A novel phylogeny and morphological reconstruction of the PIN genes and first phylogeny of the ACC-oxidases (ACOs)
Identifieur interne : 000C24 ( Main/Merge ); précédent : 000C23; suivant : 000C25A novel phylogeny and morphological reconstruction of the PIN genes and first phylogeny of the ACC-oxidases (ACOs)
Auteurs : Ronald M. Clouse [États-Unis] ; Nicola Carraro [États-Unis]Source :
- Frontiers in Plant Science [ 1664-462X ] ; 2014.
Abstract
The
Url:
DOI: 10.3389/fpls.2014.00296
PubMed: 25018760
PubMed Central: 4071234
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PMC:4071234Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A novel phylogeny and morphological reconstruction of the <italic>PIN</italic>
genes and first phylogeny of the ACC-oxidases (<italic>ACOs</italic>
)</title>
<author><name sortKey="Clouse, Ronald M" sort="Clouse, Ronald M" uniqKey="Clouse R" first="Ronald M." last="Clouse">Ronald M. Clouse</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Bioinformatics and Genomics, University of North Carolina at Charlotte</institution>
<country>Charlotte, NC, USA</country>
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<country xml:lang="fr">États-Unis</country>
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<author><name sortKey="Carraro, Nicola" sort="Carraro, Nicola" uniqKey="Carraro N" first="Nicola" last="Carraro">Nicola Carraro</name>
<affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Agronomy, Purdue University</institution>
<country>West Lafayette, IN, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
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<idno type="doi">10.3389/fpls.2014.00296</idno>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A novel phylogeny and morphological reconstruction of the <italic>PIN</italic>
genes and first phylogeny of the ACC-oxidases (<italic>ACOs</italic>
)</title>
<author><name sortKey="Clouse, Ronald M" sort="Clouse, Ronald M" uniqKey="Clouse R" first="Ronald M." last="Clouse">Ronald M. Clouse</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Bioinformatics and Genomics, University of North Carolina at Charlotte</institution>
<country>Charlotte, NC, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Carraro, Nicola" sort="Carraro, Nicola" uniqKey="Carraro N" first="Nicola" last="Carraro">Nicola Carraro</name>
<affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Agronomy, Purdue University</institution>
<country>West Lafayette, IN, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
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<series><title level="j">Frontiers in Plant Science</title>
<idno type="eISSN">1664-462X</idno>
<imprint><date when="2014">2014</date>
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<front><div type="abstract" xml:lang="en"><p>The <italic>PIN</italic>
and <italic>ACO</italic>
gene families present interesting questions about the evolution of plant physiology, including testing hypotheses about the ecological drivers of their diversification and whether unrelated genes have been recruited for similar functions. The PIN-formed proteins contribute to the polar transport of auxin, a hormone which regulates plant growth and development. <italic>PIN</italic>
loci are categorized into groups according to their protein length and structure, as well as subcellular localization. An interesting question with <italic>PIN</italic>
genes is the nature of the ancestral form and location. <italic>ACO</italic>
s are members of a superfamily of oxygenases and oxidases that catalyze the last step of ethylene synthesis, which regulates many aspects of the plant life cycle. We used publicly available <italic>PIN</italic>
and <italic>ACO</italic>
sequences to conduct phylogenetic analyses. Third codon positions of these genes in monocots have a high GC content, which could be historical but is more likely due to a mutational bias. Thus, we developed methods to extract phylogenetic information from nucleotide sequences while avoiding this convergent feature. One method consisted in using only A-T transformations, and another used only the first and second codon positions for serine, which can only take A or T and G or C, respectively. We also conducted tree-searches for both gene families using unaligned amino acid sequences and dynamic homology. <italic>PIN</italic>
genes appear to have diversified earlier than <italic>ACOs</italic>
, with monocot and dicot copies more mixed in the phylogeny. However, gymnosperm <italic>PINs</italic>
appear to be derived and not closely related to those from primitive plants. We find strong support for a long <italic>PIN</italic>
gene ancestor with short forms subsequently evolving one or more times. <italic>ACO</italic>
genes appear to have diversified mostly since the dicot-monocot split, as most genes cluster into a small number of monocot and dicot clades when the tree is rooted by genes from mosses. Gymnosperm <italic>ACO</italic>
s were recovered as closely related and derived.</p>
</div>
</front>
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<author><name sortKey="Hoyerova, K" uniqKey="Hoyerova K">K. Hoyerová</name>
</author>
<author><name sortKey="Hosek, P" uniqKey="Hosek P">P. Hosek</name>
</author>
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