Biology subjects

Ho, E. K. H.

Publications and source records attributed to Ho, E. K. H..

3 recordsLinked to original sources

bioRxiv2021

Heat shock protein gene expression is higher and more variable with thermal stress and mutation accumulation in Daphnia

Understanding the genetic architecture of the stress response and its ability to evolve in response to different stressors requires an integrative approach. Here we quantify gene expression changes in response to two stressors associated with global climate change and habitat loss--heat shock and mutation accumulation. We measure expression levels for two Heat Shock Proteins (HSP90 and HSP60)--members of an important family of conserved molecular chaperones that have been shown to play numerous roles in the cell. While HSP90 assists with protein folding, stabilization, and degradation throughout the cell, HSP60 primarily localizes to the mitochondria and mediates de novo folding and stress-induced refolding of proteins. We perform these assays in Daphnia magna originally collected from multiple genotypes and populations along a latitudinal gradient, which differ in their annual mean, maximum, and range of temperatures. We find significant differences in overall expression between loci (10-fold), in response to thermal stress (~6x increase) and with mutation accumulation (~4x increase). Importantly, stressors interact synergistically to increase gene expression levels when more than one is applied (increasing, on average, >20x). While there is no evidence for differences among the three populations assayed, individual genotypes vary considerably in HSP90 expression. Overall, our results support previous proposals that HSP90 may act as an important buffer against not only heat, but also mutation, and expands this hypothesis to include another member of the gene family acting in a different domain of the cell.

genetics↗

bioRxiv2020

Engines of change: Transposable element mutation rates are high and vary widely among genotypes and populations of Daphnia magna

Transposable elements (TEs) represent a large and dynamic portion of most eukaryotic genomes, yet little is known about their mutation rates or the correspondence between rates and long-term patterns of accrual. We compare TE activity over long and short time periods by quantifying TE profiles and mutation rates (with and without minimizing selection) among 9 genotypes from three populations of Daphnia magna sampled along a latitudinal gradient. The patterns of genome-wide variation observed in nature mirror direct estimates of rates and spectra observed in a multi-year laboratory mutation accumulation experiment, where net rates range from -11.98 to 12.79 x 10-5 per copy per generation across genotypes. Overall, gains outnumber losses and both types of events are highly deleterious based on comparing lines with and without selection minimized. The rate and spectrum of TE mutations vary widely among genotypes and across TE families/types, even within the same population. We compare TE mutation rates to previously published rates of base substitution, microsatellite mutation, and gene conversion for the same genotypes, and show a correlation only with the latter. Our study provides strong evidence for the notion that TEs represent a highly mutagenic force in the genome. Furthermore, the variation we observe underscores the need to expand the repertoire of mutations studied to include a wider array of mutation types with different underlying mechanisms in order to better understand the evolution of the mutation rate and the ways in which genetic variation is generated genome wide.

genomics↗

bioRxiv2019

Intraspecific Variation in Microsatellite Mutation Profiles in Daphnia magna

Microsatellite loci (tandem repeats of short nucleotide motifs) are highly abundant in eukaryotic genomes and are often used as genetic markers because they can exhibit variation both within and between populations. Although widely recognized for their mutability and utility, the mutation rates of microsatellites have only been empirically estimated in a few species and have rarely been compared across genotypes and populations and intraspecific differences in overall microsatellite content have rarely been explored. To investigate the accumulation of microsatellite DNA over long-and short-time periods, we quantified the abundance and genome-wide mutation rates in whole-genome sequences of 47 mutation accumulation (MA) lines and 12 non-MA lines derived from six different genotypes of the crustacean Daphnia magna collected from three populations (Finland, Germany, and Israel). Each genotype possessed a distinctive microsatellite profile and clustered according to their population of origin. During the period of mutation accumulation, we observed very high microsatellite mutation rates (a net change of -0.19 to 0.33 per copy per generation), which surpass rates reported from a closely-related congener, D. pulex, by an order of magnitude. Rates vary between microsatellite motifs and among genotypes, with those starting with high microsatellite content exhibiting greater losses and those with low microsatellite content exhibiting greater gains. Our results show that microsatellite mutation rates depend both on characteristics of the microsatellites and the genomic background. These context-dependent mutation dynamics may, in conjunction with other evolutionary forces that may differ among populations, explain the differential accumulation of repeat content in the genome over long time periods.

genomics↗