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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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Alignment of predicted amino acid sequences of the MIKCC-type MADS-box genes of peach. Sequence comparison was obtained using Clustal X and utilized for tree estimation and ancestral reconstruction. Sequences included M, I, K and C domains. A poplar gene (PtMADS27) was included as outgroup.
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Figure 2: Alignment of predicted amino acid sequences of the MIKCC-type MADS-box genes of peach. Sequence comparison was obtained using Clustal X and utilized for tree estimation and ancestral reconstruction. Sequences included M, I, K and C domains. A poplar gene (PtMADS27) was included as outgroup.

Mentions: The alignment of the complete PpDAM protein sequence revealed high amino acid sequence conservation among the peach MADS genes (Figure 2). The intron-exon structure is also conserved in all domains (Figure 3), with the exception of the C domain of PpDAM4, which contains a deletion of similar size to that present in PtMADS27. The modular domain organization of MIKC proteins is reflected in a conserved intron-exon structure [4].


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)

Alignment of predicted amino acid sequences of the MIKCC-type MADS-box genes of peach. Sequence comparison was obtained using Clustal X and utilized for tree estimation and ancestral reconstruction. Sequences included M, I, K and C domains. A poplar gene (PtMADS27) was included as outgroup.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Alignment of predicted amino acid sequences of the MIKCC-type MADS-box genes of peach. Sequence comparison was obtained using Clustal X and utilized for tree estimation and ancestral reconstruction. Sequences included M, I, K and C domains. A poplar gene (PtMADS27) was included as outgroup.
Mentions: The alignment of the complete PpDAM protein sequence revealed high amino acid sequence conservation among the peach MADS genes (Figure 2). The intron-exon structure is also conserved in all domains (Figure 3), with the exception of the C domain of PpDAM4, which contains a deletion of similar size to that present in PtMADS27. The modular domain organization of MIKC proteins is reflected in a conserved intron-exon structure [4].

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