Fungal Comparative Genomics Lab

Research Articles

L. Guo, K. S. Allen, G. Deiulio, Y. Zhang, A. M. Madeiras, R. L. Wick and L.-J. Ma* 2016. A De Novo-Assembly Based Data Analysis Pipeline for Plant Obligate Parasite Metatranscriptomic Studies. Frontiers in Plant Science. 7:925. Summplementary fasta data

L. Guo, Zhao G, Xu JR, Kistler HC, Gao L, and L.-J. Ma* 2016. Compartmentalized Gene regulatory networks of a pathogenic fungus Fusarium graminearum. New Phytologist . 211(2):527-41.

L. Guo, Breakspear A, Zhao G, Gao L, Xu J-R, Kistler HC, and L.-J. Ma* 2016. Conservation and divergence of cAMP-PKA pathways in plant pathogenic fungi Fusarium graminearum and F. verticillioides. Molecular Plant Pathology. 17(2):196-209.

Ma* L.-J. D. Geiser, R. H. Proctor, A. P. Rooney, K. O’Donnell, F. Trail, D. M. Gardiner, J. M. Manners, K. Kazan. 2013. Fusarium Pathogenimics. Annual Review of Microbiology. 167: 399-416.

Manning V, …, L.-J. Ma* , L. Ciuffetti*. 2013. Pyrenophora tritici-repentis genome reveals mechanisms that contribute to high genetic variations. G3: Genes, Genomes, Genetics. 3: 41-63.

O’Connell R.J, M.R. Thon, …, L.-J. Ma* , L.J. Vaillancourt*. 2012. Life-style transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nature Genetics. 44: 1060-1065.
***Article recommendations in F1000

Amyotte S. G., X. Tan, K. Pennerman, M. del M. Jimenez, S. J. Klosterman, L.-J. Ma , K. F. Dobinson, P. Veronese. 2012. Transposable elements in the phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification. BMC Genomics. 13: 314.

Klosterman S., K. ….. K. F. Dobinson*, L.-J. Ma*. 2011. Verticillium comparative genomics yields insights into niche adaptation by plant vascular wilt pathogens. PLoS Pathogen. 7(7): e1002137.

Desjardins C.A., et al. 2011. Gao Q. et al. 2011. Comparative Genomic Analysis of Human Fungal Pathogens Causing Paracoccidioidomycosis. PLoS Genet. 7(10): e1002345.

Gao Q. et al. 2011. Genome Sequencing and Comparative Transcriptomics of the Model Entomopathogenic Fungi Metarhizium anisopliae and M. acridum. PLoS Genet. 7(1): e1001264.

Ma L.-J. , H. Charlotte van der Does, et al. 2010. Fusarium comparative genomics reveals lineage-specific chromosomes related to pathogenicity. Nature. 465: 367-373.

Stajich J.E., et al. 2010. Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). PNAS 107:11889-11894.

Kumar L., A. Breakspear, J. Menke, C. Kistler, L.-J. Ma*, X. Xie. 2010. Systematic Discovery of regulatory motifs in Fusarium by comparison of four Fusarium genomes. BMC Genomics 11:208.

Ma L.-J.*, A. S. Ibrahim, C. Skory, M. G. Grabherr, G. Burger, F. Lang, A. Abe, M. Butler, et al. 2009 Genomic analysis of a basal fungus Rhizopus oryzae reveals whole genome duplication. PLoS Genet 5(7): e1000549.

Coleman J.J., et al. 2009. The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genet 5(8): e1000618.

Haas B, et al. 2009. Genome sequence and comparative analysis of the Irish potato famine pathogen Phytophthora infestans.Nature 461: 393-398

Cuomo, C.A., Güldener, U., Xu, J.-R., Trail, F.,Turgeon, B.G., Di Pietro, A.,Walton, J.D., Ma, L.-J, et al 2007. The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science 317: 1400-1402.

Kämper, J. R. Kahmann, M. Bölker, L.-J. Ma et al. 2006 Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 444: 97-101

Rep M., R.G. Duyvesteijn, L. Gale, T. Usgaard, B. J. Cornelissen, L.-J. Ma, T. J. Ward. 2006. The presence of GC-AG introns in Neurospora crassa and other euascomycetes determined from analyses of complete genomes: implications for automated gene prediction. Genomics. Genomics 87(3):338-47

Galagan, J. E., S. E. Calvo, C. Cuomo, L.-J. Ma, et al. 2005 Sequencing and Comparative Analysis of Aspergillus nidulans.Nature 438(7071):1105-15.

