Computational protocol: Non-dispersive phloem-protein bodies (NPBs) of Populus trichocarpa consist of a SEOR protein and do not respond to cell wounding and Ca2+

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Protocol publication

[…] Amino acid sequences of proteins and genomic nucleotide sequences were downloaded from the NCBI (https://www.ncbi.nlm.nih.gov) and phytozome databases (https://phytozome.jgi.doe.gov) for further analyses. Sequence alignments for conserved structure comparisons were conducted using CLC Sequence Viewer v.7.8.1, or earlier versions (QIAGEN, Aarhus, Denmark) with default settings. Phylogenetic analyses of the SEO/SEOR gene family for angiosperms used all putative gene family members from the above databases with gene copies aligned with MUSCLE (). Maximum likelihood (ML) analyses were performed using the JTT model in RAxML () with 100 bootstraps. The tree was rooted on the branch placing the single SEOR gene copy from Amborella sister to the rest of the angiosperm gene copies, based on the strong independent evidence for that relationship (). […]

Pipeline specifications

Software tools CLC Sequence Viewer, MUSCLE, RAxML
Databases Phytozome
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Populus trichocarpa, Arabidopsis thaliana