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Genome-wide survey and expression analysis of F-box genes in chickpea.

Gupta S, Garg V, Kant C, Bhatia S - BMC Genomics (2015)

Bottom Line: Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis.Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR.The genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi, 110067, India. shefaligupta.14@gmail.com.

ABSTRACT

Background: The F-box genes constitute one of the largest gene families in plants involved in degradation of cellular proteins. F-box proteins can recognize a wide array of substrates and regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence, among others. However, little is known about the F-box genes in the important legume crop, chickpea. The available draft genome sequence of chickpea allowed us to conduct a genome-wide survey of the F-box gene family in chickpea.

Results: A total of 285 F-box genes were identified in chickpea which were classified based on their C-terminal domain structures into 10 subfamilies. Thirteen putative novel motifs were also identified in F-box proteins with no known functional domain at their C-termini. The F-box genes were physically mapped on the 8 chickpea chromosomes and duplication events were investigated which revealed that the F-box gene family expanded largely due to tandem duplications. Phylogenetic analysis classified the chickpea F-box genes into 9 clusters. Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis. Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR.

Conclusions: The genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.

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Related in: MedlinePlus

Phylogenetic analysis of F-box genes in chickpea. The full-length amino acid sequences were aligned and the Neighbour Joining (NJ) tree was constructed using MEGA5. Bootstrap values (1,000 replicates) are placed at the nodes. Values with >50% supporting the node are indicated. Clades are divided into 9 groups A-I. Subfamilies are highlighted by colored segments. Groups B and H contained F-box proteins of FBX subfamily.
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Fig3: Phylogenetic analysis of F-box genes in chickpea. The full-length amino acid sequences were aligned and the Neighbour Joining (NJ) tree was constructed using MEGA5. Bootstrap values (1,000 replicates) are placed at the nodes. Values with >50% supporting the node are indicated. Clades are divided into 9 groups A-I. Subfamilies are highlighted by colored segments. Groups B and H contained F-box proteins of FBX subfamily.

Mentions: A neighbour-joining (NJ) tree was constructed using the full-length protein sequences of all the 285 chickpea F-box genes to study the phylogenetic relationships among them. The phylogenetic tree was divided into 9 clades (Figure 3) in which proteins with the same or similar C-terminal domain organization were found to cluster together. For example, group A mostly contained the members of FBK subfamily. Similarly, all the F-box proteins in group C belonged to FBL subfamily. All the 10 members of FBT subfamily grouped together in group D, a part of a bigger clade. Likewise, 8 members of FBP subfamily were included in group E. Most of the F-box proteins in group F belonged to FBA subfamily. Fifteen of the 17 members belonging to FBDUF subfamily clustered together in a subgroup of clade G. All the members of the FBD subfamily clustered together in group I. Interestingly, proteins with unknown domains either formed their own families (groups B and H), or were scattered within the families formed by proteins with other domains.Figure 3


Genome-wide survey and expression analysis of F-box genes in chickpea.

Gupta S, Garg V, Kant C, Bhatia S - BMC Genomics (2015)

Phylogenetic analysis of F-box genes in chickpea. The full-length amino acid sequences were aligned and the Neighbour Joining (NJ) tree was constructed using MEGA5. Bootstrap values (1,000 replicates) are placed at the nodes. Values with >50% supporting the node are indicated. Clades are divided into 9 groups A-I. Subfamilies are highlighted by colored segments. Groups B and H contained F-box proteins of FBX subfamily.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4340835&req=5

Fig3: Phylogenetic analysis of F-box genes in chickpea. The full-length amino acid sequences were aligned and the Neighbour Joining (NJ) tree was constructed using MEGA5. Bootstrap values (1,000 replicates) are placed at the nodes. Values with >50% supporting the node are indicated. Clades are divided into 9 groups A-I. Subfamilies are highlighted by colored segments. Groups B and H contained F-box proteins of FBX subfamily.
Mentions: A neighbour-joining (NJ) tree was constructed using the full-length protein sequences of all the 285 chickpea F-box genes to study the phylogenetic relationships among them. The phylogenetic tree was divided into 9 clades (Figure 3) in which proteins with the same or similar C-terminal domain organization were found to cluster together. For example, group A mostly contained the members of FBK subfamily. Similarly, all the F-box proteins in group C belonged to FBL subfamily. All the 10 members of FBT subfamily grouped together in group D, a part of a bigger clade. Likewise, 8 members of FBP subfamily were included in group E. Most of the F-box proteins in group F belonged to FBA subfamily. Fifteen of the 17 members belonging to FBDUF subfamily clustered together in a subgroup of clade G. All the members of the FBD subfamily clustered together in group I. Interestingly, proteins with unknown domains either formed their own families (groups B and H), or were scattered within the families formed by proteins with other domains.Figure 3

Bottom Line: Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis.Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR.The genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi, 110067, India. shefaligupta.14@gmail.com.

ABSTRACT

Background: The F-box genes constitute one of the largest gene families in plants involved in degradation of cellular proteins. F-box proteins can recognize a wide array of substrates and regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence, among others. However, little is known about the F-box genes in the important legume crop, chickpea. The available draft genome sequence of chickpea allowed us to conduct a genome-wide survey of the F-box gene family in chickpea.

Results: A total of 285 F-box genes were identified in chickpea which were classified based on their C-terminal domain structures into 10 subfamilies. Thirteen putative novel motifs were also identified in F-box proteins with no known functional domain at their C-termini. The F-box genes were physically mapped on the 8 chickpea chromosomes and duplication events were investigated which revealed that the F-box gene family expanded largely due to tandem duplications. Phylogenetic analysis classified the chickpea F-box genes into 9 clusters. Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis. Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR.

Conclusions: The genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.

Show MeSH
Related in: MedlinePlus