Horticultural Plant Genomics and Synthetic Biology
Team name
Horticultural Plant Genomics and Synthetic Biology
Principal Investigator
Research Objectives
Plants are natural chemists with the ability to produce a plethora of structurally diverse small molecules with bioactivities, known as natural products. Natural products of horticulture plants such as flowers, herbs and vegetables/fruits are widely enjoyed by human beings as flavors, spices, cosmetics, and medicines, shaping the human civilization and culture. Unfortunately, our use of these bioactive phytochemicals is held back by our lack of knowledge of their biosynthesis, limiting their mass production through bioengineering. Research interest of our group focuses on molecular dissection of biosynthetic pathways (genes, enzymes and regulators) of plant natural products combining genomics, bioinformatics and synthetic biology approach towards improved bioengineering of them in horticulture crops including vegetables, flowers and medicinal herbs. Our lab routinely sequence, assemble and annotate the near-complete or complete genome sequences of high-value horticulture plants and characterize the biosynthetic pathways of valuable natural products using multi-omics integrative analysis and biochemical experiments. We then de novoreconstruct and optimize the complete biochemical pathways of natural products in heterologous host systems including yeasts, E. coli and tobacco plants for fermentation and mass production. As part of an agricultural institute that aims to improve food security and quality, our lab also study the molecular mechanisms underlying interactions between plants and vascular wilt pathogenic fungi, focusing particularly on the secondary metabolites and small secreted proteins that play as virulence factors. Finally, we are also interested in the genome evolution of plants and microbes such as evolution of biosynthetic pathways and enzymes, gene clusters, and centromere repeats and transposable elements that shape the genome architecture, three-dimensional organization of genomes. The mechanisms gained through our fundamental research will be a strong foundation to developing biotechnological innovations to enhance crop growth, resilience and quality that meet the growing demand of stronger and healthier crops in the global climate change.
Team members
Ruidong Chen, Ph.D
Associate Researcher
Email: ruidong.chen@pku-iaas.edu.cn
Research Focus: Synthetic biology of natural products
Education Background:
2011-2014 Marine Biology, South China Sea Institute of Oceanology,Chinese Academy of Sciences (PhD)
2007-2010 Animal Nutrition and Feed Science,Institute of Feed Research of Chinese Academy of Agricultural Sciences(M.S.)
Dilay Hazal Ayhan, Ph.D
Assistant Researcher
Email: dilay.ayhan@pku-iaas.edu.cn
Research Focus: Bioinformatics, comparative genomics and evolution
Education Background:
2015-2021 Ph.D., Molecular and Cellular Biology, University of Massachusetts Amherst
2009-2014 B.S., Biological Sciences and Bioengineering, Sabanci University
Jingyun Jin, Ph.D
Assistant Researcher
Email: jingyun.jin@pku-iaas.edu.cn
Research Focus: Fungal natural product and secondary metabolite gene clusters
Education Background:
2014-2020 Ph.D., Graduate School of Agricultural and Life Sciences, The University of Tokyo
2009-2013 B.S, College of Biotechnology, Tianjin University of Science and Technology
Huan Wang, Ph.D
Assistant Researcher
Email: huan.wang@pku-iaas.edu.cn
Research Focus: Molecular Plant-Microbe Interactions, Fungal secondary metabolites
Education Background:
2014-2021 Ph.D., College of Plant Protection, Northwest Agriculture & Forestry University
2009-2013 B.S., College of Plant Protection, Northwest Agriculture & Forestry University
Weikai Chen, Ph.D
Assistant Researcher
Email: phyllis4yt@cau.edu.cn
Research Focus: Genome assembly, comparative genomics, evolution of metabolic gene clusters
Education Background:
2012-2018 Ph.D., College of Food Science and Nutritional Engineering, China Agricultural University
2008-2012 B.S., College of Food Science and Engineering, Ocean University of China
Changjian Du, Ph.D
Assistant Researcher
Email: changjian.du@pku-iaas.edu.cn
Research Focus: Quantitative genetics and plant breeding, Pangenome, QTL mapping
Education Background:
2020-2023 Ph.D., Chinese Academy of Forestry
2017-2020 M.S., Chinese Academy of Forestry
2012-2016B.S., Binzhou University (B.S.)
Research Projects
Genomics and Bioinformatics of Horticulture Plants
Horticulture plants are vitally important to human society, providing food, nutrients, medicine, aroma and ornament to our everyday life. Mapping the genetic codes of horticulture plants and understanding their functional and regulatory mechanisms are key to developing technologies and products for conservation and utilization of these high-value crops. Our group uses the state-of-the-art genome sequencing and analytical techniques to assemble, annotate and analyze the genomes of major horticulture plants including vegetables, flowers, fruits as well as medicinal herbs. Genomic studies of these plants will provide an essential foundation and resources to improve crops yield, quality and resistance to pests using molecular breeding and modern biotechnologies.
Synthetic Biology of Plant and Fungal Natural Products
Natural products are secondary metabolites produced by plants and microorganisms with diverse chemical structures and pharmaceutical properties used to treat various human diseases. However, most of these natural substances are hard to manufacture chemically given their complex structures and biosynthetic pathways. Using a combination of genomics, transcriptomics and metabolomics data mining, we sought to elucidate the full biosynthetic pathways of important plant and fungal natural products, followed by metabolic engineering of these pathways in heterologous hosts (yeast and tobacco). Alternatively, we study the regulatory mechanisms underlying the biosynthesis in plants and fungi and use the knowledge to guide molecular breeding of plants with high yield of these chemicals using transgenic and genome editing methods.
Research Achievements
Gapless genome assembly of Fusarium verticillioides, a filamentous fungus threatening plant and human health
Fusarium verticillioides is a filamentous fungus that causes plant diseases and harms human health through cancer-inducing mycotoxin and life-threatening Fusariosis. Given its threat to agriculture and public health, genome assembly of this fungus is critical to our understanding of its pathobiology and developing antifungal drugs. Here, we report a gap-free genome assembly of F. verticillioides using PacBio HiFi data and high-throughput chromosome capture (Hi-C) sequencing data. The assembled 42.0 Mb sequence contains eleven gapless chromosomes capturing all centromeres and 19 of all 22 telomeres. This assembly represents a significant improvement over previous version on contiguity, completeness and correctness. A total of 15,230 protein-coding genes were predicted, 6.2% of which are newly annotated genes. In addition, we identified three-dimension chromatin structures such as TADs-like structures and chromatin loops based on Hi-C data of ultra-high coverage. This gap-free genome of F. verticillioides is an excellent resource for further panoramic understanding mechanisms of fungal genome evolution, mycotoxin production and pathogenesis on plant and human host. The study was published by Scientific Data (https://www.nature.com/articles/s41597-023-02145-8).
Mycoviral gene integration converts a phytopathogenic fungus into a biocontrol agent
Mycovirus-mediated hypovirulence is a prime example of multitrophic interactions and has attracted attention for its biocontrol potential. However, direct release of mycovirus-infected fungi is risky due to potential loss of virus overtime, overshadowing its application. Besides, little is known about how hypovirulence is conferred in virus-infected fungi at the molecular level. We have discovered a mycovirus SlAV1 from plant pathogen S. lycopersici, which confers hypovirulence and pigmentation loss by inhibiting fungal biosynthesis of a phytotoxin Altersolanol A. Genomic integration and expression of a key SlAV1 gene in fungal host converts the pathogen into a biocontrol agent and provides enhanced plant resistance against virulent strains. This opens a promising and low-risk path to contain plant diseases via biocontrol. The study was published by PNAS (https://www.pnas.org/doi/10.1073/pnas.2214096119).