Our lab seeks to understand why sexual reproduction and meiotic recombination are dominant in eukaryotic species despite their heavy evolutionary costs. To address this question, our research uses the microcrustacean Daphnia as a model system to investigate the causes and consequences of obligately asexual reproduction and the evolutionary forces driving the variation of meiotic recombination rate ad different biological scales (e.g., between populations/species). To achieve these goals, our lab currently uses a combination of high-throughput genomic and single-cell sequencing, bioinformatic genomic analysis, and CRISPR-Cas gene editing. 

The genetic mechanisms underlying the origin of obligate parthenogenesis in Daphnia.

In this project, we are interested in exploring the genetic mechanisms giving rise to obligately parthenogenetic Daphnia. Our previous studies strongly suggest that the genetic incompatibility between two sexual species D. pulex and D. pulicaria is critical for the origin of obligate parthenogenesis in the hybrids of these two species.   

The evolution and genetic basis of meiotic recombination rate variation in Daphnia.

In this project, we are investigating the genetic variants regulating meiotic recombination rate variation across Daphnia populations/species and are examining whether meiotic recombination evolves in an adaptive fashion. To estimate recombination rate and identify variants associated with recombination rate variation, we are mainly using and developing single-sperm whole-genome sequencing methodologies and population genomic analysis. We will also use CRISPR-Cas genetic editing to modify genetic variants to examine their effect on recombination rate. 

CRISPR-Cas genetic editing in Daphnia.

Our lab is actively developing CRISPR-Cas gene editing methodologies for Daphnia, currently including gene knock-out, gene knock-in, and precise base editing. We have a goal of creating 1000 Daphnia mutants in the next 4-5 years and test their gene knock-out effects to gain a deeper understanding of gene function and interactions. 

How environmental mutagens affect genomic integrity.

We are interested in understanding the effect of different environmental mutagens, for example, ethyl methanesulfonate (EMS), on the mutation rate and spectrum and gene expression in Daphnia. We use mutant genomic analysis with gene knock-out mutants to understand how different genes contribute to safeguarding genome integrity against the harmful effect of mutagens.