Biology subjects

O'Donnell, S.

Publications and source records attributed to O'Donnell, S..

23 records · Page 2Linked to original sources

bioRxiv2021

Architecture and evolution of subtelomeres in the unicellular green alga Chlamydomonas reinhardtii

In most eukaryotes, subtelomeres are dynamic genomic regions populated by multi-copy sequences of different origins, which can promote segmental duplications and chromosomal rearrangements. However, their repetitive nature has complicated the efforts to sequence them, analyze their structure and infer how they evolved. Here, we use recent and forthcoming genome assemblies of Chlamydomonas reinhardtii based on long-read sequencing to comprehensively describe the subtelomere architecture of the 17 chromosomes of this model unicellular green alga. We identify three main repeated elements present at subtelomeres, which we call Sultan, Subtile and Suber, alongside three chromosome extremities with ribosomal DNA as the only identified component of their subtelomeres. The most common architecture, present in 27 out of 34 subtelomeres, is an array of 1 to 46 tandem copies of Sultan elements adjacent to the telomere and followed by a transcribed centromere-proximal Spacer sequence, a G-rich microsatellite and a region rich in transposable elements. Sequence similarity analyses suggest that Sultan elements underwent segmental duplications within each subtelomere and rearranged between subtelomeres at a much lower frequency. Comparison of genomic sequences of three laboratory strains and a wild isolate of C. reinhardtii shows that the overall subtelomeric architecture was already present in their last common ancestor, although subtelomeric rearrangements are on-going at the species level. Analysis of other green algae reveals the presence of species-specific repeated elements, highly conserved across subtelomeres and unrelated to the Sultan element, but with a subtelomere structure similar to C. reinhardtii. Overall, our work uncovers the complexity and evolution of subtelomere architecture in green algae.

genomics↗

bioRxiv2019

Larval mannitol diets increase mortality, prolong development, and decrease adult body sizes in fruit flies (Drosophila melanogaster).

Ingestion of the polyol mannitol caused sex-biased mortality in adult Drosophila melanogaster, but larval mortality was not sex-biased. High-sugar diets prolong development and generate smaller adult body sizes in D. melanogaster. We hypothesized that mannitol ingestion would generate similar developmental phenotypes as other high-carbohydrate diets. We predicted concentration-dependent effects on development similar to high-sugar diets when D. melanogaster larvae are fed mannitol, as well as a concentration-dependent amelioration of developmental effects if introduction to mannitol media is delayed past the third instar. Both male and female larvae had prolonged development and smaller adult body sizes when fed increasing concentrations of mannitol. Mannitol-induced increases in mortality were concentration dependent in 0 M to 0.8 M treatments beginning as early as 48 hours post-hatching. Larval survival, and pupation and eclosion times, were normal in 0.4 M mannitol treatments when larvae were first introduced to mannitol 72 hours post-hatching (the beginning of the third-instar); the adverse mannitol effects occurred in 0.8 M mannitol treatments, but at a lower magnitude. Female D. melanogaster adults prefer laying eggs on diets with high sugar concentrations, despite the negative effects on offspring performance. However, when given a choice, female D. melanogaster avoided laying eggs on mannitol-containing media that was otherwise identical to the control media, suggesting females perceived and avoided mannitol. In conclusion, the developmental effects of a larval mannitol diet closely resemble those of high-sugar diets, but adult female oviposition responses to mannitol in laying substrates are distinct from responses to other carbohydrates.

zoology↗

bioRxiv2019

Mannitol ingestion causes concentration-dependent, sex-specific mortality in adults of the fruit fly (Drosophila melanogaster).

Mannitol, a sugar alcohol used in commercial food products, induced sex-specific mortality in the fruit fly Drosophila melanogaster when ingested at a single concentration (1M), and female mortality was greater than male mortality. We hypothesized that sex differences in energy needs, related to reproductive costs, contribute to increased mortality in females compared to males. To test for the effects of reproductive costs, we compared longevity to 21 days of actively mating and non-mating flies fed various concentrations of mannitol. We also asked whether mannitol-induced mortality was concentration-dependent for both males and females, and if mannitols sex-specific effects were consistent across concentrations. Females and males both showed concentration-dependent increases in mortality, but female mortality was consistently higher at all concentrations above 0.75M. Fly longevity to 21 days decreased further for both sexes when housed in mixed sex vials (as compared to single sex vials), suggesting the increased energetic demands of reproduction for both sexes may increase ingestion of mannitol. Mannitol fed to larvae did not alter emerging adult sex ratios, suggesting that sex-specific mortality due to mannitol occurs only in adults.

