• Ecology & Evolution

    Ecology & Evolution

Our research in the area of Ecology and Evolution aims to address several important questions and uses a host of approaches and techniques to achieve this. Most labs use multidisciplinary approaches spanning several areas such as molecular techniques, quantitative methods, GIS, laboratory experimentation on organism development and physiology, population dynamics, genetic analyses as well as satellite imagery.

Jianping Xu
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LSB 437
(905) 525-9140 ext. 27996

Ecology and Evolutionary Genetics of Fungi The overall objective in our research is to understand how fungi evolve. We examine both the patterns of fungal evolution as well as the mechanisms responsible for the observed patterns of evolution. We study fungal populations from the environment, human hosts, clinics, and the laboratory to address a variety of issues such as the rates and effects of spontaneous mutations; the persistence and spread of mutations in natural environments and human populations; and the origins of novel traits, genotypes and species. Our research uses microbiological, molecular, ecological and quantitative genetic tools. Our current research includes the following topics: 1. Population genetics of fungi, including wild mushrooms and human and animal fungal pathogens 2. Fungal mitochondrial DNA variation and inheritance 3. Development of biomarkers for efficient identification of human fungal pathogens. 4. Genetic analyses of quantitative traits in human fungal pathogens.

Ecology & Evolution; Microbiology & Plant Biology

Lifetime Publications

(i) Peer-reviewed

(a) Books:

6. El Sheikha, A., Levin, R. and Xu, J (Editors). (2018) Molecular Techniques in Food Biology. Wiley & Sons, Inc.

5. Xu, J. (Editor) 2014. Next Generation Sequencing: Current Technologies and Applications. Caister Academic Press.

4. Singh, R. S., Xu, J., Kulathinal, R (Editors). 2012. Evolution in the fast lane: rapid evolution of genes and genetic systems. Oxford University Press.

3. Xu, J. (Editor). 2010. Microbial Population Genetics. Horizon Bioscience. UK

2. Xu, J. and Wu, Q. 2006. Essentials of Life Science. 1st Edition. Higher Education Press (Beijing) and Thomson Scientific (Toronto).

1. Xu, J. (Editor). 2005. Evolutionary Genetics of Fungi. Horizon Scientific Press. UK.

(b) Contributions to books:

29. Zhang YJ and Xu J. (2018) Molecular mechanisms of fungal adaptive evolution. In Molecular Mechanisms of Microbial Evolution: Grand Challenges in Biology and Biotechnology (eds. P. H. Rampelotto (ed.) https://doi.org/10.1007/978-3-319-69078-0_15.  Springer Nature, London, UK.

28. Hua W, Al Sheihka A, and Xu J. (2018) Molecular Techniques for Making Recombinant Enzymes Used in Food Processing. In Molecular Techniques in Food Biology (pp. 95-114). Wiley & Sons Limited.

27. Ting, J., R. Xu, and J. Xu (2018). Molecular identification and distribution of yeasts in fruits. In Molecular Techniques in Food Microbiology (pp. 115-144). Wiley & Sons Limited.

26. Dong K, Samarasinghe YAH, Hua W, Kocherry L and Xu J. 2017. Recombinant Enzymes in the Meat Industry and the Regulations of Recombinant Enzymes in Food Processing. Pp. 363-374. In Microbial Enzyme Technology in Food Applications (Editors Drs. Ramesh C. Ray and Cristina M. Rosell). CRC Press, Taylor and Francis Group, Boca Raton, Florida, USA.

25. Samarasinghe YAH, Hua W, Dong K, Kocherry L and Xu J. 2017. Recombinant Enzymes Used in Fruit and Vegetable Juice Industry. Pp. 375-395. In Microbial Enzyme Technology in Food Applications (Editors Drs. Ramesh C. Ray and Cristina M. Rosell). CRC Press, Taylor and Francis Group, Boca Raton, Florida, USA.

24. Ashu, E., Forsythe A, Vogan AA, and Xu J. 2015. Filamentous Fungi in Fermented Foods. In Fermented Foods: Biochemistry and Biotechnology. CRC Press. DOI: 10.1201/b19872-5

23. Xu, J. 2014. Microbial ecology in the age of metagenomics: an introduction. In Encyclopedia of Metagenomics. Springer.

22. Xu, J. (2012) Rapid evolution in experimental populations of all major life forms. In Rapidly Evolving Genes and Genetic Systems (eds. Singh, R. S., Xu, J., Kulathinal, R). Oxford University Press. Pp. 40-52.

21. Idnurm, A and J. Xu. (2012). Experimental and natural evolution in the Cryptococcus neoformans and Cryptococcus gattii species complex. In Evolution of Virulence in Eukaryotic Microbes (eds. David Sibley, Barbara Howlett, Joseph Heitman), Wiley/Blackwell Press, pp. 208-230

20. Litvintseva, A.P., J. Xu, and T. G. Mitchell. (2011) Population Structure and Ecology of Cryptococcus. In Cryptococcus: from human pathogen to model organism. (Editors J. Heitman, J. Kwon-Chung, J. Perfect, A. Casadevall). ASM Press. Pp. 97-112

19. Xu, J., W. Manosuthi, U. Banerjee, L-P Zhu, J.H. Chen, S. Kohno, K. Izumikawa, Y.H. Chen, S. Sungkanuparph, T. S. Harrison, M. Fisher. (2011) Cryptococcosis in Asia. In Cryptococcus: from human pathogen to model organism. (Editors J. Heitman, J. Kwon-Chung, J. Perfect, A. Casadevall). ASM Press. Pp. 287-298

18. Xu, J. (2011) Microbial ecology in the age of metagenomics.  In Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches (Editor Frans J. de Bruijn). Wiley/Blackwell

17. Luo, Y.Q., K. Lin, and J. Xu. (2010) Comparative Microbial Genomics: Analytical Tools, Population Genetic Patterns and Evolutionary Implications. Chapter 2. In Microbial Population Genetics. (Editor J. Xu), Horizon Scientific Press.

16. Eardly, B.D. and J. Xu. (2010) Population Genetics of the Symbiotic Nitrogen-fixing Bacteria Rhizobia. Chapter 5. In Microbial Population Genetics. (Editor J. Xu), Horizon Scientific Press.

15. Xu, J. (2010) Population Genetics in the Age of Metagenomics: Impact on Investigations of Viral, Bacterial, Archaeal and Eukaryotic Microbial Communities Chapter 12. In Microbial Population Genetics. (Editor J. Xu), Horizon Scientific Press.

14. Xu, J. (2009) Metagenomics and ecosystems biology: conceptual frameworks, tools, and methods. In Metagenomics: Theory, Methods and Applications (Editor Diana Marco), Caister Academic Press.

13. Xu, J. (2009) Reproduction and sex in microorganisms. Encyclopedia of Life Supporting Systems. UN-UNESCO.

12. Xu, J. (2008) Using 1-2 individual organisms to address population genetic questions. In Genetic Inheritance Patterns. Nova Publishers.

11. Xu, J. (2007) Origin, evolution and extinction of asexual fungi: experimental tests using Cryptococcus neoformans. Pp. 461-476. In Sex in Fungi. American Society for Microbiology Press.

10. Xu, J., M. Cheng, Q. Tan, and Y. Pan. (2005) Molecular population genetics of basidiomycete fungi. In Evolutionary Genetics of Fungi (J. Xu editor). Horizon Scientific Press, England. Pp. 189-220.

9. Xu, J. (2005) Fundamentals of fungal molecular population genetic analyses. In Evolutionary Genetics of Fungi (J. Xu editor). Horizon Scientific Press, England. Pp. 87-116.

8. Yan, Z. and J. Xu (2005) Fungal mitochondrial inheritance and evolution. In Evolutionary Genetics of Fungi (J. Xu editor). Horizon Scientific Press, England. Pp. 221-252.

7. Xu, J. (2004) Gene Genealogical analyses of human fungal pathogens. Pp.299-318. “Pathogenic Fungi: Structural Biology and Taxonomy" (editors Gioconda San-Blas, Richard Calderone), Horizon Scientific Press.

6. Tey, R., S. Han, Z. Yan, X. Li, K. Lazzazera, S. Sun, and J. Xu. (2003) Genotypic and phenotypic diversities of human pathogenic yeasts. Research Advances in Microbiology. Global Research Network. 3: 67-85.

5. Xu, J. (2003) Molecular population genetics of the commercial mushroom Agaricus bisporus. Research Advances in Microbiology. Global Research Network. 3:35-50

4. Mitchell, T. G. and J. Xu. (2003) Molecular methods to identify pathogenic fungi. Pp.677-702. Pathogenic Fungi in Humans and Animals (2nd Edition). Editor D. H. Howard.  Marcel Dekker, New York.

3. Xu, J. and Mitchell, T. G. 2003. Population genetic analyses of medically important fungi. Pp. 703-722. Pathogenic Fungi in Humans and Animals (2nd Edition). Editor D. H. Howard.  Marcel Dekker, New York.

