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

Roy-Zokan EM, Dyer KA, Meagher RB - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Georgia, Athens, Georgia, United States of America.

ABSTRACT
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.

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Bayesian phylogenetic analysis of the plant ADF gene family.The four ADF subclasses are highlighted in boxes. Species designations are as follows: At, Arabidopsis thaliana; Pt, Populus trichocarpa; Mg, Mimulus guttatus; Vv, Vitis vinifera; Os, Oryza sativa; Zm, Zea mays; Sm, Selaginella moellendorffii; and Php, Physcomitrella patens. 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 S1 Table.
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pone.0145917.g001: Bayesian phylogenetic analysis of the plant ADF gene family.The four ADF subclasses are highlighted in boxes. Species designations are as follows: At, Arabidopsis thaliana; Pt, Populus trichocarpa; Mg, Mimulus guttatus; Vv, Vitis vinifera; Os, Oryza sativa; Zm, Zea mays; Sm, Selaginella moellendorffii; and Php, Physcomitrella patens. 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 S1 Table.

Mentions: The phylogenetic analysis of the plant ADF variants recovered the four ancient subclasses previously described (Fig 1) [11, 12]. Of note in our analysis were the placement of the moss P. patens and lycophyte S. moellendorffii ADF variants (Fig 1). The P. patens ADF variant grouped outside of the four subclasses, while one S. moellendorffii ADF variant (Sm146459) was basal to subclasses I and II and the other S. moellendorffii ADF variant (Sm230142) was basal to subclasses III and IV (Fig 1). The two most diverse subclasses were subclasses I and II, with more ADF variants per species being represented in these two subclasses. Even though subclass III and subclass IV contain fewer ADF variants per species, each angiosperm species still had at least one ADF variant within these two subclasses (Fig 1). Finally, the phylogeny indicates that within subclasses II, III, and IV the monocot ADF variants form a distinct group from dicot ADF variants. This division between monocot and dicot ADF variants was not seen in subclass I.


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

Roy-Zokan EM, Dyer KA, Meagher RB - PLoS ONE (2015)

Bayesian phylogenetic analysis of the plant ADF gene family.The four ADF subclasses are highlighted in boxes. Species designations are as follows: At, Arabidopsis thaliana; Pt, Populus trichocarpa; Mg, Mimulus guttatus; Vv, Vitis vinifera; Os, Oryza sativa; Zm, Zea mays; Sm, Selaginella moellendorffii; and Php, Physcomitrella patens. 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 S1 Table.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4696841&req=5

pone.0145917.g001: Bayesian phylogenetic analysis of the plant ADF gene family.The four ADF subclasses are highlighted in boxes. Species designations are as follows: At, Arabidopsis thaliana; Pt, Populus trichocarpa; Mg, Mimulus guttatus; Vv, Vitis vinifera; Os, Oryza sativa; Zm, Zea mays; Sm, Selaginella moellendorffii; and Php, Physcomitrella patens. 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 S1 Table.
Mentions: The phylogenetic analysis of the plant ADF variants recovered the four ancient subclasses previously described (Fig 1) [11, 12]. Of note in our analysis were the placement of the moss P. patens and lycophyte S. moellendorffii ADF variants (Fig 1). The P. patens ADF variant grouped outside of the four subclasses, while one S. moellendorffii ADF variant (Sm146459) was basal to subclasses I and II and the other S. moellendorffii ADF variant (Sm230142) was basal to subclasses III and IV (Fig 1). The two most diverse subclasses were subclasses I and II, with more ADF variants per species being represented in these two subclasses. Even though subclass III and subclass IV contain fewer ADF variants per species, each angiosperm species still had at least one ADF variant within these two subclasses (Fig 1). Finally, the phylogeny indicates that within subclasses II, III, and IV the monocot ADF variants form a distinct group from dicot ADF variants. This division between monocot and dicot ADF variants was not seen in subclass I.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Georgia, Athens, Georgia, United States of America.

ABSTRACT
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.

Show MeSH