RT Journal Article SR Electronic T1 A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia Illucens L.) JF bioRxiv FD Cold Spring Harbor Laboratory SP 2020.11.13.381889 DO 10.1101/2020.11.13.381889 A1 Tomas N. Generalovic A1 Shane A. McCarthy A1 Ian A. Warren A1 Jonathan M.D. Wood A1 James Torrance A1 Ying Sims A1 Michael Quail A1 Kerstin Howe A1 Miha Pipan A1 Richard Durbin A1 Chris D. Jiggins YR 2020 UL http://biorxiv.org/content/early/2020/11/15/2020.11.13.381889.abstract AB Background Hermetia illucens L. (Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an increasingly important mass reared entomological resource for bioconversion of organic material into animal feed.Results We generated a high-quality chromosome-scale genome assembly of the BSF using Pacific Bioscience, 10X Genomics linked read and high-throughput chromosome conformation capture sequencing technology. Scaffolding the final assembly with Hi-C data produced a highly contiguous 1.01 Gb genome with 99.75% of scaffolds assembled into pseudo-chromosomes representing seven chromosomes with 16.01 Mb contig and 180.46 Mb scaffold N50 values. The highly complete genome obtained a BUSCO completeness of 98.6%. We masked 67.32% of the genome as repetitive sequences and annotated a total of 17,664 protein-coding genes using the BRAKER2 pipeline. We analysed an established lab population to investigate the genomic variation and architecture of the BSF revealing six autosomes and the identification of an X chromosome. Additionally, we estimated the inbreeding coefficient (1.9%) of a lab population by assessing runs of homozygosity. This revealed a plethora of inbreeding events including recent long runs of homozygosity on chromosome five.Conclusions Release of this novel chromosome-scale BSF genome assembly will provide an improved platform for further genomic studies and functional characterisation of candidate regions of artificial selection. This reference sequence will provide an essential tool for future genetic modifications, functional and population genomics.Competing Interest StatementThis study was supported in kind by Better Origin. MP is CSO at Better Origin. CDJ is a scientific advisor at Better Origin.List of abbreviationsBSFBlack Soldier FlyBSFLBlack Soldier Fly LarvaePacBioPacific BiosciencesBUSCOBenchmarking Universal Single-Copy OrthologsGCGuaninecytosineGbgigabaseMbmegabasekbkilobasebpbase pairsRNA-seqRNA-sequencingHi-Chigh-throughput chromosome conformation captureBWABurrows-Wheeler AlignerPEpaired-endSMRTsingle-molecule realtimeSRASequence Read ArchiveLINElong interspersed nuclear elementsSINEShort Interspersed Nuclear ElementsLTRlong terminal repeatSTARSpliced Transcripts Alignment to a ReferenceROHRuns Of HomozygositySNPSingle Nucleotide Polymorphism.