Next-Generation Sequencing of Coccidioides immitis Isolated during Cluster Investigation
David M. Engelthaler, Tom Chiller, James A. Schupp, Joshua Colvin, Stephen M. Beckstrom-Sternberg, Elizabeth M. Driebe, Tracy Moses, Waibhav Tembe, Shripad Sinari, James S. Beckstrom-Sternberg, Alexis Christoforides, John V. Pearson, John Carpten, Paul Keim, Ashley Peterson, Dawn Terashita, and S. Arunmozhi Balajee
Author affiliations: Author affiliations: Translational Genomics Research Institute, Phoenix, Arizona, USA (D.M. Engelthaler, J.A. Schupp, J. Colvin, S.M. Beckstrom-Sternberg, E.M. Driebe, T. Moses, W. Tembe, S. Sinari, A. Christoforides, J.V. Pearson, J. Carpten, P. Keim); Centers for Disease Control and Prevention, Atlanta, Georgia, USA (T. Chiller, S.A. Balajee); Northern Arizona University, Flagstaff, Arizona, USA (S.M. Beckstrom-Sternberg, J.S. Beckstrom-Sternberg, P. Keim); Los Angeles County Department of Public Health, Los Angeles, California, USA (A. Peterson, D. Terashita)
Figure 3. Maximum-parsimony phylogenetic analysis of 13 Coccidioides immitis genomes. MEGA4 (13) was used to conduct maximum-parsimony analysis of all single-nucleotide polymorphism (SNP) loci common to the 3 transplant isolate genomes and the 10 publicly available C. immitis genome sequences (6,10). A total of 32,695 SNP positions were identified in the final dataset, of which 17,080 were parsimony informative. The percentages of replicate trees in which the associated taxa clustered in the bootstrap test (1,000 replicates) are shown next to the branches. The tree is drawn to scale; branch lengths were calculated by using the average pathway method (14) and are in the units of the number of changes over the whole sequence. The consistency index of the tree is 0.63. Scale bar indicates nucleotide substitutions per site.
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