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A genome-wide analysis of the LBD (LATERAL ORGAN BOUNDARIES domain) gene family in Malus domestica with a functional characterization of MdLBD11.

Wang X, Zhang S, Su L, Liu X, Hao Y - PLoS ONE (2013)

Bottom Line: At the same time, the expression analysis implied that members of this apple gene family were responsive to hormones and stress and that they may participate in hormone-mediated plant organogenesis, which was demonstrated with the overexpression of the apple LBD gene MdLBD11, resulting in an abnormal phenotype.This phenotype included upward curling leaves, delayed flowering, downward-pointing flowers, siliques and other abnormal traits.Based on these data, we concluded that the MdLBD genes may play an important role in apple growth and development as in Arabidopsis and other species.

View Article: PubMed Central - PubMed

Affiliation: National Key laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong, China.

ABSTRACT
The plant-specific LBD (LATERAL ORGAN BOUNDARIES domain) genes belong to a major family of transcription factor that encode a zinc finger-like domain. It has been shown that LBD genes play crucial roles in the growth and development of Arabidopsis and other plant species. However, no detailed information concerning this family is available for apple. In the present study, we analyzed the apple (Malus domestica) genome and identified 58 LBD genes. This gene family was tested for its phylogenetic relationships with homologous genes in the Arabidopsis genome, as well as its location in the genome, structure and expression. We also transformed one MdLBD gene into Arabidopsis to evaluate its function. Like Arabidopsis, apple LBD genes also have a conserved CX2CX6CX3C zinc finger-like domain in the N terminus and can be divided into two classes. The expression profile indicated that apple LBD genes exhibited a variety of expression patterns, suggesting that they have diverse functions. At the same time, the expression analysis implied that members of this apple gene family were responsive to hormones and stress and that they may participate in hormone-mediated plant organogenesis, which was demonstrated with the overexpression of the apple LBD gene MdLBD11, resulting in an abnormal phenotype. This phenotype included upward curling leaves, delayed flowering, downward-pointing flowers, siliques and other abnormal traits. Based on these data, we concluded that the MdLBD genes may play an important role in apple growth and development as in Arabidopsis and other species.

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The phylogenetic analysis of LBD genes in apple and Arabidopsis.The amino acid sequences of the LBD proteins were aligned with Clustal X, and the phylogenetic tree was constructed using the neighbor-joining method of MEGA 5.0 software. Each node is represented by a number that indicates the bootstrap value for 1000 replicates. The scale bar represents 0.1 substitutions per sequence position. Each LBD subfamily is indicated by an arc.
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pone-0057044-g002: The phylogenetic analysis of LBD genes in apple and Arabidopsis.The amino acid sequences of the LBD proteins were aligned with Clustal X, and the phylogenetic tree was constructed using the neighbor-joining method of MEGA 5.0 software. Each node is represented by a number that indicates the bootstrap value for 1000 replicates. The scale bar represents 0.1 substitutions per sequence position. Each LBD subfamily is indicated by an arc.

Mentions: To examine the evolutionary patterns of MdLBD with those of Arabidopsis and then group them into established subfamilies, a phylogenetic tree was generated with full length protein sequences (Fig. 2). As in rice and Arabidopsis, the MdLBD clearly fell into two classes, class I and class II, which had 45 and 13 separate genes relative to 37 and 6 genes in Arabidopsis, as shown in Fig. 1. The presence of twice as many class II apple LBD genes compared with Arabidopsis indicates that this class of gene may have more functions in apple development. Class I and class II families were further divided into 8 and 2 groups. In class I, the subgroups were named from class Ia to class Ii, while class IIa and class IIb comprised the class II group. Three Arabidopsis LBD genes (AtLBD40,AtLBD41,AtLBD42) that were clustered into class IIa corresponded with only one LBD gene (MdLBD40) in apple. On the other hand, there were 12 apple LBD genes grouped in class IIb with only three genes (AtLBD37, AtLBD38, and AtLBD39) in Arabidopsis. It is reported that AtLBD37, AtLBD37, AtLBD38 and AtLBD39 function as transcript regulators in response to nitrate and regulate gene expression relative to anthocyanin biosynthesis along with nitrate uptake and transport [11]. We conclude that class IIb LBD genes may play a broader function in apple.


