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

• Published in: G3 : genes - genomes - genetics Vol. 11; no. 5
• Main Authors: Generalovic, Tomas N, McCarthy, Shane A, Warren, Ian A, Wood, Jonathan M D, Torrance, James, Sims, Ying, Quail, Michael, Howe, Kerstin, Pipan, Miha, Durbin, Richard, Jiggins, Chris D
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01-05-2021
• Subjects: Animals; Chromosomes - genetics; Diptera - genetics; Genome; Genome Report; Genomics; Repetitive Sequences, Nucleic Acid; Black Soldier Fly; Hi-C assembly; BRAKER2; genome annotation; domestication; Hermetia illucens; inbreeding; PacBio; genome assembly
• ISSN: 2160-1836; 2160-1836
• DOI: 10.1093/g3journal/jkab085

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.