1. (a) Subtree of the MetaPalette output tree for the Iowa prairie metagenome using organisms from the genus Bradyrhizobium.
(a) Subtree of the MetaPalette output tree for the Iowa prairie metagenome using organisms from the genus Bradyrhizobium. (b) Depths of alignment for reads from the soil metagenome that aligned to B. valentinum LmjM3. The outer red ring shows the %GC for B. valentinum LmjM3, and the inner blue ring shows the alignment depth (truncated to 8,000× for ease of viewing). All contigs of the reference strain B. valentinum LmjM3 were concatenated in this figure. (c) Bootstrap consensus tree topology based on nifH for 20 organisms, along with the maximum-likelihood sequence obtained from aligning the soil metagenome to the nifH gene sequence of B. valentinum LmjM3. Bootstrap values (500 replicates) are shown next to the branches. Full details regarding the formation of the tree are given in “Sequence analysis details” in Materials and Methods.
David Koslicki, and Daniel Falush mSystems 2016; doi: /mSystems