Biology subjects

Generalovic, T. N.

Publications and source records attributed to Generalovic, T. N..

4 recordsLinked to original sources

bioRxiv2025

Repeatable phenotypic but not genetic response to selection on body size in the black soldier fly

Polygenic traits are expected to show high genetic redundancy and therefore low repeatability in the genomic response to selection. We tested this prediction by selecting for large body size in the black soldier fly (Hermetia illucens). Over three replicate experiments selected for large body size, we found a strong and repeatable phenotypic response, with a mean 15% increase in body size. Selected lines also increased in larval growth rate (+19%) and average protein content (+14%), suggesting that selection on large body size does not result in strong trade-offs. In contrast to the predictability of the phenotypic response across replicates, whole genome sequencing identified a highly polygenic and non-repeatable genomic response. We identified 120, 301 and 157 outlier genomic regions in the three replicates, but high redundancy with only four shared regions. Among 12 candidate genes found in these regions, the insulin-like receptor gene (HiInR) was confirmed as regulating larval growth using a CRISPR knockout experiment. In summary, polygenic quantitative traits show high genetic redundancy, even where the phenotypic response to selection is highly repeatable.

evolutionary biology↗

bioRxiv2023

Cryptic diversity and signatures of domestication in the Black Soldier Fly (Hermetia illucens)

The Black Soldier Fly (Hermetia illucens) is the main species in the developing global industry of insects as food and feed, but little is known about its natural diversity or the genetic basis of its domestication. We obtained whole genome sequences for 54 individuals from both wild and captive populations. We identified two genetic lineages at least 3 million years divergent, revealing cryptic diversity within the species. Our study indicates that the most common populations used for commercial and academic applications are primarily derived from just one of these lineages, likely originating from a wild North American progenitor. We find that captive populations show strong reductions in genetic diversity, consistent with genome-wide effects of population bottlenecks and drift associated with rearing in captivity. Some limited evidence of gene flow between divergent lineages was observed, as well as evidence of hybridisation from domesticated populations into the wild. Our study suggests that natural genetic diversity could provide important variation for industrial purposes in this novel agricultural species. Author SummaryAnimals and plants have been domesticated by humans over thousands of years, shaping their genomes and yielding beneficial or improved traits for agriculture. Insect farming has recently reached industrial scales in order to recycle organic wastes into feed and food grade material. The Black Soldier Fly is the flagship insect species in this novel agriculture sector. However, the understanding of its evolutionary history and the genetic impact of intense farming has not been well studied to date. We examined whole genomes from populations sampled from across the worldwide distribution of Black Soldier Fly to investigate the impact of domestication and reveal the evolutionary history of the species. We found that farmed populations show distinct genomic regions showing reduced variation that could represent signatures of selection or demographic effects. We also identify two distinct lineages of Black Soldier Fly that have been diverging for millions of years, comparable to divergence between different species in other insect groups, yet show evidence of genetic exchange, indicating a lack of reproductive incompatibility in the populations tested. This work is the first to describe the genetic impact of domestication in the Black Soldier Fly and provide evolutionary insights using whole genomes. These results imply that considerable wild diversity could be harnessed for improving agricultural efficiency.

genomics↗

bioRxiv2020

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

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.

genomics↗

bioRxiv2020

A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

BackgroundDiploid genome assembly is typically impeded by heterozygosity, as it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution which exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism. FindingsWe produced a high-quality, haplotype-resolved assembly for Arctia plantaginis through trio binning. We sequenced a same-species family (F1 heterozygosity [~]1.9%) and used parental Illumina reads to bin 99.98% of offspring Pacific Biosciences reads by parental origin, before assembling each haplotype separately and scaffolding with 10X linked-reads. Both assemblies are highly contiguous (mean scaffold N50: 8.2Mb) and complete (mean BUSCO completeness: 97.3%), with complete annotations and 31 chromosomes identified through karyotyping. We employed the assembly to analyse genome-wide population structure and relationships between 40 wild resequenced individuals from five populations across Europe, revealing the Georgian population as the most genetically differentiated with the lowest genetic diversity. ConclusionsWe present the first invertebrate genome to be assembled via trio binning. This assembly is one of the highest quality genomes available for Lepidoptera, supporting trio binning as a potent strategy for assembling highly heterozygous genomes. Using this assembly, we provide genomic insights into geographic population structure of Arctia plantaginis.

genomics↗