Dean R et al. 2005. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature. 434(7036):980-6.Nature434(7036):980-6.

Rogers S.O., V. Theraisnathan, L.-J. Ma, Y. Zhao, G. Zhang, S.G. Shin, J.D. Castello, and W.T. Starmer. 2004 Comparison of protocols to decontaminate environmental ice samples for biological and molecular examinations. Appl. Environ. Microbiol.70: 2540-2544.

Ramussen, J.P., A.H. Taylor, L.-J. Ma, S. Purcell, F. Kempken, and D.E.A. Catcheside. 2004. Guest, A transposable element belonging to the Tc1/Mariner superfamily is an ancient invader of Neurospora genomes. Fungal Genetics and Biology 41:52-61.

Galagan, J.E., S.E. Calvo, K.A. Borkovich, E.U. Selker, N.D. Read, W. FitzHugh, L.-J. Ma, et al. 2003. The Genome Sequence of the Filamentous Fungus Neurospora crassa. Nature 422:859-868.

Ma, L.-J.,C.M. Catranis, W.T. Starmer and S.O. Rogers. 2000. Detection and characterization of ancient fungi entrapped in glacial ice. Mycologia 92:286-295

Ma, L.-J.,., C. M. Catranis, W. T. Starmer and S. O. Rogers. 1999. Revival and characterization of fungi from ancient polar ice. Mycologia 13:70-73

Reviews and Book Chapters

Guo L. and L.-J. Ma*.. 2014. Genomics of wheat pathogen Fusarium graminearum. In: Eds. Dean, R. and Lichens-Park A. Genomics of Plant-associated Fungi and Oomycetes. Springer, Massachusetts, United States. 102-122.

Kistler H.C., Rep M., L.-J. Ma*.. 2013. Structural dynamics of Fusarium genomes In: Fusarium: genomics, molecular and cellular biology. Eds. Brown, D.W. and Proctor, R.H., Horizon Scientific Press, Norwich, United Kingdom. pp31-41.

Ma L.-J, M. Rep and H. C. Kistler. 2012. Evolution of plant pathogenicity in Fusarium species. In Sibley, L. D., B. J. Howlett, et al.. Evolution of virulence in eukaryotic microbes. Hoboken, N.J., Wiley-Blackwell. pp485-500.

Grabherr M.G., Mauceli E., and L.-J. Ma*. Genome Sequencing and Assembly. Methods Mol. Biol. 722 J.-R. Xu and B.H. Bluhm, eds. Methods in Microbiology Vol. 722. 2011. Humana Press, pp1-9.

Ma, L.-J. and Fedorova, N.D. A practical guide to fungal genome projects: strategy, technology, cost and completion. Mycology: An International Journal on Fungal Biology. 2010 Apr 01; 1(1): 9-24. 2010.

Galagan J.E., Henn M.R., Ma, L.-J., Cuomo C.A., Birren B. 2005. Genomics of the fungal kingdom: insights into eukaryotic biology. Genome Res. 15(12):1620-31.

Ma, L.-J.,C. M. Catranis, W. T. Starmer, and S. O. Rogers. 2005. The significance and implications of filamentous fungi in glacial ice. Chapter 11, pp 159-180. In: Castello JD and Rogers SO, Life in Ancient Ice. New Jersey: Princeton University Press.

Rogers SO, L.-J. Ma, Y. Zhao, V. Theraisnathan, G. Zhang, C. Catranis, W.T. Starmer, and J.D. Castello. 2005. Recommendations for elimination of contaminants and authentication of isolates in ancient ice cores. Chapter 2, pp. 5-21. In: Castello JD and Rogers SO, Life in Ancient Ice. Princeton University Press, Princeton, NJ.

Starmer, W. T., J.W. Fell, C.M. Catranis, V. Aberdeen, L.-J. Ma, S. Zhou, and S.O. Rogers. (2005).Yeasts in the genus Rhodotorula recovered from the Greenland ice sheet. Chapter 12, pp. 181-195. In: Castello JD and Rogers SO, Life in Ancient Ice. New Jersey: Princeton University Press.

Back to top