2. Xu, J. and Mitchell, T. G.  2002. Population genetic analyses of Candida. Pp.55-64.  Chapter 4.  in "Candida and Candidiasis"(3rd edition). Editor R. Calderone, P. Magee, N. Gow, P. Fidel, D. Sanglard, S. Filler, D. Coleman and B. Merz. American Society for Microbiology Press. Washington, D. C.

1. Xu, J. and Mitchell, T. G. 2002. Strain variation and clonality in species of Candida and Cryptococcus neoformans. Pp. 739-750. Chapter 33.  in Fungal Pathogenesis: Principles and Clinical Applications. Editor Richard Calderone and R. L. Cihlar.  Marcel Dekker, Inc., New York, N.Y.

(c) Articles in Peer-Reviewed Journals (*Corresponding author)

300. Wang TH, Lv JL, Xu J, Wang XW, Zhu XQ, Guo LY*. The catalase-peroxidase PiCP1 plays a critical role in abiotic stress resistance, pathogenicity, and asexual structure development in Phytophthora infestans. Environmental Microbiology. (In Press).

299. Hitchcock M, Xu J*. 2022. Analyses of the global multilocus genotypes of the human pathogenic yeast Cryptococcus neoformans species complex. Genes. 13(11), 2045. https://doi.org/10.3390/genes13112045

298. Liu YY, Chen J, Cheng Y, Li Y, Li XW, Zhang ZB, Xu XM, Lin YF, Xu J*, Li ZM*. 2022. A simple and rapid technique of template preparation for PCR. Frontiers in Microbiology. 13:1024827 (doi: 10.3389/fmicb.2022.1024827).

297. Xu J*. 2022. Assessing Global Fungal Threats to Humans. mLife 1(3): 223-240. DOI: 10.1002/mlf2.12036.

296. Chen M, Al-Hatmi AMS, Xu J*, De Hoog SD*. 2022. Molecular epidemiology of fungal infections. Frontiers in Cellular and Infection Microbiology. Pp. 488. DOI 10.3389/978-2-88976-411-2”

295. Guo L, Tang C, Gao C, Li Z, Cheng Y, Chen J, Wang T and Xu J*. 2022. Bacterial and fungal communities within and among geographic samples of the hemp pest Psylliodes attenuata from China. Front Microbiol 13:964735. doi: 10.3389/fmicb.2022.964735

294. Zhao K, Xu J*. (In press). Analyses of genetic diversity reveal major forces impacting a local population of the gourmet mushroom Cantharellus enelensis. Mycosystema (Manuscript ID: 220266).

293. Chen M, Zhu XL, Cong Y, Chen HL, Hou Q, Hong N, Chen XC, Lei WZ, Cai J, Lu XH, Shuai LH, Li XH, Deng SW, Xu J, Liao WQ, Pan WH, Xu HP, de Hoog S. 2022. Genotypic diversity and antifungal susceptibility of Scedosporium species from clinical settings in China. Mycoses 65(12): 1159-1169. http://doi.org/10.1111/myc.13507

292. Wang Y, Xu J*. 2022. Population genomic analyses reveal evidence for limited recombination in the superbug Candida auris in nature. Computational and Structural Biotechnology Journal. 20: 3030-3040. https://doi.org/10.1016/j.csbj.2022.06.030

291. Zhao K, Korfanty GA, Xu J*, Thorn RG*. 2022. Genetic analyses of discrete geographic samples of a golden chanterelle in Canada reveal evidence for recent regional differentiation. Genes. 13(7), 1110; https://doi.org/10.3390/genes13071110

290. Forsythe A, Fontaine N, Bissonnette J, Hayashi B, Insuk C, Ghosh S, Kam G, Wong A, Lausen C*, Xu J*, Cheeptham N*. 2022. Microbial isolates with Anti-Pseudogymnoascus destructans activities from Western Canadian bat wings. Sci Rep 12, 9895 (2022). https://doi.org/10.1038/s41598-022-14223-9

289. Samarasinghe H, Korfanty G, Xu, J*. 2022. Isolation of Culturable Yeasts and Molds from Soils to Investigate Fungal Population Structure. J. Vis. Exp. 183, e63396, doi:10.3791/63396.

288. Yang GZ, Cui S, Ma N, Song YS, Ma J, Huang WJ, Zhang Y*, Xu J*. 2022. Genetic structure and triazole antifungal susceptibilities of Alternaria alternata from Greenhouses in Kunming, China. Microbiology Spectrum. 12: e0038222. doi: 10.1128/spectrum.00382-22. (https://journals.asm.org/doi/10.1128/spectrum.00382-22).

287. He YL, Chen J, Tang C, Deng Q, Guo LT, Cheng Y, Li ZM, Wang TH, Xu J*, Gao CS*. 2022. Genetic diversity and population structure of Fusarium commune causing strawberry root rot in southcentral China. Genes. 13(5):899. https://doi.org/10.3390/genes13050899

286. Li H, Xu J, Wang S, Wang P, Rao W, Hou B, Zhang Y*. Genetic Differentiation and widespread mitochondrial heteroplasmy among geographic populations of the gourmet mushroom Thelephora ganbajun from Yunnan, China. Genes. 2022; 13(5):854. https://doi.org/10.3390/genes13050854

285. Yadav A, Jain K, Wang Y, Pawar K, Kaur H, Sharma K, Tripathy V, Singh A, Xu J*, and Chowdhary A*. 2022. Candida auris on apples: diversity and clinical significance. mBio. 13(2): e00518-22 (https://doi.org/10.1128/mbio.00518-22)

284. Fisher MC, Alastruey-Izquierdo A, Berman J, Bicanic T, Bignell EM, Bowyer P, BromleyM, Brüggemann R, Garber G, Cornely OA, Gurr SJ, Harrison TS, Kuijper E, Rhodes J, Sheppard DC, Warris A, White PL, Xu J, Zwaan B, Verweij PE. 2022. Tackling the emerging threat of antifungal resistance to human health. Nature Reviews Microbiology. 20:557-571. (https://doi.org/10.1038/s41579-022-00720-1)

283. Li PD, Zhu ZR, Zhang YZ, Xu J, Wang HK, Wang ZY, Li HY*. 2022. The phyllosphere microbiome shifts toward combating melanose pathogen. Microbiome 10:56 (https://doi.org/10.1186/s40168-022-01234-x)

282. Xu J. 2022. Origins and spread of plant fungal and oomycete disease outbreaks. Journal of Plant Protection. 49(1): 283-297. DOI: 10.13802/j.cnki.zwbhxb.2022.2022810

281. Li, HD, Wen XY, Deng XL, Wu YH, Xu JP, Li X, Zhu SD, Li XF, Zhu CH, Luo F, Ma YQ, Zheng JY. 2022. Integrated proteomic and metabolomic analyses reveal significant changes in chloroplasts and mitochondria of pepper (Capsicum annuum L.) during Sclerotium rolfsii infection. J Microbiol. 60:511–525. https://doi.org/10.1007/s12275-022-1603-4

280. Liu Y, Chen Z, Li J, Zhu Z, Pang S, Xu J*, Wu J*. 2022. Extensive Diversity and Prevalent Fluconazole Resistance among Environmental Yeasts from Tropical China. Genes. 13(3), 444. https://doi.org/10.3390/genes13030444

279. Gao Q, Yan D*, Song S, Fan YY, Wang SX, Liu Y, Huang Y, Rong CB, Guo Y, Zhao S, Qin WT, Xu J*. 2022. Haplotype-resolved genome analyses reveal genetically distinct nuclei within a commercial cultivar of Lentinula edodes. Journal of Fungi. 8(2), 167; https://doi.org/10.3390/jof8020167.

278. Insuk C, Pongpamorn P, Forsythe A, Matsumoto A, Ōmura S, Pathom-aree W*, Cheeptham N*, Xu J*. 2022. Taxonomic and Metabolite Diversities of Moss-Associated Actinobacteria from Thailand. Metabolites. 12(1), 22. https://doi.org/10.3390/metabo12010022

277. Korfanty GA, Dixon M, Jia H, Yoell H, Xu, J*. 2022. Genetic Diversity and Dispersal of Aspergillus fumigatus in Arctic Soils. Genes. 13: 19. https://doi.org/10.3390/genes13010019

276. Zhong J#, Xu J#, Zhang P*. 2021. Diversity, Dispersal and Mode of Reproduction of Amanita exitialis in Southern China. Genes. 12(12):1907. https://doi.org/10.3390/genes12121907 (#, co-first authors)

275. Qiao M, Zheng H, Guo J-S, F. Castañeda-Ruiz R, Xu J, Peng J, Zhang K-Q, Yu Z-F*. 2021. Two new asexual genera and six new asexual species in the family Microthyriaceae (Dothideomycetes, Ascomycota) from China. MycoKeys 85: 1-30. https://doi.org/10.3897/mycokeys.85.70829

274. Wu G, Miyauchi S, Morin E, Kuo A, Drula E, Varga T, Kohler A, Feng B, Cao Y, Lipzen A, Daum C, Hundley H, Pangilinan J, Johnson J, Barry K, LaButti K, Ng V, Ahrendt S, Min B, Choi IG, Park HJ, Plett J, Magnuson J, Spatafora J, Nagy L, Henrissat B, Grigoriev I, Yang ZL, Xu J, Martin F*. 2021. Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales. New Phytologist. 233 (3), 1383-1400. doi: 10.1111/nph.17858

