Our research is dedicated to understanding the intricate evolutionary and functional roles of transposable elements (TEs). To achieve a comprehensive understanding of these prevalent genetic contents, we are engaged in the following research topics:

1. Characterizing TE's Activities during Stress Responses

When plants are stressed, TEs tend to be more active. We wonder what TEs are doing during these stressful times. Are they Jokers, exacerbating or exploiting the chaos, or Batmans, working to alleviate the stress? Utilizing model plant species like maize and rice, we employ a combination of methodologies, including chromatin status analysis, methylation, expression studies, comparative genomics, and molecular biology approaches to decode these questions.

A DALL-E art showcasing a stressed maize plant in a laboratory. The plant exhibits signs of wilt, and there are laboratory equipment and vials nearby, indicating a chromatin status analysis.
A DALL-E art portraying a species in its native habitat on one side and its adapted form on the other, interconnected by a DNA bridge foundationed on TEs.

2. Understanding Local Adaptation and Speciation through TEs

TEs are potent mutagens that constantly introduce kb-level mutations to the host genome, including within and nearby genes. We study TE's adaptative effects in relation to their functional consequences using comparative genomic approaches. Over evolutionary time scales, TEs have left countless footprints on host genomes and faithfully recorded significant evolutionary events, such as speciation. Some of these footprints can be utilized to understand the evolutionary history of a species. In this line of research, we try to understand TEs' contribution to evolutionary processes and utilize TEs to reconstruct evolutionary events through the creation of innovative algorithms and theoretical frameworks.

3. Development of Algorithms and Tools for Accurate TE Annotation

TEs comprise a substantial portion of plant genomes and other eukaryotic genomes. Annotating TEs accurately is challenging because 1) TEs are highly divergent even between closely related species; 2) most TEs we found in genomes are highly degraded; 3) TEs are found between genes, around genes, and within genes, resulting in challenges to accurately distinguish them from genes. Common practices of "masking" TEs (converting TE contents to Ns) often compromise the integrity of genomic research. To address these challenges, we are at the forefront of designing cutting-edge computer algorithms and developing novel software programs for precise TE annotation. We aim to enhance the applicability across diverse species and make a meaningful contribution to the field of TE studies. For more details on this work, please check out our Software page or the GitHub repository.

A DALL-E graphic featuring a computer algorithm intertwined with DNA and TEs symbols, set against a background of mathematical formulas.