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Genome-wide analysis of VQ motif-containing proteins in Moso bamboo (Phyllostachys edulis)

Main conclusion 29 Moso bamboo VQ proteins were genome-wide identified for the first time, and bioinformatics analysis was performed to investigate phylogenetic relationships and evolutionary divergence. The qRT-PCR data show that PeVQ genes response to different stress treatments. Accumulating evid... Full description

Journal Title: Planta 2017-04-17, Vol.246 (1), p.165-181
Main Author: Wang, Yujiao
Other Authors: Liu, Huanlong , Zhu, Dongyue , Gao, Yameng , Yan, Hanwei , Xiang, Yan
Format: Electronic Article Electronic Article
Language: English
Subjects:
Publisher: Berlin/Heidelberg: Springer Berlin Heidelberg
ID: ISSN: 0032-0935
Link: https://www.ncbi.nlm.nih.gov/pubmed/28417193
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recordid: cdi_proquest_miscellaneous_1889383683
title: Genome-wide analysis of VQ motif-containing proteins in Moso bamboo (Phyllostachys edulis)
format: Article
creator:
  • Wang, Yujiao
  • Liu, Huanlong
  • Zhu, Dongyue
  • Gao, Yameng
  • Yan, Hanwei
  • Xiang, Yan
subjects:
  • Abscisic acid
  • Acids
  • Agriculture
  • Analysis
  • Anopheles
  • Arabidopsis thaliana
  • Bamboo
  • Bioinformatics
  • Biological evolution
  • Biomedical and Life Sciences
  • Biotechnology
  • Cladistic analysis
  • Conserved sequence
  • Corn
  • Developmental stages
  • Divergence
  • DNA microarrays
  • Ecology
  • Evolution
  • Forestry
  • Forests and forestry
  • Gene expression
  • Gene Expression Regulation, Plant - genetics
  • Genes
  • Genetic research
  • Genome, Plant - genetics
  • Genomes
  • Genomics
  • Introns
  • Life Sciences
  • Mathematical analysis
  • Multigene Family - genetics
  • Nucleotide sequence
  • Original Article
  • Oryza sativa
  • Phylogenetics
  • Phylogeny
  • Plant Proteins - genetics
  • Plant Sciences
  • Poaceae - genetics
  • Polyethylene glycol
  • Polyethylenes
  • Polymerase chain reaction
  • Polyols
  • Profiling
  • Proteins
  • Salicylic acid
  • Subgroups
  • Tissues
  • Zea mays
ispartof: Planta, 2017-04-17, Vol.246 (1), p.165-181
description: Main conclusion 29 Moso bamboo VQ proteins were genome-wide identified for the first time, and bioinformatics analysis was performed to investigate phylogenetic relationships and evolutionary divergence. The qRT-PCR data show that PeVQ genes response to different stress treatments. Accumulating evidence suggests that VQ motif-containing proteins in rice ( Oryza sativa ), Arabidopsis ( Arabidopsis thaliana ), and maize ( Zea mays ) play fundamental roles in response to various biotic and abiotic stresses. However, little is known about the functions of VQ family proteins in Moso bamboo ( Phyllostachys edulis ). In this study, we performed a genome-wide bioinformatic analysis and expression profiling of PeVQ genes. A total of 29 VQ genes was identified and divided into seven subgroups (I–VII) based on phylogenetic analysis. Gene structure and conserved motif analysis revealed that 25 of 29 VQ genes contained no introns. Multiple sequence alignment showed that Moso bamboo VQ motif-containing proteins contained five variations of the conserved motif. The time of duplication and divergence of Moso bamboo from rice and maize was calculated using K s analysis. A heat map was generated using microarray data from 29 Moso bamboo VQ genes suggesting that these genes were expressed in different tissues or developmental stages. Quantitative real-time PCR (qRT-PCR) and promoter analysis indicated that PeVQ genes were differentially regulated following treatment with polyethylene glycol, abscisic acid and salicylic acid. Our results provide a solid foundation for further research of the specific functions of VQ motif-containing proteins in Moso bamboo.
