High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing

John M Urban,Susan A Gerbi,Michael S Foulk,Susan J Brown,Reza Mazloom,Jacob E Bliss,Allan C Spradling,Nanyan Lu,C Michelle Coleman

doi:10.1186/s12864-021-07926-2

Abstract

BackgroundThe 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.ResultsWe 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.ConclusionsWe 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.

Highlights

The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy
Data collection The somatic genome in males was targeted for the current assembly to (i) optimize the assembly of the autosomes and X chromosome by reducing the complexity introduced by the X’ and L chromosomes, and (ii) to use X haploidy in male somatic cells to partition the assembly into autosomal and X-linked sequences by coverage
The coverage, contiguity, and completeness estimates reported below are with respect to the male somatic genome

Summary

Introduction

The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. The Sciara genome has three autosomes (chromosomes II, III and IV), an X but no Y chromosome, and germline limited L chromosomes (Fig. 1) [1]. It is ~ 280 Mb in somatic cells, ~ 363 Mb in germ cells [2] (Supplemental Table S1A-D), and is ~ 38% GC [3]. In contrast to the rule that the amount of nuclear DNA is constant in all cells of an organism [4], nuclear DNA in Sciara cells exhibits copy number regulation at the levels of loci, chromosomes, and the genome. Genomic copy number varies across cell types, from canonical haploid and diploid cells to cells with 8192 synapsed chromatids [5] that form giant polytene chromosomes where locus-specific intrachromosomal DNA amplification occurs in “DNA puffs” driven by DNA rereplication [6, 7]

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Discussion

Conclusion