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The maize (Zea mays L.) AUXIN/INDOLE-3-ACETIC ACID gene family: phylogeny, synteny, and unique root-type and tissue-specific expression patterns during development.

Ludwig Y, Zhang Y, Hochholdinger F - PLoS ONE (2013)

Bottom Line: Moreover, 51 of 55 (93%) differential Aux/IAA expression patterns between different root-types followed the expression tendency: crown roots > seminal roots > primary roots > lateral roots.This pattern might imply root-type-specific regulation of Aux/IAA transcript abundance.In summary, the detailed analysis of the maize Aux/IAA gene family provides novel insights in the evolution and developmental regulation and thus the function of these genes in different root-types and tissues.

View Article: PubMed Central - PubMed

Affiliation: Crop Functional Genomics, Institute of Crop Science and Resource Conservation, Rheinische-Friedrich-Wilhelms Universit├Ąt, Bonn, Germany.

ABSTRACT
The plant hormone auxin plays a key role in the coordination of many aspects of growth and development. AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) genes encode instable primary auxin responsive regulators of plant development that display a protein structure with four characteristic domains. In the present study, a comprehensive analysis of the 34 members of the maize Aux/IAA gene family was performed. Phylogenetic reconstructions revealed two classes of Aux/IAA proteins that can be distinguished by alterations in their domain III. Seven pairs of paralogous maize Aux/IAA proteins were discovered. Comprehensive root-type and tissue-specific expression profiling revealed unique expression patterns of the diverse members of the gene family. Remarkably, five of seven pairs of paralogous genes displayed highly correlated expression patterns in roots. All but one (ZmIAA23) tested maize Aux/IAA genes were auxin inducible, displaying two types of auxin induction within three hours of treatment. Moreover, 51 of 55 (93%) differential Aux/IAA expression patterns between different root-types followed the expression tendency: crown roots > seminal roots > primary roots > lateral roots. This pattern might imply root-type-specific regulation of Aux/IAA transcript abundance. In summary, the detailed analysis of the maize Aux/IAA gene family provides novel insights in the evolution and developmental regulation and thus the function of these genes in different root-types and tissues.

Show MeSH
Unrooted phylogenetic tree and distribution of conserved domains in maize Aux/IAA proteins.The phylogenetic tree reveals two classes (A and B) of Aux/IAA proteins that differ in the sequence of domain III. The structure of the Aux/IAA proteins and the distribution of their domains are displayed to the right. The scale bar corresponds to 10 amino acids (aa). Paralogous Aux/IAA genes are encircled. The values associated to each branch are bootstrap percentages. The size bar indicates sequence divergence : 0.1 = 10%.
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pone-0078859-g001: Unrooted phylogenetic tree and distribution of conserved domains in maize Aux/IAA proteins.The phylogenetic tree reveals two classes (A and B) of Aux/IAA proteins that differ in the sequence of domain III. The structure of the Aux/IAA proteins and the distribution of their domains are displayed to the right. The scale bar corresponds to 10 amino acids (aa). Paralogous Aux/IAA genes are encircled. The values associated to each branch are bootstrap percentages. The size bar indicates sequence divergence : 0.1 = 10%.

Mentions: Phylogenetic reconstructions were based on the full-length sequences of the 34 maize Aux/IAA proteins. Two major groups of Aux/IAA proteins (class A and class B) were observed (Figure 1), which coincided with the alteration in the conserved motif in domain III (Figure S1).


The maize (Zea mays L.) AUXIN/INDOLE-3-ACETIC ACID gene family: phylogeny, synteny, and unique root-type and tissue-specific expression patterns during development.

Ludwig Y, Zhang Y, Hochholdinger F - PLoS ONE (2013)

Unrooted phylogenetic tree and distribution of conserved domains in maize Aux/IAA proteins.The phylogenetic tree reveals two classes (A and B) of Aux/IAA proteins that differ in the sequence of domain III. The structure of the Aux/IAA proteins and the distribution of their domains are displayed to the right. The scale bar corresponds to 10 amino acids (aa). Paralogous Aux/IAA genes are encircled. The values associated to each branch are bootstrap percentages. The size bar indicates sequence divergence : 0.1 = 10%.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815225&req=5

pone-0078859-g001: Unrooted phylogenetic tree and distribution of conserved domains in maize Aux/IAA proteins.The phylogenetic tree reveals two classes (A and B) of Aux/IAA proteins that differ in the sequence of domain III. The structure of the Aux/IAA proteins and the distribution of their domains are displayed to the right. The scale bar corresponds to 10 amino acids (aa). Paralogous Aux/IAA genes are encircled. The values associated to each branch are bootstrap percentages. The size bar indicates sequence divergence : 0.1 = 10%.
Mentions: Phylogenetic reconstructions were based on the full-length sequences of the 34 maize Aux/IAA proteins. Two major groups of Aux/IAA proteins (class A and class B) were observed (Figure 1), which coincided with the alteration in the conserved motif in domain III (Figure S1).

Bottom Line: Moreover, 51 of 55 (93%) differential Aux/IAA expression patterns between different root-types followed the expression tendency: crown roots > seminal roots > primary roots > lateral roots.This pattern might imply root-type-specific regulation of Aux/IAA transcript abundance.In summary, the detailed analysis of the maize Aux/IAA gene family provides novel insights in the evolution and developmental regulation and thus the function of these genes in different root-types and tissues.

View Article: PubMed Central - PubMed

Affiliation: Crop Functional Genomics, Institute of Crop Science and Resource Conservation, Rheinische-Friedrich-Wilhelms Universit├Ąt, Bonn, Germany.

ABSTRACT
The plant hormone auxin plays a key role in the coordination of many aspects of growth and development. AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) genes encode instable primary auxin responsive regulators of plant development that display a protein structure with four characteristic domains. In the present study, a comprehensive analysis of the 34 members of the maize Aux/IAA gene family was performed. Phylogenetic reconstructions revealed two classes of Aux/IAA proteins that can be distinguished by alterations in their domain III. Seven pairs of paralogous maize Aux/IAA proteins were discovered. Comprehensive root-type and tissue-specific expression profiling revealed unique expression patterns of the diverse members of the gene family. Remarkably, five of seven pairs of paralogous genes displayed highly correlated expression patterns in roots. All but one (ZmIAA23) tested maize Aux/IAA genes were auxin inducible, displaying two types of auxin induction within three hours of treatment. Moreover, 51 of 55 (93%) differential Aux/IAA expression patterns between different root-types followed the expression tendency: crown roots > seminal roots > primary roots > lateral roots. This pattern might imply root-type-specific regulation of Aux/IAA transcript abundance. In summary, the detailed analysis of the maize Aux/IAA gene family provides novel insights in the evolution and developmental regulation and thus the function of these genes in different root-types and tissues.

Show MeSH