There is significant gap in our fundamental understanding of species’ response and adaptation in the factor of population structure and environmental change. It is then crucial to elucidate the expression state and regulation of each gene in different environment, among populations and relative species to understand how evolutionary processes (mutation, genetic drift, and natural selection) combine to change organism through time. My research includes studying of the evolutionary responses of populations and organisms to changing environment, using a combination of molecular, genomics and bioinformatics approaches to characterize changes in fitness-related traits.
Firstly, studying the evolution of the Pacific oyster genome and stress-responsive transcriptomes, my study established a framework for oyster genome that contributes to environmental adaptation, including oyster-specific gene expansion, highly inducible expression, functional divergence, and adaptive divergence among populations and relatives. Secondly, CRISPR genome editing of genes associated with butterfly eyespot, an evolutionary novel trait, my results showed the presence, absence and shape of eyespots can be controlled by the activity of only two co-opted transcription factors. Further CRISPR study also eliminates context dependence and co-option of a convergent evolved wing mimicry gene. Finally, investigating the functional relationship of genetics, epigenetics and transcription, I examined the role of chromatin accessibility in gene transcription regulation using recently developed functional genomics tools including PacBio de novo genome sequencing, ATAC-seq, Histone marker and transcription factor CHIP-seq. For example, my research identified multiple candidate cis-regulatory elements that regulate temporal and spatial expression of butterfly color pattern genes. Of note, I also found independent originated enhancers drives mimicry red pattern evolution in Heliconius butterfly. Overall, my work brings us closer to know an animal under changing environment in terms of gene expression and its regulation program. My research also has implications for the species conservation and is critical to predicting how organisms will adapt to long-term environmental change.
