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

ABSTRACT: 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.

SUBMITTER: Generalovic TN

PROVIDER: S-EPMC8104945 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The black soldier fly (BSF), Hermetia illucens (L., 1758) (Diptera: Stratiomyidae), is an endemic fly species from the tropical, subtropical and warm temperate zones of America. This saprophagous species relies on its environment where it finds the decomposing matter for the larvae to grow. The polyphagous diet and the macronutrient quality (mainly lipids and proteins) of these larvae make them excellent candidates for various applications such as waste and organic material management, incorporation in animal feed or alternative energy source. Although rearing development in temperate regions requires artificial processes to continuously produce high quality eggs and larvae, few studies have been conducted on the mating and oviposition processes governing H. illucens reproduction. Research conducted in semi-artificial rearing conditions showed that the number of mating varied according to the season. It has been speculated that this behavior could be due to differences in the intensity of sunlight caused by the change of seasons. This study aims at evaluating the influence of sex-ratio, density and nycthemeral cycle on H. illucens reproduction. In order to tackle this issue, an artificial set up for oviposition to collect eggs has been developed. This egg collection system aims at centralize oviposition and simplify eggs collection. Two populations with opposite sex-ratio (male-dominant and female-dominant) were selected. Their respective eggs productions have been evaluated for five breeding densities. Eggs weights varied significantly among the densities for each opposite sex-ratio population and female dominant population produced most eggs weight from 6500 individuals /m3. Finally, four nycthemeral cycles (2, 6, 12 and 18h of daily light) were simulated to evaluate the impact of light duration on reproduction. Early oviposition pic associated with a decrease of the oviposition period are shown when H. illucens are exposed to increasing light duration. These experiments enable improvement of the understanding on artificial reproduction of H. illucens.

Project description:BackgroundThe black soldier fly (Hermetia illucens) is the most promising insect candidate for nutrient-recycling through bioconversion of organic waste into biomass, thereby improving sustainability of protein supplies for animal feed and facilitating transition to a circular economy. Contrary to conventional livestock, genetic resources of farmed insects remain poorly characterised. We present the first comprehensive population genetic characterisation of H. illucens. Based on 15 novel microsatellite markers, we genotyped and analysed 2862 individuals from 150 wild and captive populations originating from 57 countries on seven subcontinents.ResultsWe identified 16 well-distinguished genetic clusters indicating substantial global population structure. The data revealed genetic hotspots in central South America and successive northwards range expansions within the indigenous ranges of the Americas. Colonisations and naturalisations of largely unique genetic profiles occurred on all non-native continents, either preceded by demographically independent founder events from various single sources or involving admixture scenarios. A decisive primarily admixed Polynesian bridgehead population serially colonised the entire Australasian region and its secondarily admixed descendants successively mediated invasions into Africa and Europe. Conversely, captive populations from several continents traced back to a single North American origin and exhibit considerably reduced genetic diversity, although some farmed strains carry distinct genetic signatures. We highlight genetic footprints characteristic of progressing domestication due to increasing socio-economic importance of H. illucens, and ongoing introgression between domesticated strains globally traded for large-scale farming and wild populations in some regions.ConclusionsWe document the dynamic population genetic history of a cosmopolitan dipteran of South American origin shaped by striking geographic patterns. These reflect both ancient dispersal routes, and stochastic and heterogeneous anthropogenic introductions during the last century leading to pronounced diversification of worldwide structure of H. illucens. Upon the recent advent of its agronomic commercialisation, however, current human-mediated translocations of the black soldier fly largely involve genetically highly uniform domesticated strains, which meanwhile threaten the genetic integrity of differentiated unique local resources through introgression. Our in-depth reconstruction of the contemporary and historical demographic trajectories of H. illucens emphasises benchmarking potential for applied future research on this emerging model of the prospering insect-livestock sector.

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

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