Population Genomics Of Cryptococcus neoformans var. grubii Reveals New Biogeographic Relationships And Finely Maps Hybridization

作者: Joseph Heitman , Sharvari Gujja , Daniel John Lawson , Christopher A. Desjardins , Sean M. Sykes

DOI: 10.1101/132894

关键词: Chromosomal regionPhylogenetic treePopulation genomicsCryptococcus neoformansGenotypePopulationBiologyMolecular epidemiologyGeneticsLineage (evolution)

摘要: Cryptococcus neoformans var. grubii is the causative agent of cryptococcal meningitis, a significant source mortality in immunocompromised individuals, typically HIV/AIDS patients from developing countries. Despite worldwide emergence this ubiquitous infection, little known about global molecular epidemiology fungal pathogen. Here we sequence genomes 188 diverse isolates and characterized major subdivisions, their relative diversity level genetic exchange between them. While most C. belong to one three lineages (VNI, VNII, VNB), some haploid show hybrid ancestry including that appear have recently interbred, based on detection large blocks each across chromosome. Many display evidence aneuploidy, which was detected for all chromosomes. In diploid (serotype A/A) hybrids with A/D) such aneuploidies resulted loss heterozygosity, where chromosomal region represented by genotype only parental isolate. Phylogenetic population genomic analyses Brazil revealed previously “African” VNB lineage occurs naturally South American environment. This suggests migration Africa America prior its diversification, supported finding ancestral recombination events different regions. The results provide substantial structure, showing multi-continental distributions demonstrating highly dispersive nature

参考文章(89)
V. Ter-Hovhannisyan, A. Lomsadze, Y. O. Chernoff, M. Borodovsky, Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training Genome Research. ,vol. 18, pp. 1979- 1990 ,(2008) , 10.1101/GR.081612.108
Koji Yahara, Yoshikazu Furuta, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, Ichizo Kobayashi, Chromosome painting in silico in a bacterial species reveals fine population structure. Molecular Biology and Evolution. ,vol. 30, pp. 1454- 1464 ,(2013) , 10.1093/MOLBEV/MST055
R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Research. ,vol. 32, pp. 1792- 1797 ,(2004) , 10.1093/NAR/GKH340
David M. Engelthaler, Nathan D. Hicks, John D. Gillece, Chandler C. Roe, James M. Schupp, Elizabeth M. Driebe, Felix Gilgado, Fabian Carriconde, Luciana Trilles, Carolina Firacative, Popchai Ngamskulrungroj, Elizabeth Castañeda, Marcia dos Santos Lazera, Marcia S. C. Melhem, Åsa Pérez-Bercoff, Gavin Huttley, Tania C. Sorrell, Kerstin Voelz, Robin C. May, Matthew C. Fisher, George R. Thompson, Shawn R. Lockhart, Paul Keim, Wieland Meyer, Cryptococcus gattii in North American Pacific Northwest: Whole-Population Genome Analysis Provides Insights into Species Evolution and Dispersal Mbio. ,vol. 5, ,(2014) , 10.1128/MBIO.01464-14
T. Bicanic, G. Meintjes, R. Wood, M. Hayes, K. Rebe, L.-G. Bekker, T. Harrison, Fungal Burden, Early Fungicidal Activity, and Outcome in Cryptococcal Meningitis in Antiretroviral-Naive or Antiretroviral-Experienced Patients Treated with Amphotericin B or Fluconazole Clinical Infectious Diseases. ,vol. 45, pp. 76- 80 ,(2007) , 10.1086/518607
Xiaorong Lin, Sweta Patel, Anastasia P. Litvintseva, Anna Floyd, Thomas G. Mitchell, Joseph Heitman, Diploids in the Cryptococcus neoformans Serotype A Population Homozygous for the α Mating Type Originate via Unisexual Mating PLoS Pathogens. ,vol. 5, pp. e1000283- ,(2009) , 10.1371/JOURNAL.PPAT.1000283
Guanggan Hu, Joyce Wang, Jaehyuk Choi, Won Hee Jung, Iris Liu, Anastasia P Litvintseva, Tihana Bicanic, Rajeev Aurora, Thomas G Mitchell, John R Perfect, James W Kronstad, Variation in chromosome copy number influences the virulence of Cryptococcus neoformans and occurs in isolates from AIDS patients BMC Genomics. ,vol. 12, pp. 526- 526 ,(2011) , 10.1186/1471-2164-12-526
Annemarie E Brouwer, Adul Rajanuwong, Wirongrong Chierakul, George E Griffin, Robert A Larsen, Nicholas J White, Thomas S Harrison, Combination antifungal therapies for HIV-associated cryptococcal meningitis: a randomised trial The Lancet. ,vol. 363, pp. 1764- 1767 ,(2004) , 10.1016/S0140-6736(04)16301-0
Tihana Bicanic, Robin Wood, Graeme Meintjes, Kevin Rebe, Annemarie Brouwer, Angela Loyse, Linda‐Gail Bekker, Shabbar Jaffar, Thomas Harrison, High-Dose Amphotericin B with Flucytosine for the Treatment of Cryptococcal Meningitis in HIV-Infected Patients: A Randomized Trial. Clinical Infectious Diseases. ,vol. 47, pp. 123- 130 ,(2008) , 10.1086/588792