273. Chen J, Li ZM, Cheng Y, Gao CS, Guo LT, Wang TH, Xu J*. 2021. First report of Pythium aphanidermatum causing crown and root rot on industrial hemp in China. Plant Disease. doi: 10.1094/PDIS-10-21-2134-PDN

272. Xu J*. 2021. Is natural population of Candida tropicalis sexual, parasexual, and/or asexual? Frontiers in Cellular and Infection Microbiology. 11, 1066. https://doi.org/10.3389/fcimb.2021.751676

271. Fan YY, Korfanty KA, Xu J*. 2021. Genetic Analyses of Amphotericin B Susceptibility in Aspergillus fumigatus. Journal of Fungi. 7, 860. https://doi.org/10.3390/jof7100860

270. Zhang S, Bai X, Ren LY, Sun HH, Tang HP, Vaario LM*, Xu J*, Zhang YJ*. 2021. Dynamic Evolution of Eukaryotic Mitochondrial and Nuclear Genomes: A Case Study in the Gourmet Pine Mushroom Tricholoma matsutake. Environmental Microbiology. 23:7214-7230. https://doi.org/10.1111/1462-2920.15792

269. Samarasinghe H, Lu Y, Aljohani R, Al-Amad A, Yoell H, Xu J*. 2021. Global Patterns in Culturable Soil Yeast Diversity. iScience, 24(10): 103098. https://doi.org/10.1016/j.isci.2021.103098.

268. Wang TH, Ji HJ, Yu YT, Wang XJ, Cheng Y, Li ZM, Chen J, Guo LT, Xu J*, Gao CS. 2021. Development of a Loop-Mediated Isothermal Amplification Method for the Rapid Detection of Phytopythium vexans. Frontiers in Microbiology. 12: 2488. https://www.frontiersin.org/article/10.3389/fmicb.2021.720485

267. Xiong T, Zeng Y, Wang W, Li P, Gai Y, Jiao C, Zhu Z, Xu J,* Li H*. 2021. Abundant Genetic Diversity and Extensive Differentiation among Geographic Populations of the Citrus Pathogen Diaporthe citri in Southern China. Journal of Fungi. 7, 749. https://doi.org/10.3390/jof7090749

266. Wang P, Xu J, Wu G, Liu T, Yang ZL*. 2021. Genomic and Experimental Investigations of Auriscalpium and Strobilurus Fungi Reveal New Insights into Pinecone Decomposition. Journal of Fungi. 7(8):679. https://doi.org/10.3390/jof7080679

265. You M, Lin YM, Dobrin A, Xu J*. (2021) Genetic and Phenotypic Diversities in Experimental Populations of Diploid Inter-Lineage Hybrids in the Human Pathogenic Cryptococcus. Microorganisms. 9(8):1579. https://doi.org/10.3390/microorganisms9081579

264. Zhou D, Xu J*, Dong J, Li H, Wang D, Gu J, Zhang K-Q*, Zhang Y*. (2021). Historical Differentiation and Recent Hybridization in Natural Populations of the Nematode-Trapping Fungus Arthrobotrys oligospora in China. Microorganisms. 9(9):1919. https://doi.org/10.3390/microorganisms9091919

263. Chethana KWT, Jayawardena RS, Chen YJ, Konta S, Tibpromma S, Phukhamsakda C, Abeywickrama PD, Samarakoon MC, Senwanna C, Mapook A, Tang X, Gomdola D, Marasinghe DS, Padaruth OD, Balasuriya A, Xu J, Lumyong S, Hyde KD. (2021) Appressorial interactions with host and their evolution. Fungal Diversity. 110: 75–107. http://dx.doi.org/10.1007/s13225-021-00487-5

262. Manawasinghe, I.S., Phillips, A.J.L., Xu, J. Balasuriya A, Hyde KD, Stępień Harischandra DL, Karunarathna A, Yan JY, Weerasinghe J, Luo M, Dong ZY, Cheewangkoon R. (2021). Defining a species in fungal plant pathology: beyond the species level. Fungal Diversity. 109, 267–282. https://doi.org/10.1007/s13225-021-00481-x

261. Liu T, Long X, Zhou J-P, Tian D-W, Yang Y-H, Zou C-G, Xu J, Mo M-H, and Zhang K. (2021) The fungistatic mechanism of ammonia against nematode-trapping fungus Arthrobotrys oligospora, and strategy for it to survive ammonia. mSystems. 6 (5): e00879-21. https://journals.asm.org/doi/10.1128/mSystems.00879-21

260. Huang C, Zhang M, Wu X-L, Wu G, Xu J-P, Yang ZL, Li Y-C (2021) Cyanescent Gyroporus (Gyroporaceae, Boletales) from China. MycoKeys. 81: 165-183. https://doi.org/10.3897/mycokeys.81.65660

259. Zhang Y, Wang SJ, Li HX, Liu CL, Mi F, Wang RR, Mo MZ, and Xu J*. 2021. Evidence for persistent heteroplasmy and ancient recombination in the mitochondrial genomes of the edible yellow chanterelles from Southwestern China and Europe. Frontiers in Microbiology 12:699598. doi: 10.3389/fmicb.2021.699598.

258. Iyengar Y, and Xu J*. 2022. Phenotypic plasticity in the productions of virulence factors within and among serotypes in the Cryptococcus neoformans species complex. Mycopathologia 187: 65–83. 10.1007/s11046-021-00597-3

257. Zheng H, Qiao M, Xu J, and Yu Z*. 2021. Culture-based and culture-independent assessments of endophytic fungal diversity in aquatic plants in Southwest China. Frontiers in Fungal Biology. 2: 27. https://doi.org/10.3389/ffunb.2021.692549

256. Zhou D, Wang R, Li X, Peng B, Yang G, Zhang K, Zhang Y*, Xu J*. 2021. Genetic Diversity and Azole Resistance among Natural Aspergillus fumigatus Populations in Yunnan, China. Microbial Ecology. 83:869–885. https://doi.org/10.1007/s00248-021-01804-w

255. Yamamura D, Xu J*. 2021. Update on Pulmonary Cryptococcosis. Mycopathologia. 186(5): 717-728. https://doi.org/10.1007/s11046-021-00575-9

254. Leong R, Lee T-SJ, Chen Z, Zhang C, Xu J*. 2021. Global Temporal Patterns of Age Group and Sex Distributions of COVID-19. Infectious Disease Reports. 13(2):582-596. https://doi.org/10.3390/idr13020054

253. Archer M, Xu J*. 2021. Current practices for reference gene selection in RT-qPCR of Aspergillus: outlook and recommendations for the future. Genes, 12(7), 960; https://doi.org/10.3390/genes12070960

252. Chethana KWT, Jayawardena RS, Chen Y-J, Konta S, Tibpromma S, Abeywickrama PD, Gomdola D, Balasuriya A, Xu J, Lumyong S, Hyde KD. Diversity and Function of Appressoria. Pathogens. 2021; 10(6):746. https://doi.org/10.3390/pathogens10060746

251. Wu J, Gan C, Li J, Liu Y, Chen Z, Zhang Y, Yi G, Sui J, Xu J*. 2021. Species diversity and antifungal susceptibilities of oral yeasts from patients with head and neck cancer. Infection and Drug Resistance. 2021, 2279—2288 https://doi.org/10.2147/IDR.S316368

250. Fan Y, Wang Y, Korfanty GA, Archer M, Xu J*. 2021. Genome-Wide Association Analysis for Triazole Resistance in Aspergillus fumigatus. Pathogens. 10, 701. https://doi.org/10.3390/pathogens10060701

249. Hong N, Chen M, Xu J*. 2021. Molecular markers reveal epidemiological patterns and evolutionary histories of the human pathogenic CryptococcusFrontiers in Cellular and Infection Microbiology. 11: 398. (https://doi.org/10.3389/fcimb.2021.683670)

248. You M, Xu J*. 2021. What Are the Best Parents for Hybrid Progeny? An Investigation into the Human Pathogenic Fungus Cryptococcus. Journal of Fungi. 7(4): 299. https://doi.org/10.3390/jof7040299

247. Zhang Y, Mo MZ, Yang L, Mi F, Cao Y, Liu CL, Tang XZ, Wang PF, and Xu J*. 2021. Exploring the Species Diversity of Edible Mushrooms in Yunnan, Southwestern China by DNA Barcoding. Journal of Fungi. 7(4): 310. https://doi.org/10.3390/jof7040310.