language: eng
source:
identifier: ISSN: 0032-0935
fulltext: no_fulltext
issn:
  • 0032-0935
  • 1432-2048
url: Link


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titleGenome-wide analysis of VQ motif-containing proteins in Moso bamboo (Phyllostachys edulis)
creatorWang, Yujiao ; Liu, Huanlong ; Zhu, Dongyue ; Gao, Yameng ; Yan, Hanwei ; Xiang, Yan
creatorcontribWang, Yujiao ; Liu, Huanlong ; Zhu, Dongyue ; Gao, Yameng ; Yan, Hanwei ; Xiang, Yan
descriptionMain conclusion 29 Moso bamboo VQ proteins were genome-wide identified for the first time, and bioinformatics analysis was performed to investigate phylogenetic relationships and evolutionary divergence. The qRT-PCR data show that PeVQ genes response to different stress treatments. Accumulating evidence suggests that VQ motif-containing proteins in rice ( Oryza sativa ), Arabidopsis ( Arabidopsis thaliana ), and maize ( Zea mays ) play fundamental roles in response to various biotic and abiotic stresses. However, little is known about the functions of VQ family proteins in Moso bamboo ( Phyllostachys edulis ). In this study, we performed a genome-wide bioinformatic analysis and expression profiling of PeVQ genes. A total of 29 VQ genes was identified and divided into seven subgroups (I–VII) based on phylogenetic analysis. Gene structure and conserved motif analysis revealed that 25 of 29 VQ genes contained no introns. Multiple sequence alignment showed that Moso bamboo VQ motif-containing proteins contained five variations of the conserved motif. The time of duplication and divergence of Moso bamboo from rice and maize was calculated using K s analysis. A heat map was generated using microarray data from 29 Moso bamboo VQ genes suggesting that these genes were expressed in different tissues or developmental stages. Quantitative real-time PCR (qRT-PCR) and promoter analysis indicated that PeVQ genes were differentially regulated following treatment with polyethylene glycol, abscisic acid and salicylic acid. Our results provide a solid foundation for further research of the specific functions of VQ motif-containing proteins in Moso bamboo.
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subjectAbscisic acid ; Acids ; Agriculture ; Analysis ; Anopheles ; Arabidopsis thaliana ; Bamboo ; Bioinformatics ; Biological evolution ; Biomedical and Life Sciences ; Biotechnology ; Cladistic analysis ; Conserved sequence ; Corn ; Developmental stages ; Divergence ; DNA microarrays ; Ecology ; Evolution ; Forestry ; Forests and forestry ; Gene expression ; Gene Expression Regulation, Plant - genetics ; Genes ; Genetic research ; Genome, Plant - genetics ; Genomes ; Genomics ; Introns ; Life Sciences ; Mathematical analysis ; Multigene Family - genetics ; Nucleotide sequence ; Original Article ; Oryza sativa ; Phylogenetics ; Phylogeny ; Plant Proteins - genetics ; Plant Sciences ; Poaceae - genetics ; Polyethylene glycol ; Polyethylenes ; Polymerase chain reaction ; Polyols ; Profiling ; Proteins ; Salicylic acid ; Subgroups ; Tissues ; Zea mays
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descriptionMain conclusion 29 Moso bamboo VQ proteins were genome-wide identified for the first time, and bioinformatics analysis was performed to investigate phylogenetic relationships and evolutionary divergence. The qRT-PCR data show that PeVQ genes response to different stress treatments. Accumulating evidence suggests that VQ motif-containing proteins in rice ( Oryza sativa ), Arabidopsis ( Arabidopsis thaliana ), and maize ( Zea mays ) play fundamental roles in response to various biotic and abiotic stresses. However, little is known about the functions of VQ family proteins in Moso bamboo ( Phyllostachys edulis ). In this study, we performed a genome-wide bioinformatic analysis and expression profiling of PeVQ genes. A total of 29 VQ genes was identified and divided into seven subgroups (I–VII) based on phylogenetic analysis. Gene structure and conserved motif analysis revealed that 25 of 29 VQ genes contained no introns. Multiple sequence alignment showed that Moso bamboo VQ motif-containing proteins contained five variations of the conserved motif. The time of duplication and divergence of Moso bamboo from rice and maize was calculated using K s analysis. A heat map was generated using microarray data from 29 Moso bamboo VQ genes suggesting that these genes were expressed in different tissues or developmental stages. Quantitative real-time PCR (qRT-PCR) and promoter analysis indicated that PeVQ genes were differentially regulated following treatment with polyethylene glycol, abscisic acid and salicylic acid. Our results provide a solid foundation for further research of the specific functions of VQ motif-containing proteins in Moso bamboo.
