LSL N433


Fungal comparative genomics, eukaryotic genome evolution, and organism adaptation

Background and Training

PhD: State University of New York, the College of Environmental Sciences and Forestry

Postdoc: Harvard University

Research Summary

A dynamic genome with high plasticity contributes directly to the success of the organism to adapt to changing environments.  My lab studies genetic mechanisms that sustain structural and functional flexibility while maintaining the integrity of the organism using the model fungal system Fusarium oxysporum.

F. oxysporum is a highly adaptive species complex that consists of both plant and human pathogens. Collectively, members within this species complex 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 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. F. oxysporum has also been used to study host-pathogen interactions to investigate horizontal chromosome transfer in eukaryotes.

Specifically, my research combines experimental and computational biology approaches to:

  1. Study the molecular interactions within the genome and between the “core genome” and the horizontally transferred chromosomes by reconstructing regulatory network;
  2. Investigate the plant-fungal interactions using a Fusarium-Arabidopsis pathosystem for the development of optimized management strategies to control the Fusarium vascular wilt diseases; and dissect virulence factors that contribute to emerging infectious disease using Fusarium-animal model systems for the development of novel therapeutics.
  3. Dissect virulence factors that contribute to emerging infectious disease using Fusarium-animal model systems for the development of novel therapeutics.


  • Li, G., McWilliams, M., Rodrigues, M., Mearkle, B., Jaafar, N., Golla, V., Yu, H., Yang, H., Ayhan, D. H., Allen, K., Martínez-Soto, D., Springer, A., & Ma, L.-J. (2024). CUR(E)ating a New Approach to Study Fungal Effectors and Enhance Undergraduate Education through Authentic Research. BMB Education . http://doi.org/10.1002/bmb.21783
  • Abbondante S, Leal SM, Clark HL, Ratitong B, Sun Y, Ma LJ, Pearlman E. Immunity to pathogenic fungi in the eye. Semin Immunol. 2023 May;67:101753. doi: 10.1016/j.smim.2023.101753.
  • Yu, H., Yang, H., Haridas, S., Hayes, R. D., Lynch, H., Andersen, S., Li, G., Martínez-Soto, D., Milo-Cochavi, S., Hazal Ayhan, D., Zhang, Y., Grigoriev, I. V., & Ma, L.-J. (2023). Conservation and Expansion of Transcriptional Factor Repertoire in the Fusarium oxysporum Species Complex J. Fungi 2023, 9(3), 359; https://doi.org/10.3390/jof9030359
  • Martínez-Soto D, Yu H-L, Allen KS, Ma L-J*. 2023, Differential colonization of the plant vasculature between endophytic versus pathogenic Fusarium oxysporum strains. Molecular Plant-Microbe Interactions, 36(1), 4–13, https://doi.org/10.1094/MPMI-08-22-0166-SC
  • Li M, Xie L, Wang M, Lin Y, Zhong J, Zhang Y, Zeng J, Kong G, Xi P, Li H, Ma L-J*, Jiang Z*. FoQDE2-dependent milRNA promotes Fusarium oxysporum f. sp. cubense virulence by silencing a glycosyl hydrolase coding gene expression. PLoS Pathog 18, e1010157 (2022).
  • Guo L, Yu, H-L,  Wang B,  Vescio K,  DeIulio GA,  Yang H,  Berg A, Zhang L, Edel-Hermann V, Steinberg C, Kistler HC and Ma L-J**. 2021. Metatranscriptomic comparison of endophytic and pathogenic Fusarium–Arabidopsis interactions reveals plant transcriptional plasticity. MPMI  34, 1071–1083, https://doi.org/10.1094/MPMI-03-21-0063-R
  • Sohrab V#, López-Díaz C, Di Pietro A, Ma LJ, Ayhan DH. TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data. Genes (Basel). 2021. doi: 10.3390/genes12020224. PMID: 33557410.
  • Zhang Y,  He Y, Turra D, Zhou S, Ayhan DH, DeIulio AG, Guo L, Broz K, Wiederhold N, Coleman JJ, O'Donnell K, Youngster I, McAdam AJ, Savinov S, Shea T, Young S, Zeng Q, Rep M, Schwartz DC, Di Pietro A, Kistler HC, Ma L-J*. 2020. The genome of an opportunistic fungal pathogen Fusarium oxysporum carries a unique set of lineage-specific chromosomes. Communication Biology  https://doi.org/10.1038/s42003-020-0770-2
  • Liu S, Lin J, Zhang Y,  Liu N, Viljoen A, Mostert D, Zuo C, Hu C, Bi F, Gao H, Sheng O, Deng G, Yang Q, Dong T, Dou Tongxin, Yi G*, Ma L-J* and Li C*. 2020. Fusaric acid instigates the invasion of banana by Fusarium oxysporum f. sp. cubense TR4. New Phytologist 225(2), 913-929. https://doi.org/10.1111/nph.16193