zoology↗

bioRxiv2018

Reshuffling yeast chromosomes with CRISPR/Cas9

Genome engineering is a powerful approach to study how chromosomal architecture impacts phenotypes. However, quantifying the fitness impact of translocations independently from the confounding effect of base substitutions has so far remained challenging. We report a novel application of the CRISPR/Cas9 technology allowing to generate with high efficiency both uniquely targeted and multiple concomitant reciprocal translocations in the yeast genome. Targeted translocations are constructed by inducing two double-strand breaks on different chromosomes and forcing the trans-chromosomal repair through homologous recombination by chimerical donor DNAs. Multiple translocations are generated from the induction of several DSBs in LTR repeated sequences and promoting repair using endogenous uncut LTR copies as template. All engineered translocations are markerless and scarless. Targeted translocations are produced at base pair resolution and can be sequentially generated one after the other. Multiple translocations result in a large diversity of karyotypes including in some instances large segmental duplications. To test the phenotypic impact of translocations, we first recapitulated in a lab strain the SSU1/ECM34 translocation providing increased sulphite resistance to wine isolates. Surprisingly, the same translocation in a laboratory strain resulted in decreased sulphite resistance. However, adding the repeated sequences that are present in the SSU1 promoter of the resistant wine strain induced sulphite resistance in the lab strain, yet to a lower level than that of the wine isolate, implying that additional polymorphisms also contribute to the phenotype. These findings illustrate the advantage brought by our technique to untangle the phenotypic impacts of structural variations from confounding effects of base substitutions. Secondly, we showed that strains with multiple translocations display large phenotypic diversity in a wide range of environmental conditions. No coding sequence or promoter region was altered by the multiple translocations showing that simply reconfiguring chromosome architecture is sufficient to provide fitness advantages in stressful growth conditions.\n\nAUTHOR SUMMARYChromosomes are highly dynamic objects that often undergo large structural variations such as reciprocal translocations. Such rearrangements can have dramatic functional consequences, as they can disrupt genes, change their regulation or create novel fusion genes at their breakpoints. For instance, 90-95% of patients diagnosed with chronic myeloid leukemia carry the Philadelphia chromosome characterized by a reciprocal translocation between chromosomes 9 and 22. In addition, translocations reorganize the genetic information along chromosomes, which in turn can modify the 3D architecture of the genome and potentially affect its functioning. Quantifying the fitness impact of translocations independently from the confounding effect of base substitutions has so far remained challenging. Here, we report a novel CRISPR/Cas9-based technology allowing to generate with high efficiency and at a base-pair precision either uniquely targeted or multiple reciprocal translocations in yeast, without leaving any marker or scar in the genome. Engineering targeted reciprocal translocations allowed us for the first time to untangle the phenotypic impacts of large chromosomal rearrangements from that of point mutations. In addition, the generation of multiple translocations led to a large reorganization of the genetic information along the chromosomes. Although no gene was disrupted, we showed that solely shuffling the genome resulted in the emergence of fitness advantage in stressful environmental conditions.

genomics↗

bioRxiv2016

The structured diversity of specialized gut symbionts of the New World army ants

Symbiotic bacteria play important roles in the biology of their arthropod hosts. Yet the microbiota of many diverse and influential groups remain understudied, resulting in a paucity of information on the fidelities and histories of these associations. Motivated by prior findings from a smaller scale, 16S rRNA-based study, we conducted a broad phylogenetic and geographical survey of microbial communities in the ecologically dominant New World army ants (Formicidae: Dorylinae). Amplicon sequencing of the 16S rRNA gene across 28 species spanning the five New World genera showed that the microbial communities of army ants consist of very few common and abundant bacterial species. The two most abundant microbes, referred to as Unclassified Firmicutes and Unclassified Entomoplasmatales, appear to be specialized army ant associates that dominate microbial communities in the gut lumen of three host genera, Eciton, Labidus and Nomamyrmex. Both are present in other army ant genera, including those from the Old World, suggesting that army ant symbioses date back to the Cretaceous. Extensive sequencing of bacterial protein-coding genes revealed multiple strains of these symbionts co-existing within colonies, but seldom within the same individual ant. Bacterial strains formed multiple host species-specific lineages on phylogenies, which often grouped strains from distant geographic locations. These patterns deviate from those seen in other social insects, and raise intriguing questions about the influence of army ant colony swarm-founding and within-colony genetic diversity on strain co-existence, and the effects of hosting a diverse suite of symbiont strains on colony ecology.

evolutionary biology↗