246. Forsythe A, Vanderwolf KJ, and Xu J*. 2021. Landscape Genetic Connectivity and Evidence for Recombination in the North American Population of the White-Nose Syndrome Pathogen, Pseudogymnoascus destructans. Journal of Fungi. 2021, 7(3), 182. https://doi.org/10.3390/jof7030182

245. Fang DZ, Chen J, Cheng Y, Li ZM, Guo LT, Wang TH, Deng Q, Xu J*, Gao CS*. 2021. First report of Fusarium fujikuroi causing bulb rot on Lilium lancifolium in China. Plant Disease. https://doi.org/10.1094/PDIS-06-20-1197-PDN

244. Zhai Y, Zhu JX, Tan TM, Xu J, Shen AR, Yang XB, Li JL, Zeng LB*, Wei L. 2021. Isolation and characterization of antagonistic Paenibacillus polymyxa HX-140 and its biocontrol potential against Fusarium wilt of cucumber seedlings. BMC Microbiology. 21, 75. https://doi.org/10.1186/s12866-021-02131-3

243. Arora P, Singh P, Wang Y, Yadav A, Pawar K, Singh A, Padmavati G, Xu J, and Chowdhary A*. 2021. Environmental isolation of Candida auris from the coastal wetlands of Andaman Islands, India. mBio. 12:e03181-20. https://doi.org/10.1128/mBio.03181-20).

242. Pang ZQ, Chen J, Wang TH, Gao CS, Li ZM, Guo LT, Xu J*, and Cheng Y*. 2021. Linking Plant Secondary Metabolites and Plant Microbiomes: A Review. Frontiers in Plant Science. 12: 300; (DOI=10.3389/fpls.2021.621276)

241. Zhou DY, Korfanty G, Mo MZ, Wang RR, Li X, Li HX, Li SS, Wu JY, Zhang KQ, Zhang Y*, and Xu J*. 2021. Extensive Genetic Diversity and Widespread Azole Resistance in Greenhouse Populations of Aspergillus fumigatus in Yunnan, China. mSphere. 6:e00066-21. https://doi.org/10.1128/mSphere.00066-21.

240. Yadav A, Singh A, Wang Y, van Haren M, Singh A, de Groot T, Meis JF, Xu J, Chowdhary A*. 2021. Colonisation and transmission dynamics of Candida auris among chronic respiratory diseases patients hospitalised in a Chest hospital, Delhi, India: A comparative analysis of whole genome sequencing and microsatellite typing. Journal of Fungi. 2021, 7, 81. https://doi.org/10.3390/ jof7020081

239. Morin E, Murat C, Cichocki N, De la Varga H, Kohler A, Xu J, Grigoriev IV, Martin FM. 2021. The draft genomes of the black truffles Tuber brumale Vittad. and Tuber indicum Cook & Massee. Microbiology Resource Announcements. 10: e00799-20. https://doi.org/10.1128/MRA.00799-20.2

238. Liang LM*, Zhang Y, Xu J, Zhang KQ & Cao YR*. 2021. Characterization of the complete mitochondrial genome of the nematophagous fungus Purpureocillium lavendulum. Mitochondrial DNA Part B, 6:1, 33-35, DOI:10.1080/23802359.2020.1846000

237. Korfanty G, Stanley K, Lammers K, Fan YY, Xu J*. 2021. Variations in Sexual Fitness among Natural Strains of the Opportunistic Human Fungal Pathogen Aspergillus fumigatus. Infection, Genetics, Evolution. 87: 104640. https://doi.org/10.1016/j.meegid.2020.104640.

236. Zeng Y, Xiong T, Liu B, Carstens E, Chen X, Xu J*, Li H*. 2021. Genetic Diversity and Population Structure of Phyllosticta citriasiana in China. Phytopathology. 111: 850-861. https://doi.org/10.1094/PHYTO-12-18-0451-R

235. Xu Y, Chen M, Zhu J, Gerrits van den Ende B, Chen AJ, Al-Hatmi AMS, Li L, Zhang Q, Xu J, Liao W, Chen Y. 2020. Aspergillus Species in Lower Respiratory Tract of Hospitalized Patients from Shanghai, China: Species Diversity and Emerging Azole Resistance. Infect Drug Resist. 13:4663-4672. https://doi.org/10.2147/IDR.S281288

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151. Forsythe A*, Xu J. (2017). The complete mitochondrial genome sequence of the White-Nose Syndrome pathogen, Pseudogymnoascus destructans. Mitochondrial DNA Part B: Resources. http://dx.doi.org/10.1080/23802359.2017.1280706

150. El Sheikha AF*, Xu J. (2017). Traceability as a Key of Seafood Safety: Reassessment and Possible Applications. Reviews In Fisheries Science & Aquaculture. 25(2): 158-170. (http://dx.doi.org/10.1080/23308249.2016.1254158)

149. Feng B, Liu JW, Xu J, Zhao K, Ge ZW, and Yang ZL. (2016) Ecological and physical barriers shape genetic structure of the Alpine porcini (Boletus reticuloceps). Mycorrhiza. 27 (3), 261-272. DOI: 10.1007/s00572-016-0751-y

148. Xu J, Li H, Zhou GY, Liu JA. (2016). When do we call genetically distinct strains different species? - A cautionary case study of the Colletotrichum gloesporioides species complex. Fungal Genomics and Biology. 6, 146. DOI: 10.4172/2165-8056.1000146

147. Wu G, Li YC, Zhu XT, Zhao K, Han LH, Cui YY, Li F, Xu J, Yang ZL. 2016. One hundred noteworthy boletes from China. Fungal Diversity. 81: 25-188. DOI: 10.1007/s13225-016-0375-8

146. Forsythe A, Vogan AA, Xu J*. 2016. Genetic and environmental influences on the germination of basidiospores in the Cryptococcus neoformans species complex. Scientific Reports 6:33828. doi: 10.1038/srep33828.

145. Fang W, Chen M*, Liu J, Hagen F, Al-Hatmi MA, Zhang P, Guo Y, Boekhout T, Deng D, Xu J, Pan W, Liao W. 2016. Cryptococcal meningitis in systemic lupus erythematosus patients: pooled analysis and systematic review. Emerg Microbes Infect. 5(9):e95. doi: 10.1038/emi.2016.93.

144. Wang NN, Zhang YJ, Jiang X, Shu C, Hamid MI, Hussain M, Chen S, Xu J, Xiang MC*, Liu XZ. 2016. Population genetics analyses of Hirsutella rhossiliensis, a dominant parasite of cyst nematode juveniles at a continental scale. Applied and Environmental Microbiology. 82(21):6317-6325. DOI: 10.1128/AEM.01708-16

143. Wang MS, Sun XP, Yu DL, Xu J, Chung KR, Li HY*. 2016. Genomic and transcriptomic analyses of the tangerine pathotype of Alternaria alternata in response to oxidative stress. Scientific Reports 6:32437. doi: 10.1038/srep32437

142. Xu J. 2016. Fungal DNA Barcoding. Genome 59(11):913-932. DOI: 10.1139/gen-2016-0046

141. Yang R, Li Y, Li C, Xu J, Bao D*. (2016) The complete mitochondrial genome of the Basidiomycete edible fungus Pleurotus eryngii, Mitochondrial DNA Part B, 1:1, 772-774, DOI: 10.1080/23802359.2016.1238755

140. Chen M, Al-Hatmi AM, Chen Y, Ying Y, Fang W, Xu J, Hagen F, Hong N, Boekhout T, Liao W, Pan W*. 2016. Cryptococcosis and tuberculosis co-infection in mainland China. Emerg Microbes Infect. 5(9):e98. doi: 10.1038/emi.2016.95.

139. Li H, Zhou G-Y, Liu J-A, Xu J* 2016. Population genetic analyses of the fungal pathogen Colletotrichum fructicola on tea-oil trees in China. PLoS ONE 11(6): e0156841. doi:10.1371/journal.pone.0156841

138. Vogan AA, Khankhet J, Samarasinghe H, Xu J*. 2016. Identification of QTLs Associated with Virulence Related Traits and Drug Resistance in Cryptococcus neoformans. G3: Genes, Genomes, Genetics. 6(9): 2745-2759 doi:10.1534/g3.116.029595

137. Chen J, Moinard M, Xu J, Wang S, Foulongne-Oriol M, Zhao R, Hyde KD, Callac P*. (2016) Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus subrufescens. PLoS ONE 11(5): e0156250. doi:10.1371/journal.pone.0156250

136. Chang H, Ashu E, Sharma C, Kathuria S, Chowdhary A, Xu J*. 2016. Diversity and origins of Indian multi-triazole resistant strains of Aspergillus fumigatus. Mycoses. 59: 450–466. doi: 10.1111/myc.12494

135. Chen M, Zhou J, Li J, Li M, Sun J, Fang WJ, Al-Hatmi AM, Xu J, Boekhout T, Liao WQ, Pan WH*. 2016. Evaluation of five conventional and molecular approaches for diagnosis of cryptococcal meningitis in non-HIV-infected patients. Mycoses. 59(8):494-502. doi: 10.1111/myc.12497.

134. Feng B, Zhao Q, Xu J, Qin J, Yang ZL*. 2016. Drainage isolation and climate change-driven population expansion shape the genetic structures of Tuber indicum complex in the Hengduan Mountains region. Sci Rep. 6:21811. doi: 10.1038/srep21811.

