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A genome-wide analysis of the auxin/indole-3-acetic acid gene family in hexaploid bread wheat (Triticum aestivum L.).

Qiao L, Zhang X, Han X, Zhang L, Li X, Zhan H, Ma J, Luo P, Zhang W, Cui L, Li X, Chang Z - Front Plant Sci (2015)

Bottom Line: The duplicated genes have undergone an evolutionary process of purifying selection, resulting in the high conservation of copy genes among sub-genomes and functional redundancy among several members of the TaIAA family.However, functional divergence probably existed in most TaIAA members due to the diversity of the functional domain and expression pattern.Our research provides useful information for further research into the function of Aux/IAA genes in wheat.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, College of Life Science, Shanxi University Taiyuan, China ; Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Institute of Crop Science, Shanxi Academy of Agricultural Sciences Taiyuan, China.

ABSTRACT
The Auxin/indole-3-acetic acid (Aux/IAA) gene family plays key roles in the primary auxin-response process and controls a number of important traits in plants. However, the characteristics of the Aux/IAA gene family in hexaploid bread wheat (Triticum aestivum L.) have long been unknown. In this study, a comprehensive identification of the Aux/IAA gene family was performed using the latest draft genome sequence of the bread wheat "Chinese Spring." Thirty-four Aux/IAA genes were identified, 30 of which have duplicated genes on the A, B or D sub-genome, with a total of 84 Aux/IAA sequences. These predicted Aux/IAA genes were non-randomly distributed in all the wheat chromosomes except for chromosome 2D. The information of wheat Aux/IAA proteins is also described. Based on an analysis of phylogeny, expression and adaptive evolution, we prove that the Aux/IAA family in wheat has been replicated twice in the two allopolyploidization events of bread wheat, when the tandem duplication also occurred. The duplicated genes have undergone an evolutionary process of purifying selection, resulting in the high conservation of copy genes among sub-genomes and functional redundancy among several members of the TaIAA family. However, functional divergence probably existed in most TaIAA members due to the diversity of the functional domain and expression pattern. Our research provides useful information for further research into the function of Aux/IAA genes in wheat.

No MeSH data available.


Phylogenetic relationship, motif and gene structure of wheat Aux/IAA genes. (A) The phylogenetic tree of TaIAAs constructed from a complete alignment of 84 wheat Aux/IAA genes using MEGA 6.0 by the neighbor-joining method with 1000 bootstrap replicates. Bootstrap scores are indicated on the nodes and the 34 members of TaIAA, most of which contain duplicated genes, are indicated by blue or pink block. (B) The conserved motifs of TaIAAs. Motifs were identified by MEME software using the deduced amino-acid sequences of the TaIAAs. The relative position of each identified motif in all TaIAA proteins is shown as 1, 2, 3, and 4, which represented the four conserved domains of IAA. (C) Exon/intron structures of TaIAA genes. Exons are represented by black boxes and introns by black lines. The sizes of exons and introns can be estimated using the scale below.
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Figure 1: Phylogenetic relationship, motif and gene structure of wheat Aux/IAA genes. (A) The phylogenetic tree of TaIAAs constructed from a complete alignment of 84 wheat Aux/IAA genes using MEGA 6.0 by the neighbor-joining method with 1000 bootstrap replicates. Bootstrap scores are indicated on the nodes and the 34 members of TaIAA, most of which contain duplicated genes, are indicated by blue or pink block. (B) The conserved motifs of TaIAAs. Motifs were identified by MEME software using the deduced amino-acid sequences of the TaIAAs. The relative position of each identified motif in all TaIAA proteins is shown as 1, 2, 3, and 4, which represented the four conserved domains of IAA. (C) Exon/intron structures of TaIAA genes. Exons are represented by black boxes and introns by black lines. The sizes of exons and introns can be estimated using the scale below.

Mentions: A 22.8 GB local database of wheat nucleotide and protein sequences was built. By retrieving wheat protein sequence databases using the Aux/IAA HMM file, 127 non-redundant sequences were obtained. Next, 84 full-length protein sequences were detected that contained conserved Aux/IAA domains. In addition, corresponding coding sequences and genome sequences were isolated from the local nucleotide database and each Aux/IAA gene was located by searching the wheat chromosome genomic sequences using BLASTn (Table 1). An un-rooted tree of the 84 Aux/IAA full-length coding sequences was constructed (Figure 1A) to reveal the phylogenetic relationship and all the sequences were divided into 34 groups. Among them, 30 groups have two or three genes from different wheat sub-genomes, and these were regarded as different copies of one member of the Aux/IAA gene family.


