Kyriacou, R. G. | Search bioRxiv

bioRxiv2025

Evidence for Transcription and Horizontal Gene Transfer in Dipteran Germline-Restricted Chromosomes

Germline-restricted chromosomes (GRCs) constitute a unique class of chromosomes confined to reproductive cells. Arising across multiple evolutionarily distant lineages, GRCs have been identified in three insect families (non-biting midges, gall midges, and fungus gnats), each within the order Diptera. Genomic characterisation in fungus gnats has revealed GRCs to be large, gene-rich chromosomes, which, together with their persistence over millennia, implies they play important biological roles within this clade. However, transcription from these chromosomes has yet to be demonstrated, leaving key questions about their function and activity unresolved. Here, we provide the first direct evidence of GRC-linked gene expression in the fungus gnat Bradysia coprophila, integrating RNA-seq data with cytological observations across multiple developmental stages. We report that GRCs express functional genes, though overall transcription is highly limited, likely due to biological factors, such as transcriptional silencing in specific germline cell types, and technical constraints, including filtering to avoid mismapping from core chromosome paralogues. We identify 15 confidently expressed GRC-linked genes using stringent criteria, including five insect homologues of unknown function and nine resembling transposable elements, and report horizontal acquisition of a [~]290 kb bacterial-derived region on GRC2. Furthermore, we perform in vitro immunofluorescence staining and confocal microscopy, which indicate increased GRC activity in female oocytes. Overall, these findings establish GRCs in fungus gnats as transcriptionally active, albeit tightly regulated and highly dynamic, chromosomes capable of expressing both endogenous and potentially horizontally acquired genes.

genomics↗

bioRxiv2023

GC content across insect genomes: phylogenetic patterns, causes and consequences

The proportions of A:T and G:C nucleotide pairs are often unequal and can vary greatly between animal species and along chromosomes. The causes and consequences of this variation are incompletely understood. The recent release of high-quality genome sequences from the Darwin Tree of Life and other large-scale genome projects provides an opportunity for GC heterogeneity to be compared across a large number of insect species. Here we analyse GC content along chromosomes, and within protein-coding genes and codons, of 150 insect species from four holometabolous orders: Coleoptera, Diptera, Hymenoptera, and Lepidoptera. We find that protein-coding sequences have higher GC content than the genome average, and that Lepidoptera generally have higher GC content than the other three insect orders examined. GC content is higher in small chromosomes in most Lepidoptera species, but this pattern is less consistent in other orders. GC content also increases towards subtelomeric regions within protein-coding genes in Hymenoptera, Coleoptera and, most strikingly, Lepidoptera. Two species of Diptera, Bombylius major and B. discolor, have very atypical genomes with ubiquitous increase in AT content, especially at third codon positions. Despite dramatic AT-biased codon usage, we find no evidence that this has driven divergent protein evolution. We argue that the GC landscape of Lepidoptera, Hymenoptera and Coleoptera genomes is influenced by GC-biased gene conversion, strongest in Lepidoptera, with some outlier taxa affected drastically by counteracting processes.

evolutionary biology↗