Biology subjects

Wyatt, C. D. R.

Publications and source records attributed to Wyatt, C. D. R..

6 recordsLinked to original sources

bioRxiv2026

Chromosome-level genome and caste transcriptomes for Africa's most widespread social wasp (Belonogaster juncea) reveal unexpected genomic diversity

Belonogaster is an African genus of primitively eusocial wasps. They are widespread and conspicuous across sub-Saharan Africa and yet are among the least studied groups of social wasps. Here, we present the first high-quality, chromosome-level genome assembly for a representative of this genus, Belonogaster juncea, complemented by an RNA-seq analysis of brain transcription among individuals representing reproductive and non-reproductive castes. The assembled genome spans 315.8 Mb with a scaffold N50 of 7.91 Mb. The annotation contained 15,159 protein-coding genes and 20,046 isoforms, with Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 98.0% for the genome and 97.8% for the annotation. Using this new assembly, we show that the B. juncea genome differs notably from other social wasp genomes: a single satellite repeat makes up a fifth of its chromosome-scale sequence, it has the highest putative chromosome number in a sequenced wasp genome to date, and it shows high levels of syntenic breaks. We find caste neuro-transcription differences between queens and workers, revealing 573 differentially expressed genes (341 worker biased, 232 queen biased), with significant overlap in caste-specific genes when compared to Polistes dominula and Liostenogaster flavolineata. This genomic resource provides a foundation for understanding the molecular mechanisms underlying primitive eusociality and social evolution in wasps, and opens up new research opportunities for a genus of little-studied insects from the Global South.

genomics↗

bioRxiv2026

EXCON: a scalable, reproducible Nextflow pipeline for CAFE-based gene EXpansion and CONtraction analysis

Gene family expansion and contraction analysis is a commonly used approach in evolutionary comparative genomics to identify lineage-specific evolutionary pressures on gene copy/family number. CAFE is one of the most popular tools to measure changes in gene family size, but requires a high level of bioinformatics expertise, manual parameter tuning and preprocessing. Here we present EXCON, an automated, Eco-Flow community-developed Nextflow pipeline that integrates NCBI genome download, annotation quality and format pre-processing, orthologous gene family identification (Orthofinder), ultrametric tree formatting, birth-death modelling (CAFE), and GO enrichment analysis (eggNOG-mapper/TopGO) into a single, portable workflow. EXCON accepts genome assemblies and annotations, supports local, HPC and cloud-based computing environments, and requires minimal user configuration. The pipeline auto-selects appropriate CAFE lambda and error models, and separates high variance orthogroups for separate treatment. Applied to a 24-species primate dataset spanning Catarrhini, Platyrrhini and Strepsirrhini, the pipeline identified 358 rapidly evolving gene families, including a DUX (double homeobox) gene showing repeated, independent copy-number turnover across multiple lineages, consistent with the known instability of the D4Z4 macrosatellite repeat it resides in. EXCON is freely available at https://github.com/Eco-Flow/excon.

evolutionary biology↗

bioRxiv2026

nf-core/genomeqc: a best-practice pipeline for comparing genome and assembly quality

The rapid growth in publicly available genome assemblies has made selecting genomes suitable for downstream analyses increasingly challenging. Differences in assembly and annotation quality can influence gene completeness, duplication rates, contiguity, repeat representation, and other characteristics. Assessing genome quality therefore requires integrating multiple complementary quality metrics that are often generated by independent tools. Here, we present nf-core/genomeqc, a workflow for assessing and comparing genome assemblies. The pipeline accepts RefSeq/GenBank accessions for automatic genome and annotation retrieval, or local genome (FASTA) and annotation (GFF3/GTF) files. It integrates complementary analyses of assembly contiguity, gene completeness, annotation quality, repeat content and other quality metrics using tools such as BUSCO, QUAST, Merqury, and AGAT, before combining the results on a phylogenetic tree for visualisation and comparison across species. GenomeQC is implemented in Nextflow within the nf-core framework, providing an accessible, reproducible, scalable and community-driven workflow for genome quality assessment.

bioinformatics↗

bioRxiv2025

Senescent cells exhibit features of developmental signaling centres

Cellular senescence is a state that contributes to tissue patterning during development and tissue repair, but which becomes misregulated in ageing and disease. The senescence-associated secretory phenotype (SASP) mediates many of the context-dependent effects, yet its molecular composition and evolutionary origins remain incompletely understood. Here, we characterize the SASP signature of developmental senescent cells and find that it is enriched for genes encoding major developmental signaling pathways. Integrative analyses of in vitro and in vivo transcriptomes reveal that human and mouse senescent cells across diverse contexts consistently activate these developmental programs, with key morphogens constituting conserved SASP components. Functionally, we show that the SASP is sufficient to induce the expression of central developmental genes and transcription factors across multiple cell types. These findings show that senescent cells resemble developmental signaling centers and uncover developmental signaling reactivation as an evolutionarily conserved feature of senescence, providing conceptual insight into its physiological functions and its pathological impact during ageing.

cell biology↗

bioRxiv2020

Genetic toolkit for sociality predicts castes across the spectrum of social complexity in wasps

Major evolutionary transitions describe how biological complexity arises; e.g. in evolution of complex multicellular bodies, and superorganismal insect societies. Such transitions involve the evolution of division of labour, e.g. as queen and worker castes in insect societies. Castes across different evolutionary lineages are thought to be regulated by a conserved genetic toolkit. However, this hypothesis has not been tested thoroughly across the complexity spectrum of the major transition. Here we reveal, using machine learning analyses of brain transcription, evidence of a shared genetic toolkit across the spectrum of social complexity in Vespid wasps. Whilst molecular processes underpinning the simpler societies (which likely represent the origins of social living) are conserved throughout the major transition, additional processes appear to come into play in more complex societies. Such fundamental shifts in regulatory processes with complexity may typify other major evolutionary transitions, such as the evolution of multicellularity.

evolutionary biology↗

bioRxiv2020

The molecular basis of socially-mediated phenotypic plasticity in a eusocial paper wasp

Phenotypic plasticity, the ability to produce multiple phenotypes from a single genotype, represents an excellent model with which to examine the relationship between gene expression and phenotypes. Despite this, analyses of the molecular bases of plasticity have been limited by the challenges of linking individual phenotypes with individual-level gene expression profiles, especially in the case of complex social phenotypes. Here, we tackle this challenge by analysing the individual-level gene expression profiles of Polistes dominula paper wasps following the loss of a queen, a perturbation that induces some individuals to undergo a significant phenotypic shift and become replacement reproductives. Using a machine learning approach, we find a strong response of caste-associated gene expression to queen loss, wherein individuals expression profiles become intermediate between queen and worker states. Importantly, this change occurs even in individuals that appear phenotypically unaffected. Part of this response is explained by individual attributes, most prominently age. These results demonstrate that large changes in gene expression may occur in the absence of detectable phenotypic changes, resulting here in a socially mediated de-differentiation of individuals at the transcriptomic but not the phenotypic level. Our findings also highlight the complexity of the relationship between gene expression and phenotype, where transcriptomes are neither a direct reflection of the genotype nor a proxy for the molecular underpinnings of the external phenotype.

bioinformatics↗