Phylogenetic gene tree figures from Chapter 3 of the University of Copenhagen PhD thesis 'Understanding Specialized Metabolism in Faba Bean: From Biosynthetic Pathways to Crop Improvement'

Dataset description

This dataset comprises a set of images of gene trees analysing the polyphenol oxidase (PPO) and amino acid transporter (AAT) gene families across angiosperms, in particular legumes. The purpose of this set of figures is to provide the full gene trees that are the source of subsampled gene trees presented in Chapter 3 of the PhD thesis of Denise Blume, Understanding Specialized Metabolism in Faba Bean: From Biosynthetic Pathways to Crop Improvement.

This dataset includes:

• 'Gene_trees' directory:
• Supplementary Figure 13. Taxon-labeled maximum likelihood legume PPO gene tree with amino acid branch lengths and support values.pdf
• Supplementary Figure 14. Taxon-labeled maximum likelihood angiosperm PPO gene tree inferred from amino acid sequences.pdf
• Supplementary Figure 15. Taxon-labeled maximum likelihood angiosperm PPO gene tree inferred from nucleotide sequences.pdf
• Supplementary Figure 16. Taxon-labeled maximum likelihood angiosperm AAT gene tree with amino acid branch lengths and support values.pdf
• LICENSE.txt

Figure legends

Supplementary Figure 13. Taxon-labeled maximum likelihood legume PPO gene tree with amino acid branch lengths and support values. Branch values are support from 1000 rapid bootstrap replicates and the SH-aLRT, respectively (RBS/SH-aLRT). Branch lengths are expected substitutions per site.

Supplementary Figure 14. Taxon-labeled maximum likelihood angiosperm PPO gene tree inferred from amino acid sequences. Branch values are support from 1000 rapid bootstrap replicates and the SH-aLRT, respectively (RBS/SH-aLRT). Branch lengths are expected substitutions per site.

Supplementary Figure 15. Taxon-labeled maximum likelihood angiosperm PPO gene tree inferred from nucleotide sequences. Branch values are support from 1000 rapid bootstrap replicates and the SH-aLRT, respectively (RBS/SH-aLRT). Branch lengths are expected substitutions per site.

Supplementary Figure 16. Taxon-labeled maximum likelihood angiosperm AAT gene tree with amino acid branch lengths and support values. Branch values are support from 1000 rapid bootstrap replicates and the SH-aLRT, respectively (RBS/SH-aLRT). Branch lengths are expected substitutions per site.

Technical details

Image files are provided in Portable Document Format (PDF/A) and can be opened using any standard PDF viewer (e.g. Adobe Acrobat Reader, Preview on macOS, Adobe Acrobat Pro, or Foxit PDF Editor).