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

No Thumbnail Available
Change log
Generalovic, Tomas N  ORCID logo  https://orcid.org/0000-0002-8983-1024
McCarthy, Shane A 
Warren, Ian A 
Wood, Jonathan MD 
Torrance, James 

Hermetia illucens L. (Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an increasingly important species for bioconversion of organic material into animal feed. 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 pseudochromosomes representing seven chromosomes with 16.01 Mb contig and 180.46 Mb scaffold N50 values. The highly complete genome obtained a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 98.6%. We masked 67.32% of the genome as repetitive sequences and annotated a total of 16,478 protein-coding genes using the BRAKER2 pipeline. We analyzed an established lab population to investigate the genomic variation and architecture of the BSF revealing six autosomes and an X chromosome. Additionally, we estimated the inbreeding coefficient (1.9%) of the lab population by assessing runs of homozygosity. This provided evidence for inbreeding events including long runs of homozygosity on chromosome 5. The release of this novel chromosome-scale BSF genome assembly will provide an improved resource for further genomic studies, functional characterization of genes of interest and genetic modification of this economically important species.

Hermetia illucens, BRAKER2, Black Soldier Fly, Hi-C assembly, PacBio, domestication, genome annotation, genome assembly, inbreeding, Animals, Chromosomes, Diptera, Genome, Genomics, Repetitive Sequences, Nucleic Acid
Journal Title
G3 (Bethesda)
Conference Name
Journal ISSN
Volume Title
Oxford University Press (OUP)
All rights reserved
Biotechnology and Biological Sciences Research Council (BB/S507635/1)
Wellcome Trust (unknown)
Biotechnology and Biological Sciences Research Council (BB/M011194/1)
European Research Council (339873)
TNG was supported by the Biotechnology and Biological Sciences Research Council BB/M011194/1. CDJ and IAW were supported by ERC Speciation Genetics Advanced Grant 339873. JMDW, K.H, J.T, Y.S and M.Q were supported by the Wellcome Trust core grant 206194. SAM and RD were supported by Wellcome grant WT207492 to perform genome assembly.