Biology subjects

Coate, J. E.

Publications and source records attributed to Coate, J. E..

4 recordsLinked to original sources

bioRxiv2022

Estimating somatic mutation rates by Duplex Sequencing in non-model organisms: Daphnia magna as a case study

Somatic mutations are evolutionarily important as determinants of individual organismal fitness, as well as being a focus of clinical research on age-related disease, such as cancer. Identifying somatic mutations and quantifying mutation rates, however, is extremely challenging and genome-wide somatic mutation rates have only been reported for a few model organisms. Here, we describe the application of Duplex Sequencing on bottlenecked WGS libraries to quantify genome-wide somatic base substitution rates in Daphnia magna. Daphnia, historically an ecological model system, has more recently been the focus of mutation studies, in part because of its high germline mutation rates. Using our protocol and pipeline, we estimate a somatic mutation rate of 2.14 x 10-7 substitutions per site (in a genotype where the germline rate is 3.60 x 10-9 substitutions per site per generation). To obtain this estimate, we tested multiple dilution levels to maximize sequencing efficiency, and developed bioinformatic filters needed to minimize false positives when a high quality reference genome is not available. In addition to laying the groundwork for estimating genotypic variation in rates of somatic mutations within D. magna, we provide a framework for quantifying somatic mutations in other non-model systems, and also highlight recent innovations to single molecule sequencing that will help to further refine such estimates.

bioinformatics↗

bioRxiv2021

Induction of autotetraploidy and microbiome associations mediate differential responses to pathogens

It has become increasingly clear that the microbiome plays a critical role in shaping the host organisms response to disease. There also exists mounting evidence that an organisms ploidy level is important in their response to pathogens and parasites. However, no study has determined if or how these two factors influence one another. We investigate the effect of whole-genome duplication in Arabidopsis thaliana on their above-ground (phyllosphere) microbiome, and determine the interacting impacts of ploidy and the microbiome on disease outcome. Using seven independently derived synthetic auto-tetraploid Arabidopsis accessions, a synthetic leaf-associated bacterial community, and the model pathogen Pseudomonas syringae pv. Tomato DC3000, we confirm that polyploids are generally more resistant to pathogens, but illustrate that this resistance may be in part due to a decrease in the reliance on beneficial bacteria. Polyploids fare better against the pathogen than diploids regardless of microbial inoculation, while we observed that diploids harboring an intact microbiome have lower pathogen densities than those without. We then use RNA sequencing to show that diploids have many more differentially expressed defense-related genes in the presence of their phyllosphere microbiota, while polyploids exhibit constitutively activated defenses regardless of exposure to the synthetic community. These results imply that whole-genome duplication can disrupt historical host-microbiome associations, and suggest that a potential cause or consequence of disruption is a heightened capacity for pathogen defense that is less impacted by the microbiome.

plant biology↗

bioRxiv2020

Expression partitioning of duplicate genes at single cell resolution in Arabidopsis roots

Gene duplication is a key evolutionary phenomenon, prevalent in all organisms but particularly so in plants, where whole genome duplication (WGD; polyploidy) is a major force in genome evolution. Much effort has been expended in attempting to understand the evolution of duplicate genes, addressing such questions as why some paralogue pairs rapidly return to single copy status whereas, in other pairs, paralogues are retained and may (or may not) diverge in expression pattern or function. The effect of a gene--its site of expression and thus the initial locus of its function--occurs at the level of a cell comprising a single cell type at a given state of the cells development. Thus, it is critical to understand the expression of duplicated gene pairs at a cellular level of resolution. Using Arabidopsis thaliana root single cell transcriptomic data we identify 36 cell clusters, each representing a cell type at a particular developmental state, and analyze expression patterns of over 11,000 duplicate gene pairs produced by three cycles of polyploidy as well as by various types of single gene duplication mechanisms. We categorize paralogue pairs by their patterns of expression, identifying pairs showing strongly biased paralogue/homoeologue expression in different cell clusters. Notably, the precision of cell-level expression data permits the identification of pairs showing alternate bias, with each paralogue comprising 90% or greater of the pairs expression in different cell clusters, consistent with subfunctionalization at the cell type or cell state level, and, in some cases, at the level of individual cells. We identify a set of over 7,000 genes whose expression in all 36 cell clusters suggests that the single copy ancestor of each was also expressed in all root cells. With this cell-level expression information we hypothesize that there have been major shifts in expression for the majority of duplicated genes, to different degrees depending, as expected, on gene function and duplication type, but also on the particular cell type and state.

plant biology↗

bioRxiv2019

Gene balance predicts transcriptional responses immediately following ploidy change in Arabidopsis thaliana

The Gene Balance Hypothesis postulates that there is selection on gene copy number (gene dosage) to preserve stoichiometric balance among interacting proteins. This presupposes that gene product abundance is governed by gene dosage, and that the way in which gene product abundance is governed by gene dosage is consistent for all genes in a dosage-sensitive network or complex. Gene dosage responses, however, have rarely been quantified and the available data suggest that they are highly variable. We sequenced the transcriptomes of two synthetic autopolyploid accessions of Arabidopsis thaliana and their diploid progenitors, as well as one natural tetraploid and its synthetic diploid produced via haploid induction, to estimate transcriptome size and gene dosage responses immediately following ploidy change. We demonstrate that overall transcriptome size does not exhibit a simple doubling in response to genome doubling, and that individual gene dosage responses are highly variable in all three accessions, indicating that expression is not strictly coupled with gene dosage. Nonetheless, putatively dosage-sensitive gene groups (GO terms, metabolic networks, gene families, and predicted interacting protein pairs) exhibit both smaller and more coordinated dosage responses than do putatively dosage-insensitive gene groups, suggesting that constraints on dosage balance operate immediately following whole genome duplication. This supports the hypothesis that duplicate gene retention patterns are shaped by selection to preserve dosage balance.

plant biology↗