Biology subjects

Chong, R. A.

Publications and source records attributed to Chong, R. A..

3 recordsLinked to original sources

bioRxiv2025

Comparative genomic analysis of Cluster AZ Arthrobacter phages

Bacteria in the Arthrobacter genus belong to the phylum Actinobacteria and are primarily soil-dwelling. Over 600 bacteriophages infecting Arthrobacter hosts have been isolated and sequenced, and genomic analyses show these phages to be highly diverse with mosaic genome architectures. We describe here a group of 32 Arthrobacter phages grouped in Cluster AZ, isolated on four different Arthrobacter strains all with siphoviral morphologies. The Cluster AZ phages exhibit a spectrum of diversity and can be subdivided into four subclusters. The diversity in minor tail protein and endolysin genes correlates partly with isolation host strain and may be predictive of the host range of these phages. Most of the Cluster AZ phages are temperate, form stable lysogens, and encode an integrase; however, an immunity repressor gene has not been identified. The intracluster diversity was analyzed in-depth at the whole genome level and through individual genes. As more Arthrobacter phages are isolated and analyzed they continue to provide new insights into phage evolution.

genomics↗

bioRxiv2021

Metamorphosis imposes variable constraints on genome expansion

Genome size varies ~ 100,000-fold across eukaryotes and has long been hypothesized to be influenced by metamorphosis in animals. Transposable element accumulation has been identified as a major driver of increase, but the nature of constraints limiting the size of genomes has remained unclear, even as traits such as cell size and rate of development co-vary strongly with genome size. Salamanders, which possess diverse metamorphic and non-metamorphic life histories, have the largest vertebrate genomes -- 3 to 40 times that of humans -- as well as the largest range of variation in genome size. We tested 13 biologically-inspired hypotheses exploring how the form of metamorphosis imposes varying constraints on genome expansion in a broadly representative phylogeny containing 118 species of salamanders. We show that metamorphosis during which animals undergo the most extensive and synchronous remodeling imposes the most severe constraint against genome expansion, with the severity of constraint decreasing with reduced extent and synchronicity of remodeling. More generally, our work demonstrates the potential for broader interpretation of phylogenetic comparative analysis in exploring the balance of multiple evolutionary pressures shaping phenotypic evolution.

evolutionary biology↗

bioRxiv2017

Unexpected variation across mitochondrial gene trees and evidence for systematic error: How much gene tree variation is biological?

The use of large genomic datasets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of these biological versus methodological factors in explaining gene tree variation is a major unresolved question in phylogenetics. Using mitochondrial genomes to control for biological causes of gene tree variation, we estimate the extent of gene tree discordance driven by systematic error and employ posterior prediction to highlight the role of model fit. We find that the amount of discordance among mitochondrial gene trees is similar to the amount of discordance found in other studies that assume only biological causes of variation. This similarity suggests that the role of systematic error in generating gene tree variation is underappreciated and that critical evaluation of the fit between assumed models and the data used for inference is important for the resolution of unresolved phylogenetic questions.

evolutionary biology↗