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In a previous comprehensive study on Peronospora phylogeny [41], backbone resolution of the phylogenetic trees was relatively low.
Considering only supported clades (PB > 70%, LB > 70% and PP > 95%), the backbone resolution of the phylogenetic tree generated from the combined dataset was higher than the tree inferred from ITS.
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To test this hypothesis, we employed Scrollsaw, a phylogenetic approach that has been shown to produce backbone resolution between paralogs of large gene families where only short regions of homology are available (Elias et al. 2012; Gabernet-Castello et al. 2013).
To improve phylogenetic resolution of the backbone, more DNA markers or next generation sequencing data should be applied.
11 For the ten- and twelve-helix bundles, the measured end-to-end distances were identical to the measured contour lengths within the resolution of the bundlese thecing measured
The remaining 28S sequences are distributed over the whole tree and provided good resolution of the backbone, which is why we decided to include them despite a high level of missing data.
Diagnostic restriction digests and FIGE was further carried to verify the genomic integrity of the clones and confirm pLD53 backbone resolution.
The phylogenetic analysis described above of the Sec24 tree (supplementary fig. S3, Supplementary Material online) failed to show backbone resolution between paralogs.
Resolution of the conflict: Discussion.
However, in all analyses the resolution of backbone branches was generally poorly supported or unresolved.
It should be noted that inclusion of the peptides with resolution of 2 3 Å should not have a significant influence on the backbone quality of the libraries and thus the prediction of peptide backbone, as according to X-ray crystallography, the positions of backbone and many side chains are clear in the electron density map at 2 3 Å resolution [39].
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