133. Du XH, Zhao Q, Xu J, Yang ZL*. 2016. High inbreeding, limited recombination and divergent evolutionary patterns between two sympatric morel species in China. Sci Rep. 6:22434. doi: 10.1038/srep22434

132. Mi F, Zhang Y, Yang D, Tang X, Wang P, He X, Zhang Y, Dong J, Cao Y, Liu C, Zhang KQ, Xu J*. 2016. Evidence for Inbreeding and Genetic Differentiation among Geographic Populations of the Saprophytic Mushroom Trogia venenata from Southwestern China. PLoS One. 11(2):e0149507. doi: 10.1371/journal.pone.0149507

131. Xu J*, Wang PF. 2015. Mitochondrial inheritance in basidiomycete fungi. Fungal Biology Reviews. 29(3–4): 209-219 http://dx.doi.org/10.1016/j.fbr.2015.02.001

130. Ashu E, Xu J*. 2015. The roles of sexual and asexual reproduction in the origin and dissemination of strains causing fungal infectious disease outbreaks. Infection, Genetics and Evolution. 36: 199–209

129. Li J, Zou C, Xu J, Ji X, Niu X, Yang J, Huang X, Zhang KQ*. 2015. Molecular mechanisms of nematode-nematophagous microbe interactions: basis for biological control of plant-parasitic nematodes. Annu Rev Phytopathol. 53:67-95

128. Wang PF, Zhang Y, Mi F, Tang XZ, He XX, Cao Y, Liu CL, Yang D, Dong JY, Zhang KQ & Xu J*. 2015. Recent advances in population genetics of ectomycorrhizal mushrooms Russula spp. Mycology 6(2): 110-120

127. Tang XZ, Mi F, Zhang Y, He XX, Cao Y, Wang PF, Liu CL, Yang D, Dong JY, Zhang KQ, Xu J*. 2015. Diversity, population genetics, and evolution of macrofungi associated with animals. Mycology 6(2): 94-109; DOI:10.1080/21501203.2015.1043968

126. Zhang P*, Tang L-P, Cai Q and Xu J. 2015. A review on the diversity, phylogeography and population genetics of Amanita mushrooms. Mycology 6 (2): 86-93

125. Xu J*, Li H. 2015. Current perspectives on mitochondrial inheritance in fungi. Cell Health and Cytoskeleton. 7: 143—154

124. Cao Y, Zhang Y, Yu Z, Wang P, Tang X, He X, Mi F, Liu C, Yang D, Xu J*. 2015. Genome Sequence of Phlebopus portentosus Strain PP33, a cultivated Bolete. Genome Announc. 23;3(2). pii: e00326-15. doi: 10.1128/genomeA.00326-15.

123. Cui YY, Feng B, Wu G, Xu J, Yang ZL*. 2015. Porcini mushrooms (Boletus sect. Boletus) from China. Fungal Diversity 81(1): 189–212; DOI:10.1007/s13225-015-0336-7

122. Zhang Y, Zhang S, Zhang G, Liu X, Wang C, Xu J*. 2015. Comparison of mitochondrial genomes provides insights into intron dynamics and evolution in the caterpillar fungus Cordyceps militaris. Fungal Genet Biol. 77:95-107.

121. Wang ZX, Wilson A, Xu J*. 2015. Mitochondrial DNA Inheritance in the Human Fungal Pathogen Cryptococcus gattii. Fungal Genet Biol. 75:1-10.

120. Diao YZ, Zhang C, Xu J, Lin D, Liu L, Mtung'e OG, Liu XL* 2015. Genetic differentiation and recombination among geographic populations of the fungal pathogen Colletotrichum truncatum from chili peppers in China. Evolutionary Applications. 8(1):108-118 (DOI: 10.1111/eva.12233)

119. Wang X, Li GH, Zou CG, Ji XL, Liu T, Zhao PJ, Liang LM, Xu J, An ZQ, Zheng X, Qin YK, Tian MQ, Xu YY, Ma YC, Yu ZF, Huang XW, Liu SQ, Niu XM, Yang JK, Huang Y, and Zhang KQ*. (2014) Bacteria can mobilize nematode-trapping fungi to kill nematodes. Nature Communications. 5:5776 doi: 10.1038/ncomms6776.

118. Zhang YJ, Zhang S, Li YL, Ma SL, Wang CS, Xiang MC, Liu X, An ZQ, Xu J*, and Liu XZ*. 2014. Phylogeography and evolution of a fungal-insect association on the Tibetan Plateau. Molecular Ecology. 23: 5337-5355 (onlinelibrary.wiley.com/doi/10.1111/mec.12940/abstract

117. Vogan AA and Xu J.* 2014. Evidence for genetic incompatibilities associated with post-zygotic reproductive isolation in the human fungal pathogen Cryptococcus neoformans. Genome 57: 335–344 (dx.doi.org/10.1139/gen-2014-0077)

116. Schoch CL et al. 2014. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi. Database 2014, bau061.

115. Khankhet J, Vanderwolf KJ, McAlpine DF, McBurney S, Overy DP, Slavic D, and Xu J.* 2014. Clonal expansion of the Pseudogymnoascus destructans genotype in North America is accompanied by significant variation in phenotypic expression. PLOS ONE 9(8): e104684 (DOI: 10.1371/journal.pone.0104684)

114. Xu J. 2014. Genomics and Fungal Speciation: What Can We Expect in the Clinical Laboratory? Current Clinical Microbiology Reports. Doi: 10.1007/s40588-014-0004-9 (Invited Review)

113. Sharma C, Muralidhar S, Xu J, Meis J, and Chowdhary A. (2014) Multilocus sequence typing of Candida africana from patients with vulvovaginal candidiasis in New Delhi, India. Mycoses, doi: 10.1111/myc.12193.

112. Wu JY, Guo H, Yi GH, Zhou LM, He XW, Huang XX, Wang HM, Xue WL & Xu J* (2014) Prevalent drug resistance among oral yeasts from asymptomatic patients in Hainan, China. Mycopathologia. 177, 299-307

111. Wu G, Feng B, Xu J, Zhu XT, Li YC, Zeng NK, Hosen MI, Yang ZL. (2014) Molecular phylogenetic analyses redefine seven major clades and reveal 22 new generic clades in the fungal family Boletaceae. Fungal Diversity. DOI 10.1007/s13225-014-0283-8

110. Venu I, Durisko Z, Xu J and Dukas R. (2014). Social attraction mediated by fruit flies’ microbiome. J. Exp. Biol. 217, 1346-1352. (Highlighted by Nature)

109. Chen SX, Wang CM, Xu J, and Yang ZL. (2014) Molecular characterization of pHRDV1, a new virus-like mobile genetic element closely related to pleomorphic viruses in haloarchaea. Extremophiles. 18:195-206. DOI 10.1007/s00792-013-0599-4

108. Carvalho, C., Yang, J., Vogan, A., Maganti H, Yamamura, D., and Xu J*. 2014. Clinical and Tree Hollow Populations of Human Pathogenic Yeasts in Hamilton, Ontario, Canada Are Different. Mycoses. 57(5):271-283. Doi:10.1111/myc.12156

107. Cao, Y., Zhang, Y., Yu, Z., Mi, F., Liu, C., Tang, X., Long, Y., He, X., Wang, P., and Xu, J*. 2013. Structure, Gene Flow, and Recombination among Geographic Populations of a Russula virescens Ally from Southwestern China. PLoS ONE 8(9): e73174. doi:10.1371/journal.pone.0073174

106. Wang, H., Xu, J., Guo, H., Wu, J., Yi, G., Pei, H., Niu, L., Li, Y. 2013. Patterns of human oral yeast species distribution on Hainan Island in China. Mycopathologia. 176:359-368. Online version: http://dx.doi.org/10.1007/s11046-013-9703-7

105. Chowdhary A, Kathuria S, Xu J, Meis JF. 2013. Emergence of Azole Resistant Aspergillus fumigatus Strains due to Agricultural Azole Use Creates an Increasing Threat to Human Health. PLoS Pathogen 9(10): e1003633. doi:10.1371/journal.ppat.1003633.

