Biology subjects

Singh, N. D.

Publications and source records attributed to Singh, N. D..

4 recordsLinked to original sources

bioRxiv2022

Candidate Genes Underlying Wolbachia-Associated Plastic Recombination Revealed by Ovarian Transcriptomics of D. melanogaster

Phenotypic plasticity is prevalent in nature and can facilitate the acclimation of organisms to changing environments. Recombination rate is plastic in a diversity of organisms and under a variety of stressful conditions. However, the recent finding that Wolbachia pipientis induces plastic recombination in Drosophila melanogaster was surprising because Wolbachia is not strictly considered a stressor to this host. We investigate the molecular mechanisms of Wolbachia-associated plastic recombination by comparing the ovarian transcriptomes of D. melanogaster infected and uninfected with Wolbachia. Our data suggest that infection explains a small amount of transcriptional variation but specifically affects genes related to cell cycle, translation, and metabolism. We also find enrichment of cell division and recombination processes among genes with infection-associated differential expression. Broadly, the transcriptomic changes identified in this study provide insight for the mechanisms of microbe-mediated plastic recombination, an important but poorly understood facet of host-microbe dynamics. Significance StatementThough it is documented that Wolbachia is associated with increased recombination in D. melanogaster, the underlying mechanisms remain unknown. Here we use ovarian transcriptomics in Wolbachia-infected and uninfected flies to identify candidate genes underlying Wolbachia-associated plastic recombination. We find that infection alters ovarian gene expression in subtle ways, and also identify exciting candidate genes for functional analysis in subsequent work. These candidate genes may be the first step in determining the molecular mechanisms underlying Wolbachia-associated plastic recombination. Moreover, our data contribute to the growing body of knowledge surrounding how Wolbachia affects host gene expression, and highlights how context-dependent these effects are.

evolutionary biology↗

bioRxiv2022

Variation in fine scale recombination rate in temperature-evolved Drosophila melanogaster populations in response to selection.

Meiotic recombination plays a critical evolutionary role in maintaining fitness in response to selective pressures due to changing environments. Variation in recombination rate has been observed amongst and between species and populations and within genomes across numerous taxa. Studies have demonstrated a link between changes in recombination rate and selection but the extent to which fine scale recombination rate varies between evolved populations during the evolutionary period in response to selection is under active research. Here we utilize a set of three temperature-evolved Drosophila melanogaster populations that were shown to have diverged in several phenotypes including recombination rate based on the temperature regime in which they evolved. Using whole genome sequencing data of these populations, we generated fine scale recombination maps of the three populations. We compare recombination rates and patterns among the three populations and show that they have diverged at fine scales but are conserved at broader scales. We further demonstrate a correlation between recombination rates and genomic variation in the three populations and observe variation in putative warm-spots between the populations with these enhanced areas and associated genes overlapping areas previously shown to have diverged in the three populations due to selection. These data support the existence of recombination modifiers in these populations which are subject to selection during evolutionary change.

evolutionary biology↗

bioRxiv2021

Diet effects on mouse sperm: a warning for recombination studies

Meiotic recombination is a critical process for sexually reproducing organisms. This exchange of genetic information between homologous chromosomes during meiosis is important not only because it generates genetic diversity, but also because it is often required for proper chromosome segregation. Consequently, the frequency and distribution of crossovers are tightly controlled to ensure fertility and offspring viability. However, in many systems it has been shown that environmental factors can alter the frequency of crossover events. Two studies in flies and yeast point to nutritional status affecting the frequency of crossing over. However, this question remains unexplored in mammals. Here we test how crossover frequency varies in response to diet in Mus musculus males. We use immunohistochemistry to estimate crossover frequency in multiple genotypes under two diet treatments. Our results indicate that while crossover frequency was unaffected by diet in some strains, other strains were sensitive even to small composition changes between two common laboratory chows. Therefore, recombination is both resistant and sensitive to certain dietary changes in a strain-dependent manner and, hence, this response is genetically determined. Our study is the first to report a nutrition effect on genome-wide levels of recombination. Moreover, our work highlights the importance of controlling diet in recombination studies and may point to diet as a potential source of variability among studies, which is relevant for reproducibility.

genetics↗

bioRxiv2021

Diet-induced changes in titer support a threshold effect of Wolbachia-associated plastic recombination in Drosophila melanogaster

Plastic recombination in Drosophila melanogaster has been associated with a variety of extrinsic and intrinsic factors such as temperature, starvation, and parasite infection. The bacterial endosymbiont Wolbachia pipientis has also been associated with plastic recombination in D. melanogaster. Wolbachia infection is pervasive in arthropods and this infection induces a variety of phenotypes in its hosts, the strength of which can depend on bacterial concentration, or titer. Here we test the hypothesis that the magnitude of Wolbachia-associated plastic recombination in D. melanogaster depends on titer. To manipulate titer, we raised Wolbachia-infected and uninfected flies on diets that have previously been shown to increase or decrease Wolbachia titer relative to controls. We measured recombination in treated and control individuals using a standard backcrossing scheme with two X-linked visible markers. Our results recapitulate previous findings that Wolbachia infection is associated with increased recombination rate across the yellow-vermillion interval of the X chromosome. Our data show no significant effect of diet or diet by Wolbachia interactions on recombination, suggesting that diet-induced changes in Wolbachia titer have no effect on the magnitude of plastic recombination. These findings represent the first step toward investigating the mechanisms behind Wolbachia-associated plastic recombination and demonstrate that the effect may be threshold-based as opposed to dose-dependent.

evolutionary biology↗