A genome-wide analysis of the auxin/indole-3-acetic acid gene family in hexaploid bread wheat (Triticum aestivum L.).

Qiao L, Zhang X, Han X, Zhang L, Li X, Zhan H, Ma J, Luo P, Zhang W, Cui L, Li X, Chang Z - Front Plant Sci (2015)

Phylogenetic relationship, motif and gene structure of wheat Aux/IAA genes. (A) The phylogenetic tree of TaIAAs constructed from a complete alignment of 84 wheat Aux/IAA genes using MEGA 6.0 by the neighbor-joining method with 1000 bootstrap replicates. Bootstrap scores are indicated on the nodes and the 34 members of TaIAA, most of which contain duplicated genes, are indicated by blue or pink block. (B) The conserved motifs of TaIAAs. Motifs were identified by MEME software using the deduced amino-acid sequences of the TaIAAs. The relative position of each identified motif in all TaIAA proteins is shown as 1, 2, 3, and 4, which represented the four conserved domains of IAA. (C) Exon/intron structures of TaIAA genes. Exons are represented by black boxes and introns by black lines. The sizes of exons and introns can be estimated using the scale below.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4588698&req=5

Figure 1: Phylogenetic relationship, motif and gene structure of wheat Aux/IAA genes. (A) The phylogenetic tree of TaIAAs constructed from a complete alignment of 84 wheat Aux/IAA genes using MEGA 6.0 by the neighbor-joining method with 1000 bootstrap replicates. Bootstrap scores are indicated on the nodes and the 34 members of TaIAA, most of which contain duplicated genes, are indicated by blue or pink block. (B) The conserved motifs of TaIAAs. Motifs were identified by MEME software using the deduced amino-acid sequences of the TaIAAs. The relative position of each identified motif in all TaIAA proteins is shown as 1, 2, 3, and 4, which represented the four conserved domains of IAA. (C) Exon/intron structures of TaIAA genes. Exons are represented by black boxes and introns by black lines. The sizes of exons and introns can be estimated using the scale below.
Mentions: A 22.8 GB local database of wheat nucleotide and protein sequences was built. By retrieving wheat protein sequence databases using the Aux/IAA HMM file, 127 non-redundant sequences were obtained. Next, 84 full-length protein sequences were detected that contained conserved Aux/IAA domains. In addition, corresponding coding sequences and genome sequences were isolated from the local nucleotide database and each Aux/IAA gene was located by searching the wheat chromosome genomic sequences using BLASTn (Table 1). An un-rooted tree of the 84 Aux/IAA full-length coding sequences was constructed (Figure 1A) to reveal the phylogenetic relationship and all the sequences were divided into 34 groups. Among them, 30 groups have two or three genes from different wheat sub-genomes, and these were regarded as different copies of one member of the Aux/IAA gene family.

Bottom Line: The duplicated genes have undergone an evolutionary process of purifying selection, resulting in the high conservation of copy genes among sub-genomes and functional redundancy among several members of the TaIAA family.However, functional divergence probably existed in most TaIAA members due to the diversity of the functional domain and expression pattern.Our research provides useful information for further research into the function of Aux/IAA genes in wheat.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, College of Life Science, Shanxi University Taiyuan, China ; Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Institute of Crop Science, Shanxi Academy of Agricultural Sciences Taiyuan, China.

ABSTRACT
The Auxin/indole-3-acetic acid (Aux/IAA) gene family plays key roles in the primary auxin-response process and controls a number of important traits in plants. However, the characteristics of the Aux/IAA gene family in hexaploid bread wheat (Triticum aestivum L.) have long been unknown. In this study, a comprehensive identification of the Aux/IAA gene family was performed using the latest draft genome sequence of the bread wheat "Chinese Spring." Thirty-four Aux/IAA genes were identified, 30 of which have duplicated genes on the A, B or D sub-genome, with a total of 84 Aux/IAA sequences. These predicted Aux/IAA genes were non-randomly distributed in all the wheat chromosomes except for chromosome 2D. The information of wheat Aux/IAA proteins is also described. Based on an analysis of phylogeny, expression and adaptive evolution, we prove that the Aux/IAA family in wheat has been replicated twice in the two allopolyploidization events of bread wheat, when the tandem duplication also occurred. The duplicated genes have undergone an evolutionary process of purifying selection, resulting in the high conservation of copy genes among sub-genomes and functional redundancy among several members of the TaIAA family. However, functional divergence probably existed in most TaIAA members due to the diversity of the functional domain and expression pattern. Our research provides useful information for further research into the function of Aux/IAA genes in wheat.

No MeSH data available.