top of page

Genome Mining

Screen Shot 2017-12-22 at 11.56.43.png
Screen Shot 2017-12-22 at 11.56.51.png
Screenshot 2019-02-25 at 15.55.08.png

Plants are estimated to synthesize ove one million  small molecules, but less than 0.1% of their synthetic pathways are known. How and why plants synthesize such astounding metabolism are less understood.

​

 

~ 10% genes are encoding enzymes in A. thaliana, the best model plant ever. Most of them are functionally unknown, no speak of their potential ecological roles. The situation in other non-model plants should be even worse.

 

Using bioinformatics, I am developing new pipelines to discover new enzymes, novel pathways and advanced networks.

Cytochromes P450

Cytochromes P450 (CYPs) are evolved in almost every primary and specialized pathway in plants, which reflects the diversity and complexity of plant metabolism greatly. My PhD thesis was titled as “Evolutionary mechanisms of plant adaptation illustrated by cytochrome P450 genes under purifying or relaxed selection”. Two papers were published out of my PhD work so far, one is characterizing a well-conserved P450 that is essential for plant volatile emission; the other is using evolutionary theory to trace the enzyme evolving history and discover new-to-nature functions of CYPs.

715A1GFP HDEL RFP04_c1+2+3_edited.jpg

ER localised cytochrome P450

AtCYP715A1-GFP

HDEL-RFP (ER marker)

co-expressed in N. benthamiana leaves

Specialized Pathway

View More

lignin pathway

Ca. 20-30% of carbon are fixed by the lignin pathway in plants. While lignin is essential for plant erect growth and water transportation, it constitutes the major cell wall recalcitrance to cellulase digestibility present in the second generation biofuel industry. We are manupilating the lignin biosynthesis network in order to enginner better plants subject to easy fermatation process.

flavoid pathway

triterpene pathway

lipids pathway

Biochemical Evolution

View More

Evolution of plant metabolites: from phylogenomics to functional validations

Plants have evolved specialized metabolites since the first land plants over 450 million years ago. They then expanded the accumulation of specialized compounds enormously following the radiation of plants. Now, we can find plants in every corner of this planet earth with various growth conditions.

​

My research aims at understanding how plants have achived in producing such a big number (estimated over 1 million) of small molecules at the molecular level. Using combinations of phylogenomics, biochemistry and genetics in multiple plant lineages and species, I expect to discover new pathways, unknown chemical structures and novel strategies that plants have used to adapt to the blue planet earth. 

Gene Duplication for Innovation

Biosynthetic gene cluster (BGC)

It has been shown until recently that non-homologous genes encoding a full metabolic pathway can be evolved in proximity on genomic loci in plants. Now those genes are called biosynthetic gene clusters (BGCs). A real conundrum that has fascinated me, however, is how and why plants have assembled BGCs in the context of most of other well-known metabolic pathway genes are scattered on genomes.

Biodiversity Protection

Natural compounds often appear in small quantities in plants, most often, in limited lineages and/or species. Medicinal properties of some natural molecules are biomarker of their host plants, but the resulting surge in global demand of these high-value compounds can drive some of the source plants to extinction. There are urgent necessities

bottom of page