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1Acids
2Agriculture
3Analysis
4Anopheles
5Arabidopsis thaliana
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7Bioinformatics
8Biological evolution
9Biomedical and Life Sciences
10Biotechnology
11Cladistic analysis
12Conserved sequence
13Corn
14Developmental stages
15Divergence
16DNA microarrays
17Ecology
18Evolution
19Forestry
20Forests and forestry
21Gene expression
22Gene Expression Regulation, Plant - genetics
23Genes
24Genetic research
25Genome, Plant - genetics
26Genomes
27Genomics
28Introns
29Life Sciences
30Mathematical analysis
31Multigene Family - genetics
32Nucleotide sequence
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34Oryza sativa
35Phylogenetics
36Phylogeny
37Plant Proteins - genetics
38Plant Sciences
39Poaceae - genetics
40Polyethylene glycol
41Polyethylenes
42Polymerase chain reaction
43Polyols
44Profiling
45Proteins
46Salicylic acid
47Subgroups
48Tissues
49Zea mays
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2Agriculture
3Analysis
4Anopheles
5Arabidopsis thaliana
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8Biological evolution
9Biomedical and Life Sciences
10Biotechnology
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12Conserved sequence
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16DNA microarrays
17Ecology
18Evolution
19Forestry
20Forests and forestry
21Gene expression
22Gene Expression Regulation, Plant - genetics
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39Poaceae - genetics
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42Polymerase chain reaction
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46Salicylic acid
47Subgroups
48Tissues
49Zea mays
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abstractMain conclusion 29 Moso bamboo VQ proteins were genome-wide identified for the first time, and bioinformatics analysis was performed to investigate phylogenetic relationships and evolutionary divergence. The qRT-PCR data show that PeVQ genes response to different stress treatments. Accumulating evidence suggests that VQ motif-containing proteins in rice ( Oryza sativa ), Arabidopsis ( Arabidopsis thaliana ), and maize ( Zea mays ) play fundamental roles in response to various biotic and abiotic stresses. However, little is known about the functions of VQ family proteins in Moso bamboo ( Phyllostachys edulis ). In this study, we performed a genome-wide bioinformatic analysis and expression profiling of PeVQ genes. A total of 29 VQ genes was identified and divided into seven subgroups (I–VII) based on phylogenetic analysis. Gene structure and conserved motif analysis revealed that 25 of 29 VQ genes contained no introns. Multiple sequence alignment showed that Moso bamboo VQ motif-containing proteins contained five variations of the conserved motif. The time of duplication and divergence of Moso bamboo from rice and maize was calculated using K s analysis. A heat map was generated using microarray data from 29 Moso bamboo VQ genes suggesting that these genes were expressed in different tissues or developmental stages. Quantitative real-time PCR (qRT-PCR) and promoter analysis indicated that PeVQ genes were differentially regulated following treatment with polyethylene glycol, abscisic acid and salicylic acid. Our results provide a solid foundation for further research of the specific functions of VQ motif-containing proteins in Moso bamboo.
copBerlin/Heidelberg
pubSpringer Berlin Heidelberg
pmid28417193
doi10.1007/s00425-017-2693-9