumina assemblies using 7 short-read assemblers and 50 long-read assemblies of PacBio and MinION sequence data using 6 long-read assemblers. We ranked assemblies using a battery of reference-free metrics, and scaffolded a subset of the highest-ranking assemblies using BioNano Genomics optical maps. RNA-seq datasets from multiple life stages and both sexes facilitated genome annotation. Moreover, we anchored nearly half of the <i>Sciara</i> genome sequence into chromosomes. Finally, we used the signal level of both the PacBio and Oxford Nanopore data to explore the presence or absence of DNA modifications in the <i>Sciara</i> genome since DNA modifications may play a role in imprinting in <i>Sciara</i>, as they do in mammals. These data serve as the foundation for future research by the growing community studying the unique features of this emerging model system.