104. Zhang S, Zhang YJ, Bhushan S, Xu JP, Wang CS, Liu XZ. 2013. Ophiocordyceps sinensis and Cordyceps militaris: research advances, issues and perspectives. Mycosystema. 32 (4), 577-597

103. Zhang Y, Zhang K, Cao Y, Qiao M, Xu J, and Yu Z. 2013. Genetic diversity and recombination in natural populations of the nematode-trapping fungus Arthrobotrys oligospora from China. Ecology and Evolution 3(2):312-325

102. Vogan A, Khankhet J, Xu J* 2013. Evidence for Mitotic Recombination within the Basidia of a Hybrid Cross of Cryptococcus neoformans. PLoS ONE: 8(5): e62790. doi:10.1371/journal.pone.0062790

101. Chang H, Pun N, Xu J*. 2013. Attractions of nematodes to yeasts are influenced by both nematodes and yeasts. Mycology. 4(2): 73-81. DOI:10.1080/21501203.2013.798698

100. Ferandon C, Xu J, Barroso G*. 2013. The 135 kbp mitochondrial genome of Agaricus bisporus is the largest known eukaryotic reservoir of group I introns and plasmid-related sequences. Fungal Genetics and Biology. 55: 85–91

99. Xu J*, Zhang Y, and Pun N. 2013. Mitochondrial recombination in natural populations of the button mushroom Agaricus bisporus. Fungal Genetics and Biology. 55: 92–97

98. Chowdhary A, Kathuria S, Xu J, Sharma C, Sundar G, Singh PK, Gaur SN, Hagen F, Klaassen CH, Meis JF*. 2012. Clonal expansion and emergence of environmental multiple-triazole-resistant Aspergillus fumigatus strains carrying the TR34/L98H mutations in the cyp51A gene in India. PLoS ONE 7(12): e52871. doi:10.1371/journal.pone.0052871

97. Zhang Y., Y. Li, G. Wu, B. Feng, S. Yoell, Z. Yu, K. Zhang and J. Xu*. 2012. Evidence Against Barium in the Mushroom Trogia venenata as a Cause of the Yunnan Sudden Unexpected Deaths. Applied and Environmental Microbiology. 78 (24): 8834-8835

96. Morin E, Annegret Kohler, Adam Baker, Marie Foulogne-Oriol, Vincent Lombard, Robin A Ohm, Aleksandrina Patyshakuliyeva, Annick Brun, Andrea Aerts, Andrew M Bailey, Christophe Billette, Pedro M Coutinho, Harshavardhan Doddapaneni, Jane Grimwood, Kristiina Hilden, Ursula Kuees, Kurt M. LaButti, Alla Lapidus, Erika A Lindquist, Susan M Lucas, Taina Lundell, Claude Murat, Robert Riley, Asaf A. Salamov, Jeremy Schmutz, Venkataramanan Subramanian, Han A.B. Wosten, Jianping Xu, Daniel Eastwood, Gary D Foster, Anton SM Sonnenberg, Dan Cullen, Ronald P de Vries, Bernard Henrissat, Kerry Burton, Rick W Kerrigan, Mike P Challen, Igor V. Grigoriev, Francis M. Martin*. 2012. Genome sequence of the Button Mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche”. Proc Natl Acad Sci (USA). 109 (43): 17501-17506.

95. Feng B, Xu J, Wu G, Zeng N-K, Li Y-C, Tolgor B, Kost GW, Yang Z-L*. 2012. DNA sequence analyses reveal abundant diversity, endemism and evidence for Asian origin of the Porcini mushrooms. PLoS ONE 7(5): e37567. doi:10.1371/journal.pone.0037567

94. Wilson, A. J, Xu J*. 2012. Mitochondrial inheritance: diverse patterns and mechanisms with an emphasis on fungi. Mycology. 3: 158-166

93. Xu J*, Yoell H. 2012. Onychomycosis: an overview with a focus on diagnosis. Experimental and Laboratory Medicine. 30:111-118

92. Schoch CL*, and the Fungal Barcode Consortium (one of ~100 collaborators). 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci (USA). 109:6241-6246

91. Zhang, Y., Yu, Z.-F., Xu, J., and Zhang, K-Q*. 2012. Divergence and dispersal of the nematode-trapping fungus Arthrobotrys oligospora from China. Environmental Microbiology Report 3:763-773.

90. Maganti, H*, D. Bartfai, J. Xu. 2012. Ecological structuring of yeasts associated with trees around Hamilton, Ontario, Canada. FEMS Yeast Research 12:9-19

89. Ge S-H., J. Xie, J. Xu; J. Li; D-M Li, L-L Zong; Y-C Zheng, F-Y Bai*. 2012. Prevalence of specific and phylogenetically closely related genotypes in the population of Candida albicans associated with genital candidiasis in China. Fungal Genetics and Biology. 49(1):86-93

88. Ma, H-C., J-R. Wu, X. Zeng, D. Zhang, Z. Xiong, and J. Xu*. 2012. Diversity and stress-tolerance of symbiotic nitrogen-fixing bacteria from legumes in the Dry-Hot Valleys of southwest China. African Journal of Microbiology Research. 6:1675-1684

87. Yang, J., L. Wang, X. Ji, Y. Feng, X. Li, C. Zou, J. Xu, Y. Ren, Q. Mi, J. Wu, S. Liu, Y. Liu, X. Huang, H. Wang, X. Niu, J. Li, L. Liang, Y. Luo, K. Ji, W. Zhou, Z. Yu, G. Li, Y. Liu, L. Li, M. Qiao, L. Feng, and K. Zhang*. 2011. Genomic and proteomic analyses of the fungus Arthrobotrys oligospora provide insights into nematode-trap formation. PLoS Pathogen 7(9): e1002179. doi:10.1371/journal.ppat.1002179

86. Chowdhary A, S.S. Hiremath, S. Sun, T. Kowshiki, H.S. Randhawa, and J. Xu*. 2011. Genetic differentiation, recombination and clonal expansion in environmental populations of Cryptococcus gattii in India. Environmental Microbiology 13(7):1875-88. doi: 10.1111/j.1462-2920.2011.02510.x

85. Chowdhary, A.*, H. S. Randhawa, G. Sundar, S. Kathuria, A. Prakash, Z. U. Khan, S. SUN & J. Xu. 2011. In vitro antifungal susceptibility profiles and genotypes of 308 clinical and environmental isolates of Cryptococcus neoformans var. grubii and Cryptococcus gattii serotype B from north-western India. Journal of Medical Microbiology 60:961-967.

84. Rajkumar S.S., R.J. Rudd, J.C. Okoniewski, J. Xu, S. Chaturvedi, and V. Chaturvedi*. 2011. Dispersal of a single, clonal genotype of Geomyces destructans among New York bats with geomycosis (White Nose Syndrome). Emerging Infectious Diseases http://www.cdc.gov/EID/content/17/7/1273.htm; DOI: 10.3201/eid1707.102056

83. Maganti H, D. Yamamura, and J. Xu*. 2011. Prevalent nosocomial clusters among causative agents for candidemia in Hamilton, Canada. Medical Mycology 49(5):530-538. DOI:10.3109/13693786.2010.547880

82. Cao CW, Liang L*, Wang WJ, Luo H, Huang SB, Liu DH, Xu J, Henk DA, Fisher MC. 2011. Common reservoirs for Penicillium marneffei infection in humans and rodents, China. Emerging Infectious Diseases 17:209-214.

81. Randhawa, H. S.*, T. Kowshik, A. Chowdhary, K. Preeti Sinha, Z. U. Khan, J. Xu. 2011. Seasonal variations in prevalence of Cryptococcus neoformans var. grubii and Cryptococcus gattii in decayed wood inside trunk hollows of diverse tree species in north- western India: a retrospective study. Medical Mycology 49:320-323

80. Qiao M, Zhang Y, Li SF, Baral H.-O., Weber E., Su HY, Xu J, Zhang KQ, Yu ZF. 2012. Orbilia blumenaviensis and its Arthrobotrys anamorph. Mycological Progress. 11: 255–262. DOI: 10.1007/s11557-011-0744-3.

79. Qin L, Qiao M, Yang Y, Yang GZ, Lu KP, Zhang KQ, Xu J, Yu ZF. 2010. Dactylella pseudobrevistipitata, a new species from China. Annals of Microbiology. On line: DOI: 10.1007/s13213-010-0177-2.

78. Niu, QH, Huang XW, Zhang L, Xu J, Yang DM, Wei KB, Niu XM, An ZQ, Bennett JW, Zou CG, Yang JK, and Zhang KQ*. 2010. A Trojan horse mechanism of bacterial pathogenesis against nematodes. PNAS 107: 16631–16636. Published online 2010 August 23. doi: 10.1073/pnas.1007276107 (www.pnas.org/cgi/doi/10.1073/pnas.1007276107)

77. Li MC, Liang JF, Li YC, Feng B, Yang ZL, James TY, and Xu J*. 2010. Genetic diversity of Dahongjun, the commercially important "Big Red Mushroom" from southern China. PLoS ONE 5(5): e10684. doi:10.1371/journal.pone.0010684

76. Nayak R* and Xu J. 2010. Effects of sertraline hydrochloride and fluconazole combinations on Cryptococcus neoformans and Cryptococcus gattii. Mycology 1: 99-105

75. Ge SH, Wan Z, Li J, Xu J, Li RY, and Bai FY*. 2010. Correlation between Azole Susceptibilities, Genotypes and ERG11 Mutations in Candida albicans Isolates Associated with Vulvovaginal Candidiasis in China. Antimicrobial Agents and Chemotherapy 54:3126-3131

74. Fan JY, Guo LY*, Xu J, Luo Y, Michailides TJ. 2010. Genetic Diversity of Populations of Monilinia fructicola (Fungi, Ascomycota, Helotiales) from China. J Eukaryotic Microbiology 57: 206-212.

