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Summary The black soldier fly, Hermetia illucens, is an emerging biotechnological agent with its larvae being effective converters of organic waste into usable bio‐products including protein and lipids. To date, most operations use unimproved commercial populations produced by mass rearing, without cognisance of specific breeding strategies. The genetic and phenotypic consequences of these commercial practices remain unknown and could have a significant impact on long‐term population viability and productivity. The aim of this study was thus to assess the genetic and phenotypic changes during the early phases of colony establishment and domestication in the black soldier fly. An experimental colony was established from wild founder flies and a new microsatellite marker panel was developed to assess population genetic parameters along with the phenotypic characteristics of each generational cohort under captive breeding. The experimental colony was characterised by a small effective population size, subsequent loss of genetic diversity and rapid genetic and phenotypic differentiation between the generational cohorts. Ultimately, the population collapsed by the fifth generation, most likely owing to the adverse effect of inbreeding depression following the fixation of deleterious alleles. Species with r‐selected life history characteristics (e.g. short life‐span, high fecundity and low larval survival) are known to pose particular challenges for genetic management. The current study suggests that sufficient genetic and phenotypic variations exist in the wild population and that domestication and strain development could be achieved with careful population augmentation and selection during the early stages of colony establishment.

BackgroundBlow flies (Diptera: Calliphoridae) are important medical, veterinary and forensic insects encompassing 8 % of the species diversity observed in the calyptrate insects. Few genomic resources exist to understand the diversity and evolution of this group.ResultsWe present the hybrid (short and long reads) draft assemblies of the male and female genomes of the common North American blow fly, Phormia regina (Diptera: Calliphoridae). The 550 and 534 Mb draft assemblies contained 8312 and 9490 predicted genes in the female and male genomes, respectively; including > 93 % conserved eukaryotic genes. Putative X and Y chromosomes (21 and 14 Mb, respectively) were assembled and annotated. The P. regina genomes appear to contain few mobile genetic elements, an almost complete absence of SINEs, and most of the repetitive landscape consists of simple repetitive sequences. Candidate gene approaches were undertaken to annotate insecticide resistance, sex-determining, chemoreceptors, and antimicrobial peptides.ConclusionsThis work yielded a robust, reliable reference calliphorid genome from a species located in the middle of a calliphorid phylogeny. By adding an additional blow fly genome, the ability to tease apart what might be true of general calliphorids vs. what is specific of two distinct lineages now exists. This resource will provide a strong foundation for future studies into the evolution, population structure, behavior, and physiology of all blow flies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3187-z) contains supplementary material, which is available to authorized users.

The yellow mealworm, the larval stage of the darkling beetle Tenebrio molitor, shows great promise as an alternative source of animal protein. Herein we present the 312 Mb draft genome assembled using 10x Genomics linked-read technology to inform research efforts and to provide resources to optimise yellow mealworm for mass production and consumption. The genome with a contig N50 of 39,478 bp contains 89% of conserved arthropod genes among the > 20,000 genes assembled (complete and partial genes). This draft assembly represents a valuable resource to understanding T. molitor biology as a means of producing alternative, sustainable protein for the growing population and in the face of changing climates.

The production of male and female offspring is often determined by the presence of specific sex chromosomes which control sex-specific expression, and sex chromosomes evolve through reduced recombination and specialized gene content. Here we present the genomes of Chrysomya rufifacies, a monogenic blow fly (females produce female or male offspring, exclusively) by separately sequencing and assembling each type of female and the male. The genomes (> 25X coverage) do not appear to have any sex-linked Muller F elements (typical for many Diptera) and exhibit little differentiation between groups supporting the morphological assessments of C. rufifacies homomorphic chromosomes. Males in this species are associated with a unimodal coverage distribution while females exhibit bimodal coverage distributions, suggesting a potential difference in genomic architecture. The presence of the individual-sex draft genomes herein provides new clues regarding the origination and evolution of the diverse sex-determining mechanisms observed within Diptera. Additional genomic analysis of sex chromosomes and sex-determining genes of other blow flies will allow a refined evolutionary understanding of how flies with a typical X/Y heterogametic amphogeny (male and female offspring in similar ratios) sex determination systems evolved into one with a dominant factor that results in single sex progeny in a chromosomally monomorphic system.