AnimalPhylo

Newick output of the MrBayes phylogenetic analysis for the vertebrate and invertebrate ADF/CFL gene sequences. This was the newick file that was used for fitmodel analyses

TranslatedOriginal

This is the original alignment, translated to amino acid sequence, that was used for our phylogenetic and fitModeL analyses

PlantADFFitmodel

Plant ADF sequence file used as input into fitmodel analyses

Phylogenetic Patterns of Codon Evolution in the ACTIN-DEPOLYMERIZING FACTOR/COFILIN (ADF/CFL) Gene Family

<div><p>The actin-depolymerizing factor/cofilin (ADF/CFL) gene family encodes a diverse group of relatively small proteins. Once known strictly as modulators of actin filament dynamics, recent research has demonstrated that these proteins are involved in a variety of cellular processes, from signal transduction to the cytonuclear trafficking of actin. In both plant and animal lineages, expression patterns of paralogs in the ADF/CFL gene family vary among tissue types and developmental stages. In this study we use computational approaches to investigate the evolutionary forces responsible for the diversification of the ADF/CFL gene family. Estimating the rate of non-synonymous to synonymous mutations (dN/dS) across phylogenetic lineages revealed that the majority of ADF/CFL codon positions were under strong purifying selection, with rare episodic events of accelerated protein evolution. In both plants and animals these instances of accelerated evolution were ADF/CFL subclass specific, and all of the sites under selection were located in regions of the protein that could serve in new functional roles. We suggest these sites may have been important in the functional diversification of ADF/CFL proteins.</p></div

PlantADFPhylo

Newick output of the MrBayes phylogenetic analysis for the plant ADF gene sequences. This was the newick file that was used for fitmodel analyses

Three dimensional protein models of ADF/CFL proteins highlighting sites with accelerated rates of evolution (ω₃ rate category) in pink.

<p>(A) <i>Z</i>. <i>mays</i> ADF5 proteins with codon position 26 highlighted. (B) <i>H</i>. <i>sapiens</i> CFL1 protein with codon position 125 highlighted. (<b>C</b>) <i>D</i>. <i>rerio</i> CFL2 protein with codon position 69 highlighted.</p

The number of branches with the highest probability of being in the ω3 rate category plotted across each codon position for the (A) plant ADF and (B) animal CFL/ADF protein variants.

<p>A linear representation of the secondary structure is depicted directly below each graph, where open cylinders represent α-helices and black arrows represent β-sheets. Conserved binding regions are depicted below the secondary structures, with black bars represent F-actin binding regions, dark gray bars represent regions that are involved in both G-actin and F-actin binding, light gray bars are regions involved in only G-actin binding, and the dark gray bar with asterisks is the nuclear localization sequence. Tertiary structure and binding domains are based on [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145917#pone.0145917.ref033" target="_blank">33</a>] and [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145917#pone.0145917.ref034" target="_blank">34</a>]. The numbering of codon positions is based on protein sequence alignments used for phylogenetic analyses and selection analyses.</p

Bayesian phylogenetic analysis of the plant ADF gene family.

<p>The four ADF subclasses are highlighted in boxes. Species designations are as follows: At, <i>Arabidopsis thaliana</i>; Pt, <i>Populus trichocarpa</i>; Mg, <i>Mimulus guttatus</i>; Vv, <i>Vitis vinifera</i>; Os, <i>Oryza sativa</i>; Zm, <i>Zea mays</i>; Sm, <i>Selaginella moellendorffii</i>; and Php, <i>Physcomitrella patens</i>. ADF family number is given next to species designation when available. For those sequences that did not have a published family number on NCBI, the accession number is given. Accession numbers for all plant ADF variants used in analyses can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145917#pone.0145917.s002" target="_blank">S1 Table</a>.</p

AnimalFitmodel

Vertebrate and invertebrate ADF/CFL sequence file used as input into fitmodel analyses

AnimalFigure3and4

Excel file of the animal ADF/CFL fitmodel data set used to produce figures 3 and 4 of the manuscript. Please see associated readme file for more details