A genome-wide analysis of the LBD (LATERAL ORGAN BOUNDARIES domain) gene family in Malus domestica with a functional characterization of MdLBD11.

Wang X, Zhang S, Su L, Liu X, Hao Y - PLoS ONE (2013)

The phylogenetic analysis of LBD genes in apple and Arabidopsis.The amino acid sequences of the LBD proteins were aligned with Clustal X, and the phylogenetic tree was constructed using the neighbor-joining method of MEGA 5.0 software. Each node is represented by a number that indicates the bootstrap value for 1000 replicates. The scale bar represents 0.1 substitutions per sequence position. Each LBD subfamily is indicated by an arc.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3585328&req=5

pone-0057044-g002: The phylogenetic analysis of LBD genes in apple and Arabidopsis.The amino acid sequences of the LBD proteins were aligned with Clustal X, and the phylogenetic tree was constructed using the neighbor-joining method of MEGA 5.0 software. Each node is represented by a number that indicates the bootstrap value for 1000 replicates. The scale bar represents 0.1 substitutions per sequence position. Each LBD subfamily is indicated by an arc.
Mentions: To examine the evolutionary patterns of MdLBD with those of Arabidopsis and then group them into established subfamilies, a phylogenetic tree was generated with full length protein sequences (Fig. 2). As in rice and Arabidopsis, the MdLBD clearly fell into two classes, class I and class II, which had 45 and 13 separate genes relative to 37 and 6 genes in Arabidopsis, as shown in Fig. 1. The presence of twice as many class II apple LBD genes compared with Arabidopsis indicates that this class of gene may have more functions in apple development. Class I and class II families were further divided into 8 and 2 groups. In class I, the subgroups were named from class Ia to class Ii, while class IIa and class IIb comprised the class II group. Three Arabidopsis LBD genes (AtLBD40,AtLBD41,AtLBD42) that were clustered into class IIa corresponded with only one LBD gene (MdLBD40) in apple. On the other hand, there were 12 apple LBD genes grouped in class IIb with only three genes (AtLBD37, AtLBD38, and AtLBD39) in Arabidopsis. It is reported that AtLBD37, AtLBD37, AtLBD38 and AtLBD39 function as transcript regulators in response to nitrate and regulate gene expression relative to anthocyanin biosynthesis along with nitrate uptake and transport [11]. We conclude that class IIb LBD genes may play a broader function in apple.

Bottom Line: At the same time, the expression analysis implied that members of this apple gene family were responsive to hormones and stress and that they may participate in hormone-mediated plant organogenesis, which was demonstrated with the overexpression of the apple LBD gene MdLBD11, resulting in an abnormal phenotype.This phenotype included upward curling leaves, delayed flowering, downward-pointing flowers, siliques and other abnormal traits.Based on these data, we concluded that the MdLBD genes may play an important role in apple growth and development as in Arabidopsis and other species.

View Article: PubMed Central - PubMed

Affiliation: National Key laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong, China.

ABSTRACT
The plant-specific LBD (LATERAL ORGAN BOUNDARIES domain) genes belong to a major family of transcription factor that encode a zinc finger-like domain. It has been shown that LBD genes play crucial roles in the growth and development of Arabidopsis and other plant species. However, no detailed information concerning this family is available for apple. In the present study, we analyzed the apple (Malus domestica) genome and identified 58 LBD genes. This gene family was tested for its phylogenetic relationships with homologous genes in the Arabidopsis genome, as well as its location in the genome, structure and expression. We also transformed one MdLBD gene into Arabidopsis to evaluate its function. Like Arabidopsis, apple LBD genes also have a conserved CX2CX6CX3C zinc finger-like domain in the N terminus and can be divided into two classes. The expression profile indicated that apple LBD genes exhibited a variety of expression patterns, suggesting that they have diverse functions. At the same time, the expression analysis implied that members of this apple gene family were responsive to hormones and stress and that they may participate in hormone-mediated plant organogenesis, which was demonstrated with the overexpression of the apple LBD gene MdLBD11, resulting in an abnormal phenotype. This phenotype included upward curling leaves, delayed flowering, downward-pointing flowers, siliques and other abnormal traits. Based on these data, we concluded that the MdLBD genes may play an important role in apple growth and development as in Arabidopsis and other species.

Show MeSH
Related in: MedlinePlus