Protect our Life

The rapid detection of microbial pathogens infecting crops or contaminating fresh produces will ensure the mission of protecting our crops and securing our consumed food. I am interested in developing and refining rapidly and highly sensitive Next Generation Sequencing (NGS) metagenomics based assays for detection and quantification of various microorganisms from crops to fresh consumed food. This NGS-based diagnosis tool is a Whole genome culture-independent diagnostic test (WG-CIDT) and the target microorganisms include virus, bacteria, fungus and parasite.

The used sequencing platforms include MinION (Oxford Nanopore Technologies); MiSeq (Illumina), Ion Personal Genome Machine (PGM)/S5 (Thermo Fisher). Furthermore, detection of pathogens from the sequence data is accomplished by mining the data from various sequencing platforms, which is ultimately used for the creation, validation and maintenance of genomics datasets for a highly curated customized database.

Climatic and environmental conditions under which crops are grown may have resulted in the emerging of new diseases. The advanced genetic and statistical methods have facilitated global screening to study new pathogens. Mixed pathogen infection are common in plants and the mixtures of synergistic and antagonistic interactions usually create unpredictable biological and epidemiological consequences. Thus I am interested in using comparative genomics and phylogenetic tools to study the pathogen relatedness and phylogenetic based evolutionary analyses, which is useful for the epidemiology and surveillance of diseases.

Complete genome assemblies of microorganism isolates were obtained from hybrid assembly of both Nanopore long reads and Illumina short reads. Pairwise genome comparison, whole genome alignment and average nucleotide identity analyses will be applied for comparative genomics analysis. Combing other available genome sequences, taxonomy based phylogenetic/phylogenomic studies are useful for the rapid identification and classification and also to understand the relationships between the organisms.

A rapid and systemic virulence evaluation tool for comprehensively assessing the foodborne pathogens is a powerful tool for evaluating large and persistent foodborne outbreaks to ensure food safety. Based on the documented 227 VGs and 80 Salmonella enterica reference genomes, we have developed the sequence-based AmpliSeq_{Salm_227VG} tool that can be used to simultaneously interrogate the presence/absence of 227 VGs of various Salmonella isolates.

One of my future research interest is to expand the AmpliSeq based rapid confirmatory testing and assessing the potential pathogenicity of interested pathogens. It will facilitate the research on identification and application of serovar-specific genome biomarkers using various bioinformatics tools.

In both plant and animal systems, only a small portion of the transcripts encode proteins, whereas a large portion of the transcripts is generally termed non-protein-coding RNAs (ncRNAs). From an RNA-Seq based transcriptomic analysis, I have demonstrated both a protein coding gene WRKY61 and a ncRNAs LINC-AP2 playing crucial roles in regulating Turnip Crinkle Virus infection.

I am very interested in the viruses infecting grapevines, fruit trees and small fruit crops of regulatory concern. Better understanding plant-virus interactions will help developing improved disease management methods and provide foundations for studying virus epidemiology/ecology in the field. It is critical for the building of sustainable, resilient and profitable agricultural systems.