Biology subjects

Simmonds, T.

Publications and source records attributed to Simmonds, T..

3 recordsLinked to original sources

bioRxiv2026

The tortured past of young polymorphic sex chromosomes revealed through multiple de novo genome assemblies of the mountain pine beetle

Neo-sex chromosomes provide a powerful system for studying the early stages of sex chromosome evolution and the genomic mechanisms that may contribute to reproductive isolation. Using PacBio long-read HiFi sequencing, Hi-C scaffolding, and sex-specific transcriptomic data, we generated six chromosome-level assemblies (male and female from three populations) of the mountain pine beetle (Dendroctonus ponderosae), a species known to harbor three partially reproductively isolated neo-Y haplogroups. These assemblies reveal that the large neo-X and neo-Y chromosomes formed through sequential fusions of the ancestral X with three autosomes, with recombination cessation occurring at [~]8.6, [~]6.3, and [~]4.3 MYA for each event. Comparative analyses show that while neo-X chromosomes remain largely collinear across populations, neo-Ys exhibit dramatic structural divergence, with 900-1,200 inverted segments per haplogroup and only [~]65% of sequence able to be aligned to the neo-X. Repeat analyses demonstrate moderate TE accumulation on the neo-Y, particularly LTR elements, and gene mapping analyses reveal extensive degeneration: [~]62% of neo-Y genes exhibit gene loss, fragmentation, or disruptive mutations. All populations retain a single pseudoautosomal region (PAR), though PAR size and gene content vary due to neo-Y specific rearrangements. Across neo-Ys, 27 genes are uniquely missing in the Western haplogroup, including previously identified candidates implicated in hybrid male sterility. Broader comparisons among neo-Ys show widespread structural variation, population specific patterns of degeneration, and limited gene family expansions. Together, these results provide the first full characterization of neo-sex chromosome evolution in D. ponderosae, revealing rapid, lineage specific neo-Y degeneration and highlighting the potential for sex chromosome divergence to contribute to emerging reproductive incompatibilities within a single species.

genomics↗

bioRxiv2025

Genome report: chromosome-scale genome assembly of the Olive fly Bactrocera oleae (Diptera: Tephritidae)

The olive fruit fly, Bactrocera oleae (Rossi) (Diptera: Tephritidae), is a specialist of fruits of the genus Olea and is a major pest of commercial olives due to their adverse impacts to olive production. In support of genomic and physiological research of the olive fly, we sequenced, assembled, and annotated two independent genomes, one from a wild-collected male and one from a wild-collected female. The resulting genomes are highly contiguous, collinear, and complete, attesting to the accuracy and quality of both assemblies. In addition to the autosomes captured as single contigs, the X and Y chromosomes were also captured as evidenced by the X chromosome showing diploid coverage in the female assembly compared to haploid coverage in the male assembly and the Y chromosome being entirely absent from the female assembly. These assemblies represent the first full chromosome-level assembly for Olive fly. In addition, a complete genome assembly of a known obligate symbiont to the olive fly, Candidatus Erwinia dacicola, was fully captured. The Ca. E. dacicola we report here is the most contiguous to date, represented with a gapless chromosome and two separate gapless plasmids. These genome assemblies, along with bacterial symbiont assembly, provide foundational resources for future genetic and genomic research in support of its management as an agricultural pest.

genomics↗

bioRxiv2024

Utilizing full-length 16S rRNA sequencing to assess the impact of diet formulation and age on targeted gut microbiome colonization in laboratory and mass-reared Mediterranean fruit flies

Insect gut microbiomes have important roles in overall host health and how hosts function in the environment. In laboratory and mass-reared insects, gut microbiomes can differ in composition and function compared to wild conspecifics. For fruit flies, like the Mediterranean fruit fly (medfly; Ceratitis capitata), these changes can influence male performance and behavior. Overall, understanding factors that influence the ability of bacteria to colonize hosts is an important for the establishment of lost or novel microbiota into mass-reared insects. The goal of this study was to evaluate how host age and diet inoculation method influenced bacterial establishment in laboratory and mass-reared medfly. We used an Enterobacter strain with antibiotic resistance and coupled it with full-length PacBio 16S rRNA sequencing to track the establishment of a specific isolates under different adult dietary conditions. We also used two longstanding reared lines of medfly in our study. Our results identified that diet had a strong interaction with age. Host medfly fed a liquid diet with the target bacteria were able to be colonized regardless of age, but those fed a slurry-based diet and separate water source were more resilient. This was consistent for both fly rearing lines used in the study. 16S rRNA sequencing corroborated the establishment of the specific strain, but also revealed some species/strain-level variation of Enterobacter sequences associated with the flies. Additionally, our study illustrates that long-read 16S rRNA sequencing may afford improved characterization of species- and strain-level distribution of Enterobacteriaceae in insects. ImportanceInsects form intimate relationships with gut microorganisms that can help facilitate several important roles. The goals of our study were to evaluate factors that influence microbial establishment in lines of the Mediterranean fruit fly (medfly), an important pest species throughout the world. Mass-reared insects for sterile insect technique often possess gut microbiomes that substantially differ from wild flies, which can impact their performance in pest control contexts. Here, we show that liquid-based formulations can be utilized to manipulate the gut microbiota of mass-reared medfly. Furthermore, using near full-length 16S rRNA metabarcoding sequencing, we uncovered strain-level diversity of that was not immediately obvious using other approaches. This is a notable finding, as it suggests that full-length 16S rRNA approaches can have marked improvements for some taxa compared to fewer hypervariable regions at approximately the same cost. Our results provide new avenues for exploring and interrogating medfly-microbiome interactions.

microbiology↗