73. Liang, J. F., Yang, Z. L.*, Xu J and Z-W Ge. 2010. Two new unusual Leucoagaricus species (Agaricaceae) from tropical China with blue-green staining reactions. Mycologia 102: 1141-1152

72. Wu, J. R., H.C. Ma,M. LÜ, S.F. Han, Y.Y. Zhu, H. Jin, J.F. Liang, L. Liu, and J. Xu*. 2010.  Rhizoctonia fungi enhance the growth of the endangered orchid Cymbidium goeringii. Botany 88: 20-29

71. Skosireva, I., T. Y. James, S. Sun, and J. Xu*. 2010. Mitochondrial inheritance in haploid x non-haploid crosses in Cryptococcus neoformans. Current Genetics 56:163-176

70. Xu, J.*, Cadorin, M., Liang, Y-J, and Yang, Z.L.. 2010. DNA-based geographical typing of the gourmet mushroom Tricholoma matsutake traded in China. Mycoscience 51:248–251. DOI 10.1007/s10267-009-0024-0)

69. Wang, Q.M.. J. Xu, H.M. Wang, J. Li, F.Y. Bai*. 2009. Torulaspora quercuum sp. nov. and Candida pseudohumilis sp. nov., novel yeasts from human and forest habitats. FEMS Yeast Research 9:1322-1326

68. Guo, H., S. Sun, B. Eardly, T. Finan, and J. Xu*, 2009. Genome variation in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti. Genome 52:862-875

67. Liang*, J. F., J. Xu, and Z. L. Yang. 2009. Divergence, dispersal and recombination in Lepiota cristata from China. Fungal Diversity 38:105–124

66. Xu, J*., Z. Yan, and H. Guo. 2009. Divergence, hybridization, and recombination in the mitochondrial genome of the human pathogenic yeast Cryptococcus gattii. Molecular Ecology 18: 2628-2642

65. Li, M. and Xu, J*. 2009. Molecular ecology of ectomycorrhizal fungi: molecular markers, genets and ecological importance. Acta Botanica Yunnanica 31: 193-209

64. Sun, S. and J. Xu*. 2009. Chromosomal rearrangements between serotype A and D strains in Cryptococcus neoformans. PLoS ONE. 4(5): e5524

63. Sha, T., J. Xu*, M. G. Palanichamy, H.-B. Zhang, T. Li, Z.-W. Zhao, Y.-P. Zhang*. 2008. Genetic diversity of an endemic gourmet mushroom Thelephora ganbajun from southwestern China. Microbiology-SGM 154, 3460-3468

62. Ciccotelli*, W., Haider S., and Xu, J. 2008. A traveler in time: phylogenetic analysis diagnoses the first case of reactivated sub-acute disseminated African histoplasmosis in an immunocompromised host from Tanzania. Canadian Journal of Infectious Diseases and Medical Microbiology. 19: 313-315

61. Ásmundsdóttir, L. R., Erlendsdóttir, H., Haraldsson, G., Guo, H., Xu, J., Gottfredsson*. M. 2008. Molecular epidemiology of candidemia: Evidence for smoldering nosocomial clustering. Clinical Infectious Diseases 47:17-24

60. M. I. Bidartondo et al. [one of 256 authors] (2008). Preserving Accuracy in GenBank. Science 319, 1616. DOI: 10.1126/science.319.5870.1616a

59. Hiremath, S. S., A. Chowdhary, T. Kowshik, H. S. Randhawa, S. Sun and J. Xu* 2008 Long-distance dispersal and recombination in environmental populations of Cryptococcus neoformans var. grubii from India. Microbiology-SGM. 154: 1513-1524

58. Randhawa, H. S., T. Kowshik, A. Chowdhary, K. Preeti Sinha, Z. U. Khan, S. Sun and J. Xu, 2008 The expanding host tree species spectrum of Cryptococcus gattii and Cryptococcus neoformans and their isolations from surrounding soil in India. Medical Mycology 18: 1-11

57. Shahid, M., Han, S., Yoell, H., and Xu, J*. 2008. Fitness distribution and transgressive segregation across 40 environmental conditions in a hybrid progeny population of the human pathogenic yeast Cryptococcus neoformans. Genome 51:272-281

56. Xu, J*., Sha, T., Li, Y.-C., Zhao, Z.-W., and Yang, Z.- L. 2008. Recombination and genetic differentiation among natural populations of the ectomycorrhizal mushroom Tricholoma matsutake from southwestern China. Molecular Ecology 17: 1238-1247

55. He YH, Xu J, Wang SJ, Zhou GY & Liu JA. 2014. Optimization of medium components for production of chitin deacetylase by Bacillus amyloliquefaciens Z7, using response surface methodology, Biotechnology & Biotechnological Equipment, 28:2, 242-247, DOI: 10.1080/13102818.2014.907659

54. Lian L, Tian B, Xiong R, Zhu M, Xu J. Zhang K. 2007. Proteases from Bacillus: a new insight into the mechanism of action for rhizobacterial suppression of nematode populations. Letters in Applied Microbiology, 45: 262-269. https://doi.org/10.1111/j.1472-765X.2007.02184.x

53. Sun, S., and Xu, J*. 2007. Genetic analyses of a hybrid cross between serotypes A and D strains of the human pathogenic fungus Cryptococcus neoformans. Genetics 177:1475-1486

52. Li, G., Zhang, K*., Xu, J., Dong, J., and Liu, Y. 2007. Nematicidal substances from fungi. Recent Patents in Biotechnology 1: 212-233

51. Wang, H., Guo, H., Sun, S., and Xu, J*. 2007. Abundant sequence variation around the mitochondrial origin of replication in the human opportunistic yeast pathogen Candida albicans from a tropical island in China. Fungal Genetics and Biology 44:991-1001

50. Wang, H., Wang, Y., Chen, J., Zhan, Z., Li, Y., and Xu, J*. 2007. Oral yeast flora and their ITS sequence diversity among a large cohort of medical students in Hainan, China. Mycopathologia. 164:65-72

49. Xu, J*., Guo, H., and Yang, Z-L*. 2007. Single nucleotide polymorphisms in the ectomycorrhizal mushroom Tricholoma matsutake. Microbiology 153:2002-2012 (cover photo)

48. Yan, Z., Hull, C. M., Sun, S., Heitman, J., and Xu, J*. 2007. The mating type-specific homeodomain genes SXI1 and SXI2a coordinately control uniparental mitochondrial inheritance in Cryptococcus neoformans. Current Genetics 51:187-195

47. Yan, Z., Sun, S., Shahid, M., and Xu, J*. 2007. Environment factors can influence mitochondrial inheritance in the fungus Cryptococcus neoformans. Fungal Genetics and Biology 44:315-322

46. Xu, J. 2006. Evolution of microbial pathogens. Emerging Infectious Diseases. 8:1306-1307

45. Randawa HS*, Kowshik T, Preeti Sinha K, Chowdhary A, Khan ZU, Yan Z, Xu J, Kumar A. 2006. Distribution of Cryptococcus gattii and Cryptococcus neoformans in decayed trunk wood of Syzygium cumini trees in north-western India. Medical Mycology. 44:623-630

44. Sun, S., Guo, H., and Xu, J*. 2006. Multiple gene genealogical analyses reveal both common and distinct population genetic patterns among replicons in the nitrogen-fixing bacterium Sinorhizobium meliloti. Microbiology. 152:3245-3259

43. Xu, J. 2006. Extracting haplotypes from diploid organisms. Current Issues in Molecular Biology. 8:113-122

42. Xu, J. 2006. Fundamentals of fungal molecular population genetic analyses. Current Issues in Molecular Biology. 8:75-89

41. Lan, L. and Xu, J*. 2006. Multiple gene genealogical analyses suggest divergence and recent clonal dispersal in the opportunistic human pathogen Candida guilliermondii. Microbiology. 152:1539-1549

40. Xu, J. 2006. Microbial ecology in the age of genomics and metagenomics: concepts, tools and recent advances. Molecular Ecology 15:1713-1731

39. Xu, J. 2005. Cost of interacting with sexual partners in a facultative sexual microbe.  Genetics. 171:1597-1604

38. Xu, J. 2005. The inheritance of organelle genes and genomes: patterns and mechanisms.  Genome. 48:951-958

37. Kidd, S.E., Guo, H., Bartlett, K., Xu, J., Kronstad, J. W*. 2005. Comparative gene genealogies indicate that two clonal lineages of Cryptococcus gattii in British Columbia resemble strains from other geographical areas.  Eukaryotic Cell 4: 1629-1638

36. Guo, H., Sun, S., Finan, T.M. and Xu, J*. 2005. Novel DNA sequences from natural strains of the nitrogen-fixing symbiotic bacterium Sinorhizobium melilotiApplied and Environmental Microbiology. 71:7130-7138

35. Xu, J. 2004. Genotype-environment interactions of spontaneous mutations affecting vegetative fitness in the human pathogenic fungus Cryptococcus neoformans. Genetics 168:1177-1188.

34. Yan, Z, Hull, C. M., Heitman, J., Sun, S. and Xu, J*. 2004. SXI1 controls uniparental mitochondrial inheritance in Cryptococcus neoformansCurrent Biology. 14:R743-R744.

33. Xu, J. 2004. The prevalence and evolution of sex in microorganisms. Genome 47:775-780

32. Xu, J*. and Mitchell, T. G. 2003. Comparative gene genealogical analyses of strains of serotype AD identify recombination in populations of serotypes A and D in the human pathogenic yeast Cryptococcus neoformans.  Microbiology. 149:2147-2154.

