bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.03.13.642958

Castes and developmental stages of the harvester ant P. californicus differ in genome-wide and gene specific DNA methylation

Chavarria, T.·Errbii, M.·Rinke, J.·Schrader, L.·Gadau, J.
View original source ↗Export metadata ↓

Abstract

DNA methylation in social insects has been proposed as a key mechanism underlying both reproductive and non-reproductive caste determination by regulating gene expression in response to environmental cues. So far, studies on DNA methylation in social insects have yielded mixed results, with some studies finding no effect on caste determination or worker behaviour while others have reported such effects. In order to link DNA methylation to either process one first needs to show variation in DNA methylation between castes and developmental stages. This study determined cytosin methylation in a CpG context (CmpG) in the harvester ant Pogonomyrmex californicus using ONT (Oxford Nanopore Sequencing) sequencing in larvae, pupae, workers and queens, moreover we compared accuracy of methylation with the gold standard WGBS (Whole Genome Bisulfite Sequencing). Methylation sites were highly correlated between WGBS and ONT (r2=0.8). Overall, the P. californicus genome showed low levels of methylation (3%) which is comparable to what has been found in other Hymenopterans. DNA methylation was significantly increased in gene bodies and in particular exons and showed a significant decrease at the transcription start site and promotor region. Introns, intergenic regions and transposable elements have the lowest levels of DNA methylation. Gene body methylation was positively correlated with gene expression in queens, which is in accordance with other studies and the opposite of what is found in vertebrate studies. Both castes and developmental stages showed significant variation and differences in gene body methylation frequencies. Furthermore, castes and stages which have a high metabolic rate (queens and pupae) show higher DNA methylation, suggesting plasticity and an active role of DNA methylation in gene regulation and in extension caste regulation.

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Chavarria, T., Errbii, M., Rinke, J., Schrader, L., Gadau, J.. 2025-03-15. Castes and developmental stages of the harvester ant P. californicus differ in genome-wide and gene specific DNA methylation. https://doi.org/10.1101/2025.03.13.642958

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Structural variation in repeat elements is widespread in normal human tissues and in tumorigenesis

Somatic mosaicism contributes to genomic variation, yet postzygotic structural variants remain under-characterized. We performed long- and short-read WGS from multiple individuals (n=47 normal tissues; n=168 samples) and identified mosaic structural variants in all individuals and germ layers, impacting a median 285.2 kb/genome. Nearly half of breakpoints were independently validated, with tissue distributions reflecting both early and late developmental origins. Most mosaic variants were repeat-mediated and 8.3% overlapped functional elements, an enrichment compared to germline variants. To extend these analyses in samples where long-read sequencing is infeasible, we measured repeat alterations from short-read sequencing, recapitulating mosaic tissue-specific differences. We characterized tumor- and tissue- specific variation in repeats across 15 cancer types and found tumor-related repeat variation to be similar in scale to that of normal mosaic variation. Tracking repeat changes in cell-free DNA provided a noninvasive approach for tumor monitoring. Our analyses revealed widespread repeat-driven structural variation in health and disease.

genomics↗
bioRxiv2026

RNA isoform-resolved multiplexed sequencing with bioorthogonal barcoding

RNA isoform dysregulation drives disease pathogenesis and is the target of FDA-approved splice-switching therapeutics. However, multiplexed sequencing methods discard splice junction information because only 3' termini are barcoded and counted. Here, we repurpose acylation and click chemistries to conjugate bioorthogonal barcodes (bobcodes) directly onto multiple internal positions along cellular RNAs. Bobcoded RNAs from multiple samples are pooled for multiplexed cDNA synthesis, during which reverse transcriptase switches from each RNA template onto its tethered bobcode with greater than 99% accuracy in species mixing experiments. Bobcode attachment intervals set cDNA insert sizes without a library fragmentation step, and priming with poly(dT) or random hexamers selects between 3'-end counting and full-length isoform capture. A bioorthogonal barcode-sequencing (BOB-seq v0.1) drug screen identifies transcriptome-wide on- and off-target RNA splicing effects and outperforms existing multiplexing RNA sequencing methods in workflow simplicity, sample-to-sample variability, and barcoding accuracy. Bobcodes add isoform resolution to scalable multiplexed RNA sequencing.

genomics↗
bioRxiv2026

Structural polymorphism and population-variable coding capacity of HERV-K(HML-2) in human pangenomes

Approximately 8% of the human genome is derived from ancient retroviral infections. The most recently integrated of these endogenous retroviruses is the HERV-K(HML-2) clade, whose expression has been associated with cancer, amyotrophic lateral sclerosis, and embryogenesis. Studies of HERV expression, particularly HML-2, have relied predominantly on short-read sequencing. However, the high similarity among HML-2 proviruses prevents many short reads from being assigned uniquely to individual loci. We therefore compared haplotype-resolved long-read genome assemblies from 292 donors to resolve variation in proviral structure and coding capacity. Several loci previously thought to be fixed were structurally polymorphic. Tandem arrays occurred at 13 loci and contained up to six proviral copies in a single array. At 8q11.23, we identified a previously undescribed full-length provirus in one haplotype. All 583 other haplotypes carried a solo-LTR. We found that standard reference genomes failed to represent the coding capacity retained in many individuals, whose proviruses contained intact open reading frames despite disruptive mutations in the reference sequences. Short-read genotypes left 32.5% of the tested donor-variant pairs unresolved at sites associated with viral reading frames. These findings show why HML-2 expression must be interpreted in the context of the structural and coding alleles each individual carries.

genomics↗