Supplementary Dataset for Saeed et al. 2021: Evolution and Functions of Plant U-box proteins (PUBs): From protein quality control to signalling

This record contains additional information and a supplementary dataset of sequence alignment files and phylograms that support the publication:

Saeed B, Trenner J, Monaghan J, Quint M, Shabek N, Trujillo M. 2021. Evolution and Functions of Plant U-box proteins (PUBs): From protein quality control to signalling. (submitted to Annual Review of Plant Biology)

included files:

Additional information.pdf

This file contains Supplementary Methods and References for the phylogenetic analyses.

Ubox_full_protein_maximum_likelihood_phylogram_linear.pdf

A multiple protein sequence alignment by MAFFT (22) of 1121 U-box protein sequences from 21 species and four outgroup sequences containing a RING finger domain (A. thaliana RBX1, A. thaliana RMA1, S. cerevisiae RAD18, Homo sapiens TRAF6 ) was used to infer a phylogenetic tree by maximum likelihood with IQ-TREE (31, 32). The implemented ultrafast bootstrap approximation, set to 2000 bootstrap samples, was used for branch support (17). The consensus tree was annotated using iTOL (25).

Ubox_domain_maximum_likelihood_phylogram_linear.pdf

In order to analyse specifically the evolution of the U-box domain, the U-box domain of the final 1121 U-box protein sequences as well as the RING finger domain of the four outgroup sequences were isolated and aligned by MAFFT (22). The U-box domain alignment was then used to infer a phylogenetic tree by maximum likelihood with IQ-TREE (31, 32). The implemented ultrafast bootstrap approximation, set to 2000 bootstrap samples, was used for branch support (17). The consensus tree was annotated using iTOL (25). This tree was used to interpret the evolutionary history of U-box proteins in the main text.

MAFFT_alignment _1121seqs_Ubox_full_protein_plus_4seqs_RING_outgroup.fasta

Multiple protein sequences alignment by MAFFT (22) of 1121 U-box full length protein sequences and four RING finger protein sequences, FASTA formatted.

MAFFT_alignment _1121seqs_Ubox_domain_plus_4seqs_RING_outgroup.fasta

Multiple protein sequences alignment by MAFFT (22) of U-box domain sequences of 1121 U-box protein and four RING finger domain sequences of outgroup sequences, FASTA formatted.

Ubox_protein_sequences_information.xlsx

Spreadsheet with sequence ID information and source databases.