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Li-Jun Ma

Co-PI

Dr. Ma is the PI of the UMass Amherst Ma lab has directed many fungal genome projects and has unparalleled experience in handling genomics data and deep understanding of fungal genome evolution. In addition to her success in fungal comparative genomics, she has directed RNA-seq and transcriptomics projects. Recent research from the Ma lab includes solidified several computational pipelines to assemble genomes, analyze metatranscriptomics data, and reconstruct regulatory networks. With the establishment of these computational capacities, I have applied these tools through the collaboration with Dr. Simon at Rutgers University to identify responsible resistance gene from a Basil Downy Mildew (BDM) resistant cultivar ‘Mirihani’ (MRI) using meta-transcriptomic approaches. Comparative analyses with RNAseq data of resistant line MRI or susceptible line SB22 inoculated with the BDM pathogen Peronospora belbahrii confirmed that the meta-transcriptomics method is effective in differentiating plant and pathogen transcripts out of mixed RNA samples, and powerful in elucidating host-pathogen interactions during the course of infection. The profile of the pathogen transcripts retained a similar pattern among all MRI inoculated samples, reflecting its limited growth. In the contrast, the profiles of the pathogen transcripts continuously increased in SB22 inoculated samples, indicating an increased pathogen pressure in a susceptible host. RNAseq data suggest that P. belbahrii is able to severely block the SA synthesis pathway through downregulating the expression of isochorismate pyruvate lyase (PAL) gene (100-fold decrease in both MRI and SB22). However, the resistant cultivar MRI was able to upregulate the isochorismate synthase (ICS1) gene (20-fold increase) for the SA biosynthesis, rescuing plant defense and resulting in resistance.

 

RELEVANT PUBLICATIONS

  1. Ayhan DH, Martínez-Soto D, Rickelton K, Sohrab V, Kotera S, Arie T, Abbodante S, Marshall ME, Rocha M, Shlezinger N, Pearlman E, and Ma L-J*. 2022. A comprehensive comparison of one plant and one human pathogenic isolates of Fusarium oxysporum. (To be submitted, pdf is availalbe)
  2. Yu H-L, Haridas S, Hayes R, Lynch H, Andersen S, Liu A, Martínez-Soto D, Milo Cochavi S, Ayhan DH, Zhang Y, Grigoriev I, Ma L-J*. 2022, Conservation and Expansion of Transcription Factor Repertoire in the Fusarium oxysporum Species Complex. (To be submitted, pdf is availalbe)
  3. Allen KS, DeIulio GA, Pyne R, Maman J, Guo L, Wick RL, Simon J, Gershenson A, Ma L-J*. 2022, Identification of novel basil downy mildew resistance genes using de novo comparative transcriptomics. MPMI (Submitted pdf is availalbe)
  4. Martínez-Soto D, Yu H-L, Allen KS, Ma L-J*. 2022, Differential colonization of the plant vasculature between endophytic versus pathogenic Fusarium oxysporum MPMI (Submitted pdf is availalbe)
  5. Yu H-L, Ayhan DH, Martínez-Soto D, Milo Cochavi S, Ma L-J*. 2022. Accessory chromosomes of the Fusarium oxysporum species complex and their contribution to host niche adaptation. Springer Book: Plant Relationships – Fungal-Plant Interactions (Accepted)
  6. 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
  7. Yong Zhang, Pei-Lun Kao#, Akaansha Rampal#, Sibongile Mafu, Sergey N. Savinov , and Ma L-J*. 2021. High-throughput screening assays to identify plant natural products with antifungal properties against Fusarium oxysporum. In Jeffery Colman (Eds). Fusarium Wilt, Methods in Molecular Biology, Springer Nature. 
  8. 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.
  9. Viljoen, A., Ma, L.-J., & Molina, A. B. 2020. Fusarium wilt (Panama disease) and monoculture banana production: Resurgence of a century-old disease. In A. Records & J. Ristaino (Eds.), Emerging plant diseases and global food security. St Paul: APS Press.159-184.
  10. Yang H, Yu H, Ma L-J*. Accessory Chromosomes in Fusarium oxysporum. Phytopathology 110:1488-1496. https://doi.org/10.1094/PHYTO-03-20-0069-IA
  11. Yu H‡, Ayhan DH‡, Diener A., Ma L-J*. Genome Sequence of Fusarium oxysporum f. sp. matthiolae, a Brassicaceae Pathogen. Molecular Plant-Microbe Interactions 33(4): 569-572. https://doi.org/10.1094/MPMI-11-19-0324-A
  12. 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*. 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
  13. 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 sp. cubense TR4. New Phytologist 225(2), 913-929. https://doi.org/10.1111/nph.16193
  14. Ma, L-J* and Xu JR. 2019. Shuttling effector genes through mini-chromosomes. PLoS Genet 15(9): e1008345. https://doi.org/10.1371/journal.pgen.1008345
  15. Gao S, Gold SE, Wisecaver JH, Zhang Y‡, Guo L‡, Ma L-J, Rokas A, Glenn AE*. 2019. Genome-wide analysis of Fusarium verticillioides reveals inter-kingdom contribution of horizontal gene transfer to the expansion of metabolism. Fungal Genetics and Biology 128, 60-73.
  16. Milo-Cochavi S, Pareek M, Delulio G‡, Almog Y, Anand G, Ma L-J, Covo S*. 2019. The response to the DNA damaging agent methyl methanesulfonate in a fungal plant pathogen. Fungal Biology 123 (5), 408-422
  17. Anand G, Waiger D, Vital N, Maman J‡, Ma L-J, Covo S*. 2019. How does Fusarium oxysporum sense and respond to nicotinaldehyde, an inhibitor of the NAD+ salvage biosynthesis pathway? Frontiers in Microbiology 10, 329
  18. Zhang Y‡, Guo L‡ and Ma L-J*. A computational protocol to analyze meta-transcriptomic data capturing fungal-host interactions. In Methods in Molecular Biology vol. 1848. Eds: Ma WB and Wolpert T. Springer pp 207-233
  19. Ayhan DH‡, Lpez-Daz C, Di Pietro A, Ma L-J*. Improved assembly of reference genomeFusarium oxysporum f. sp. lycopersici strain Fol4287. Microbiol. Resour. Announc. 7:e00910-18. https://doi.org/10.1128/MRA.00910-18.
  20. Zhao G, Guo L‡, Zhang Y‡, Gao L, and Ma L-J. Identifying TF Binding Motifs from Partial Set of Target Genes and its Application to Regulatory Network Inference, IEEE/ACM Transactions on Computational Biology and Bioinformatics. doi: 10.1109/TCBB.2018.2882377
  21. DeIulio GA‡, Guo L‡, Zhang Y‡, Goldberg JM, Kistler HC, Ma L-J*. Kinome expansion in the Fusarium oxysporum species complex driven by accessary chromosomes. mSphere 13;3(3). pii: e00231-18. doi: 10.1128/mSphere.00231-18.