31. Montour, L. Tey, R. and Xu, J*. 2003. Isolation of Candida dubliniensis in an aboriginal community in Ontario, Canada.  Journal of Clinical Microbiology. 41:3423-3426.

30. Gottfredsson, M*., Vredenburgh, J., Xu, J., Schell, W. A., Perfect, J. R. 2003. Candidemia in women with breast carcinoma treated with high-dose chemotherapy and autologous bone marrow transplantation. Cancer. 98:24-30.

29. Yan, Z. and Xu, J*. 2003. Mitochondria are transmitted from MATa parent in sexual crosses of the human pathogenic fungus Cryptococcus neoformansGenetics 163, 1315-1325.

28. Xu, J. and Mitchell, T. G*. 2003. Geographic differences in human oral yeast flora. Clinical Infectious Diseases 36: 221-224.

27. Li, X., Yan, Z., and Xu, J*. 2003. Quantitative variation in biofilms among strains in natural populations of Candida albicans. Microbiology 149: 353-362.

26. Khan, Z.U*., Al-Anezi, A. A., Chandy, R. and Xu, J. 2003.  Disseminated cryptococcosis in an AIDS patient caused by a canavanine-resistant strain of Cryptococcus neoformans var. grubii. Journal of Medical Microbiology 52: 271-275.

25. Xu, J. 2002. Estimating the spontaneous mutation rate of loss of sex in the human pathogenic fungus Cryptococcus neoformansGenetics 162:1157-1167.

24. Xu, J. 2002. Mitochondrial DNA polymorphisms in the human pathogenic fungus Cryptococcus neoformansCurrent Genetics 41:43-47.

23. Kam, A., and Xu, J*. 2002. Diversity of commensal yeasts from within and between healthy hosts.  Diagnostic Microbiology and Infectious Diseases 43:19-28.

22. Xu, J*., Desmerger, C., and Callac, P. 2002. Fine scale genetic analyses reveal unexpected spatial-temporal heterogeneity in two natural populations of the commercial mushroom Agaricus bisporus. Microbiology 148:1253-1262.

21. Yan, Z., Li X, and Xu, J*. 2002. Geographic distribution of mating type alleles of Cryptococcus neoformans in four areas of the United States.  Journal of Clinical Microbiology 40:965-972.

20. Xu, J*., Luo, G., Vilgalys R., Brandt, M. E., and Mitchell, T. G. 2002. Multiple origins of hybrid strains of Cryptococcus neoformans with serotype AD.  Microbiology 148:203-212.

19. Forche, A., Xu, J., Vilgalys R., and Mitchell, T. G*. 2001. Development and characterization of a genetic linkage map of Cryptococcus neoformans var. neoformans using amplified fragment length polymorphisms (AFLP) and other markers.  Fungal Genetics and Biology.  31:189-203.

18. Xu, J*., Onyewu, C., Yoell, H. J., Ali, R. Y., Vilgalys, R., and Mitchell, T. G. 2001. Dynamic and heterogeneous mutations to fluconazole resistance in Cryptococcus neoformans. Antimicrobial Agents and Chemotherapy. 45:420-427.

17. McEwen JG*, Taylor JW, Carter D, Xu J, Felipe MSS, Vilgalys R, Mitchell TG, Kasuga T, White T, Bui T, Soares CMA.  2000. Molecular typing of pathogenic fungi. Medical Mycology 38(sppl 1):189-197.

16. Xu, J. Vilgalys, R., and Mitchell, T. G*. 2000.  Multiple gene genealogies reveal recent dispersion and hybridization in the human pathogenic fungus Cryptococcus neoformans. Molecular Ecology.  9:1471-1481.

15. Xu, J., Ramos, A., Vilgalys, R. and Mitchell, T. G*. 2000. Clonal and spontaneous origins of fluconazole resistance in Candida albicans. Journal of Clinical Microbiology.  38:1214-1220.

14. Xu, J., Ali, R., Gregory, D., Amick, D., Lambert, S., Yoell, H., Vilgalys, R. and Mitchell, T. G*. 2000. Uniparental mitochondrial transmission in sexual crosses in Cryptococcus neoformans. Current Microbiology.  40:269-273. DOI: 10.1007/s002849910053

13. Kerrigan, R. W*., Callac, P., Xu, J., and Noble, R. 1999.  Population and phylogenetic structure within the Agaricus subfloccosus complex. Mycological Research.  103:1515-1523.

12. Xu, J., Boyd, C. M., Livingstone, E., Meyer, W., Madden, J. F., and Mitchell, T. G*. 1999. Species and genotypic diversities and similarities of pathogenic yeasts colonizing women. Journal of Clinical Microbiology. 37:3835-3843.

11. Xu, J., Vilgalys, R. and Mitchell, T. G*. 1999. Lack of genetic differentiation between two geographic samples of Candida albicans isolated from patients infected with the Human Immunodeficiency Virus. Journal of Bacteriology.  181:1369-1373.

10. Xu, J., Mitchell, T. G. and Vilgalys, R*. 1999.  PCR-RFLP analyses reveal both extensive clonality and local genetic differentiation in Candida albicans. Molecular Ecology. 8:59-74.

9. Xu, J., Vilgalys, R., and Mitchell, T. G*. 1998.  Colony size can be used to determine the minimum inhibitory concentration of fluconazole for pathogenic yeasts.  Journal of Clinical Microbiology 36:2383-2385.

8. Xu, J., Kerrigan, R. W., Sonnenberg, A. S., Callac, P., Horgen, P. A. and Anderson, J. B*. 1998. Mitochondrial DNA variation in natural populations of the mushroom Agaricus bisporus.  Molecular Ecology 7:19-33.

7. Xu, J., Kerrigan, R. W., Callac, P., Horgen, P. A., and Anderson, J. B*. 1997.  The genetic structure of natural populations of Agaricus bisporus. the commercial button mushroom. Journal of Heredity 88:482-488.

6. Xu, J., Horgen, P. A., and Anderson, J. B*. 1996b.  Variation in mating interactions in Agaricus bisporusThe Cultivated Mushroom Research Newsletter 3:23-30.

5. Xu, J., Horgen, P. A., and Anderson, J. B*. 1996a.  Somatic recombination in the cultivated mushroom Agaricus bisporusMycological Research 100: 188-192.

4. Xu, J. 1995.  Analysis of inbreeding depression in Agaricus bisporusGenetics 141:137-145.

3. Xu, J*., Yoell, H. J., and Anderson, J. B. 1994.  An efficient protocol for isolating DNA from higher fungi.  Trends in Genetics 10:26-27.

2. Xu, J., Kerrigan, R. W., Horgen, P. A., and Anderson, J. B*. 1993b.  Localization of the mating type gene in Agaricus bisporusApplied and Environmental Microbiology.  59: 3044-3049.

1. Xu, J., Horgen, P. A., and Anderson, J. B*. 1993a.  Media and temperature effects on mating interactions of Agaricus bisporus   The Cultivated Mushroom Research Newsletter. 1: 25-32.

(ii) Not Peer-Reviewed

       (a) Books

       (b) Contributions to books

       (c) Journal articles

10. Xu J, Wang T, Gao C, Cheng Y, Guo L. 2020. Fiber crops. https://encyclopedia.pub/item/revision/ac19b2ebaa1101929cf6d6819edd481b

9. Xu J. 2020. Fungal pigments. https://encyclopedia.pub/item/revision/9e7b2da9972be066f3cdea3e1bcf9495

8. Xu J, Zhang Y. Fungi–Nematode Interactions. https://encyclopedia.pub/item/revision/95957976fb1b9a21f35d3726dd2e5723

7. Xu J. 2017. The life and work of Dr. Fan Qingsheng: a pioneer in antibiotics research, agricultural microbiology, systems agriculture, and agricultural education in China. Protein and Cell. DOI 10.1007/s13238-017-0374-x

6. Adamowicz SJ*, Chain FJ, Clare EL, Deiner K, Dincă V, Elías-Gutiérrez M, Hausmann A, Hogg ID, Kekkonen M, Lijtmaer DA, Naaum A, Steinke D, Valdez-Moreno M, Van der Bank M, Wilson JJ, Xu J. 2016. From Barcodes to Biomes: Special Issues from the 6th International Barcode of Life Conference. Genome. 59(11):v-ix. doi: 10.1139/gen-2016-0159

5. Cheng XY, Zhang LS, Tian T, Li H, Harvey C, Xu J*, He JS*. Insights from a biology field course at McMaster University. Theory and Practice of Contemporary Education, 2016, 8(12): 44-47. DOI:10.13582/j.cnki.1674-5884.2016.12.01

4. Xu J, Cai L. 2015. Diversity, population genetics, and phylogeography of selected wild mushrooms. Mycology 6(2): 77

3. Xu J. 2010. DNA barcoding, fungal diversity, and authentication of wild gourmet mushrooms. Acta Agriculturae Universitatis Jiangxiensis. 32 (5): 1010-1017.

2. Xu, J. 2010. Molecular, developmental, and evolutionary genetic studies highlight rapid evolution of genes and genetic systems. Genome 53 (10): 848-852

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