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Phylogenetic analysis and molecular evolution of the dormancy associated MADS-box genes from peach.

Jiménez S, Lawton-Rauh AL, Reighard GL, Abbott AG, Bielenberg DG - BMC Plant Biol. (2009)

Bottom Line: Dormancy associated MADS-box (DAM) genes are candidates for the regulation of growth cessation and terminal bud formation in peach.Phylogenetic analyses suggest that the peach SVP/StMADS11-like gene family, which contains significantly more members than annual model plants, expanded through serial tandem gene duplication.In addition, this pattern of selection suggests that the DAM genes are important for peach growth and development.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Horticulture, Clemson University, Clemson, SC 29634-0319, USA. sergij@clemson.edu

ABSTRACT

Background: Dormancy associated MADS-box (DAM) genes are candidates for the regulation of growth cessation and terminal bud formation in peach. These genes are not expressed in the peach mutant evergrowing, which fails to cease growth and enter dormancy under dormancy-inducing conditions. We analyzed the phylogenetic relationships among and the rates and patterns of molecular evolution within DAM genes in the phylogenetic context of the MADS-box gene family.

Results: The peach DAM genes grouped with the SVP/StMADS11 lineage of type II MIKCC MADS-box genes. Phylogenetic analyses suggest that the peach SVP/StMADS11-like gene family, which contains significantly more members than annual model plants, expanded through serial tandem gene duplication. We found evidence of strong purifying selection acting to constrain functional divergence among the peach DAM genes and only a single codon, located in the C-terminal region, under significant positive selection.

Conclusion: Because all DAM genes are expressed in peach and are subjected to strong purifying selection we suggest that the duplicated genes have been maintained by subfunctionalization and/or neofunctionalization. In addition, this pattern of selection suggests that the DAM genes are important for peach growth and development.

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Ancestral reconstruction in the region of the positively selected site 239 in PpDAM genes. Sequence corresponds with the rectangular region of Figure 2. Ancestral names of sequences correspond to internal nodes of Figure 4. The posterior probability for the reconstructed amino acid at an internal node is indicated. Non-variable sites are not highlighted.
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Figure 5: Ancestral reconstruction in the region of the positively selected site 239 in PpDAM genes. Sequence corresponds with the rectangular region of Figure 2. Ancestral names of sequences correspond to internal nodes of Figure 4. The posterior probability for the reconstructed amino acid at an internal node is indicated. Non-variable sites are not highlighted.

Mentions: The Naïve empirical Bayes of M3 and M8 models suggested one potential site under significant positive selection (Table 2): a serine-aspartate change of the C-terminal region (amino acid position 239 in Figure 2). A maximum likelihood-based estimated reconstruction of ancestral sequences around this site is shown in Figure 5. Identical changes (S to D) at amino acid 239 are present in PpDAM1 and PpDAM3. In this section of the alignment, ancestral sequences of PpDAM genes shared the same nucleotides with a probability higher than 0.95, except near PpDAM1 and PpDAM3 genes at the potential positively selected site. However, ancestral sequences of PpDAM genes did not shared the same nucleotides (probability higher than 0.90) in the non-positive selected positions 238 and 240 around this site (Figure 5).


Phylogenetic analysis and molecular evolution of the dormancy associated MADS-box genes from peach.

Jiménez S, Lawton-Rauh AL, Reighard GL, Abbott AG, Bielenberg DG - BMC Plant Biol. (2009)

Ancestral reconstruction in the region of the positively selected site 239 in PpDAM genes. Sequence corresponds with the rectangular region of Figure 2. Ancestral names of sequences correspond to internal nodes of Figure 4. The posterior probability for the reconstructed amino acid at an internal node is indicated. Non-variable sites are not highlighted.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2713236&req=5

Figure 5: Ancestral reconstruction in the region of the positively selected site 239 in PpDAM genes. Sequence corresponds with the rectangular region of Figure 2. Ancestral names of sequences correspond to internal nodes of Figure 4. The posterior probability for the reconstructed amino acid at an internal node is indicated. Non-variable sites are not highlighted.
Mentions: The Naïve empirical Bayes of M3 and M8 models suggested one potential site under significant positive selection (Table 2): a serine-aspartate change of the C-terminal region (amino acid position 239 in Figure 2). A maximum likelihood-based estimated reconstruction of ancestral sequences around this site is shown in Figure 5. Identical changes (S to D) at amino acid 239 are present in PpDAM1 and PpDAM3. In this section of the alignment, ancestral sequences of PpDAM genes shared the same nucleotides with a probability higher than 0.95, except near PpDAM1 and PpDAM3 genes at the potential positively selected site. However, ancestral sequences of PpDAM genes did not shared the same nucleotides (probability higher than 0.90) in the non-positive selected positions 238 and 240 around this site (Figure 5).

Bottom Line: Dormancy associated MADS-box (DAM) genes are candidates for the regulation of growth cessation and terminal bud formation in peach.Phylogenetic analyses suggest that the peach SVP/StMADS11-like gene family, which contains significantly more members than annual model plants, expanded through serial tandem gene duplication.In addition, this pattern of selection suggests that the DAM genes are important for peach growth and development.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Horticulture, Clemson University, Clemson, SC 29634-0319, USA. sergij@clemson.edu

ABSTRACT

Background: Dormancy associated MADS-box (DAM) genes are candidates for the regulation of growth cessation and terminal bud formation in peach. These genes are not expressed in the peach mutant evergrowing, which fails to cease growth and enter dormancy under dormancy-inducing conditions. We analyzed the phylogenetic relationships among and the rates and patterns of molecular evolution within DAM genes in the phylogenetic context of the MADS-box gene family.

Results: The peach DAM genes grouped with the SVP/StMADS11 lineage of type II MIKCC MADS-box genes. Phylogenetic analyses suggest that the peach SVP/StMADS11-like gene family, which contains significantly more members than annual model plants, expanded through serial tandem gene duplication. We found evidence of strong purifying selection acting to constrain functional divergence among the peach DAM genes and only a single codon, located in the C-terminal region, under significant positive selection.

Conclusion: Because all DAM genes are expressed in peach and are subjected to strong purifying selection we suggest that the duplicated genes have been maintained by subfunctionalization and/or neofunctionalization. In addition, this pattern of selection suggests that the DAM genes are important for peach growth and development.

Show MeSH
Related in: MedlinePlus