Phylogenetic detection of novel Cryptomycota in an Iowa (United States) aquifer and from previously collected marine and freshwater targeted high-throughput sequencing sets
Article first published online: 5 MAR 2013
© 2013 John Wiley & Sons Ltd and Society for Applied Microbiology
Volume 15, Issue 8, pages 2333–2341, August 2013
How to Cite
Livermore, J. A. and Mattes, T. E. (2013), Phylogenetic detection of novel Cryptomycota in an Iowa (United States) aquifer and from previously collected marine and freshwater targeted high-throughput sequencing sets. Environmental Microbiology, 15: 2333–2341. doi: 10.1111/1462-2920.12106
- Issue published online: 2 AUG 2013
- Article first published online: 5 MAR 2013
- Accepted manuscript online: 6 FEB 2013 08:58AM EST
- Manuscript Accepted: 27 JAN 2013
- Manuscript Revised: 19 DEC 2012
- Manuscript Received: 19 OCT 2012
- National Science Foundation. Grant Number: CBET-1007476
Fig. S1. PhyML Maximum likelihood phylogeny (GTR model) of 18S rRNA gene sequences references (from Jones et al., 2011b, 1536 nucleotide alignment). Bootstrap values (500 replicates) are shown on all branches. The out-group and other fungal references sequences are the same as those used in Jones and colleagues (2011b).
Fig. S2. PhyML Maximum likelihood phylogeny (GTR model) of 18S rRNA gene OTUs from targeted pyrosequencing with Cryptomycota reference sequences (Jones et al., 2011b, 313 nucleotide alignment). Aquifer sequences are highlighted with circles on branches with bootstrap values (500 replicates) greater 50% and larger circles denoting higher bootstrap value.
Fig. S3. Linear regressions based on Tamura Nei 1993 distances computed using two different hypervariable regions to compare a sequence pair of Cryptomycota sequences. Top left comparison of V4 and V3 distances per sequence, Top right: comparison of V9 and V3 distances, Bottom: comparison of V9 and V4 distance.
Fig. S4. High resolution, zoomable version of Fig. 3. FastTree summary phylogeny of reference Cryptomycota sequences from a previous study and candidate sequences from 13 pyrosequencing sets. Pink names indicate marine sequences, blue names indicate freshwaters sequences, and yellow names indicate locations of sequences from the Iowa Aquifer. Dots on a branch indicate SH (Shimodaira–Hasegawa) test > 0.7, Brown circles on perimeter indicate reference sequences.
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