A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia IllucensL.)

Abstract

BackgroundHermetia 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.ResultsWe 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.ConclusionsRelease 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.

Grasshopper genome reveals long-term conservation of the X chromosome and temporal variation in X chromosome evolution

“…The proportion of X-linked genes of each species with the genomic location of L. migratoria homologs identified by reciprocal best hit. Genome comparisons include Schistocerca gregaria (Verlinden et al 2020), Teleogryllus oceanicus (Pascoal et al 2020), Laodelphax striatellus (Zhu et al 2017), Sogatella furcifera (Wang et al 2017), Nilaparvata lugens (Ye et al 2021), Pachypsylla venusta (Li et al 2020), Tribolium castaneum (Richards et al 2008), Harmonia axyridis (M. Chen et al 2021), Photinus pyralis (Fallon et al 2018), Hermetia illucens (Generalovic et al 2021) and Drosophila melanogaster (Celniker et al 2002). …”

“…Harmonia axyridis(M. , Photinus pyralis (Fallon et al 2018), Hermetia illucens (Generalovic et al 2021) and Drosophila melanogaster (Celniker et al 2002).…”

Twenty-seven ZAD-ZNF genes of Drosophila melanogaster are orthologous to the embryo polarity determining mosquito gene cucoid

“…In the genomes of lower Brachycera, we identified five cucoid loci on chromosome 6 of the soldier fly Hermetia illucens ( Hil_cucoid_1-5 , GenBank accession numbers: XP_037925088.1, XP_037925165.1, XP_037924715.1, CAD7093451.1, XP_037922166.1) (62) ( Fig 6C ) and four cucoid loci in the robber fly Proctacanthus coquilleti (Pco_cucoid_1-4) (63) ( S2 Table ), which seem to be orthologous to Hermetia cucoid orthologs 1, 2, 3, and 4/5, respectively ( S5 Figure ). The lower brachyceran Cucoid proteins 1 and 2 are most similar to CG9215, but retain conserved introns and are therefore potentially orthologous to CG9215/Zif , whereas the lower brachyceran Cucoid orthologs 3 and 4 are most similar to CG4424 and CG14711, respectively.…”

“…(62) (Fig 6C) and four cucoid loci in the robber fly Proctacanthus coquilleti (Pco_cucoid_1-4) (63) (S2 Table), which seem to be orthologous to Hermetia cucoid orthologs 1, 2, 3, and 4/5, respectively (S5 Figure). The lower brachyceran Cucoid proteins 1 and 2 are most similar to CG9215, but retain conserved introns and are therefore potentially orthologous to CG9215/Zif, whereas the lower brachyceran Cucoid orthologs 3 and 4 are most similar to CG4424 and CG14711, respectively.…”

The Natural History of the Black Soldier Fly, Hermetia Illucens: Insights From Complete Mitochondrial Genome Sequences

“…Finally, based on 15 microsatellite markers, 16 genetic clusters were found with hot spots in South America 33 . Other works focused on more fundamental aspects of BSF and assembled a reference mitochondrial genome and a chromosomal-scale nuclear genome 34,35,36 .…”