Person:
Ma, Li-Jun

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Job Title
Assistant Professor, Department of Biochemistry and Molecular Biology
Last Name
Ma
First Name
Li-Jun
Discipline
Biochemistry
Molecular Biology
Expertise
Eukaryotic genome evolution
Fungal comparative genomics
Organism adaptation
Introduction
The focus of my laboratory is to understand genomic plasticity that enables organism niche adaptation using a model fungal system Fusarium oxysporum.
Genomic plasticity contributes directly to the adaptability of an organism to survive in changing environments. My research group studies eukaryotic genome evolution with a focus on understanding the genetic mechanisms that sustain structural and functional flexibility while maintaining the integrity of the organism. F. oxysporum is a highly adaptive species complex that consists of members that cause destructive and intractable wilt diseases across a diverse spectrum of plant hosts, including numerous economically important crops: e.g., cotton, canola, melons, and tomato. During the past two decades, F. oxysporum strains have also emerged as opportunistic pathogens causing life-threatening infections in immunocompromised patients. However, any single pathogenic form exhibits strong host specificity. Comparative genomics demonstrated that horizontal transfer of pathogenicity chromosomes conveys such host-specific pathogenicity (Ma et al, 2010). The pathogenicity chromosomes encoded in each pathogenic form provide a focal point for investigating the genetic mechanisms that underlie pathogenesis and have established F. oxysporum as an effective model to investigate horizontal chromosome transfer in eukaryotes.
Specifically, we will combine the experimental and computational biology approaches to:
study the molecular interactions between the “core genome” and the horizontally transferred chromosomes by probing regulatory network;
investigate the plant-fungal interactions using a Fusarium-Arabidopsis pathosystem; and
optimize management strategies to control the Fusarium diseases.
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  • Publication
    TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data
    (2021-01-01) Sohrab, Vista; López-Díaz, Cristina; Pietro, Antonio Di; Ma, Li-Jun; Ayhan, Dilay Hazal
    Transposable elements (TEs) are mobile elements capable of introducing genetic changes rapidly. Their importance has been documented in many biological processes, such as introducing genetic instability, altering patterns of gene expression, and accelerating genome evolution. Increasing appreciation of TEs has resulted in a growing number of bioinformatics software to identify insertion events. However, the application of existing tools is limited by either narrow-focused design of the package, too many dependencies on other tools, or prior knowledge required as input files that may not be readily available to all users. Here, we reported a simple pipeline, TEfinder, developed for the detection of new TE insertions with minimal software and input file dependencies. The external software requirements are BEDTools, SAMtools, and Picard. Necessary input files include the reference genome sequence in FASTA format, an alignment file from paired-end reads, existing TEs in GTF format, and a text file of TE names. We tested TEfinder among several evolving populations of Fusarium oxysporum generated through a short-term adaptation study. Our results demonstrate that this easy-to-use tool can effectively detect new TE insertion events, making it accessible and practical for TE analysis.