This preprint is under consideration at BMC Plant Biology. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
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Research Article
Yuan Li
College of Landscape Architecture and life Science/Insititute of special Plants, Chongqing University of Arts and Sciences, Chongqing
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background:
AP2/ERF transcription factors perform indispensable functions in various biological processes, such as plant growth, development, biotic and abiotic stresses responses. The AP2/ERF transcription factor family has been identified in many plants, and several AP2/ERF transcription factors from Arabidopsis (Arabidopsis thaliana) have been functionally characterized. However, little research has been conducted on the AP2/ERF genes of ginger (Zingiber officinale), which is an important edible and medicinal horticultural plant. The recently published whole genome sequence of ginger allowed us to study the tissue and expression profiles of AP2/ERF genes in ginger on a genome-wide basis.
Results:
In this study, 163 AP2/ERF genes of ginger (ZoAP2/ERF) were identified and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. According to the number conserved domains and gene structure, the AP2/ERF genes were divided into three subfamilies by phylogenetic analysis, namely, AP2 (35 members), ERF (125 members) and RAV (3 members). A total of 10 motifs were detected in ginger AP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes.
Conclusion:
A comprehensive analysis of AP2/ERF gene expression patterns in different tissues and rhizome development stages by transcriptom sequence and quantitative real-time PCR (qRT-PCR) showed that they played an important role in the growth and development of ginger, and genes that might regulate rhizome and flower development were preliminarily identified. This systematic analysis establishes a foundation for further studies of the functional characteristics of ZoAP2/ERF genes and improvement of ginger.
Keywords
Ginger, ZoAP2/ERF, Inflorescence /Rhizome development, Expression patterns
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No competing interests reported.
This is a list of supplementary files associated with this preprint. Click to download.
- Additionalfile1FigS1SchematicrepresentationsforthechromosomaldistributionofgingerAP2ERFgenes.jpg
Additional file1: Table S1: List of the 163 ZoAP2ERF genes identified in this study
- Additionalfile2TableS1Listofthe163ZoAP2ERFgenesidentifiedinthisstudy.xls
Additional file2: Fig S1: Schematic representations for the chromosomal distribution of ginger AP2ERF genes.
- Additionalfile3FigS2AlignmentofmultipleZoAP2ERFandselectedAP2domainaminoacidsequences.jpg
Additional file3: Fig S2: Alignment of multiple ZoAP2ERF and selected AP2 domain amino acid sequences
- Additionalfile4FigS3AnalysisanddistributionofconservedmotifsingingerAP2ERFproteins..png
Additional file4: Fig S3: Analysis and distribution of conserved motifs in ginger AP2ERF proteins.
- Additionalfile5TableS2ListofthetandemrepeatgenepairsofAP2ERFinginger.xls
Additional file5: Table S2: List of the tandem repeat gene pairs of AP2ERF in ginger.
- Additionalfile6FigS4.AnalysisanddistributioofconservedmotifinAP2subgroupofgingerandotherspecies.png
Additional file6: Fig S4: Analysis and distributio of conserved motif in AP2 subgroup of ginger and other species.
- Additionalfile7FigS5AnalysisanddistributioofconservedmotifinERFsubgroupofgingerandotherspecies.png
Additional file7: Fig S5: Analysis and distributio of conserved motif in ERF subgroup of ginger and other species.
- Additionalfile8FigS6AnalysisanddistributioofconservedmotifinRAVsubgroupofgingerandotherspecies.png
Additional file8: Fig S6: Analysis and distributio of conserved motif in RAV subgroup of ginger and other species.
- Additionalfile9TableS3GingerandotherspeciesAP2ERFsyntenygenepairslist.xls
Additional file9: Table S3: Ginger and other species AP2ERF synteny gene pairs list.
- Additionalfile10TableS4KaKsratio.xls
Additional file10: Table S4: Ka/Ks ratio.
- Additionalfile11TableS5TheprimersequencesofqRTPCR.xls
Additional file11: Table S5: The primer sequences of qRT-PCR.
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CURRENT STATUS: Under Review
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Editorial decision: Major revision
On 14 Apr, 2021
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Received 07 Apr, 2021
Reviewers agreed
On 24 Mar, 2021
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Editor invited
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This preprint is under consideration at BMC Plant Biology. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research Article
Yuan Li
College of Landscape Architecture and life Science/Insititute of special Plants, Chongqing University of Arts and Sciences, Chongqing
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 1
Posted 24 Mar, 2021
No community comments so far
Editorial decision: Major revision
On 14 Apr, 2021
Reviews received
Received 07 Apr, 2021
Reviewers agreed
On 24 Mar, 2021
Reviewers invited
Invitations sent on 22 Mar, 2021
Editor assigned
On 22 Mar, 2021
Editor invited
On 22 Mar, 2021
Submission checks complete
On 22 Mar, 2021
First submitted
On 23 Feb, 2021
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background:
AP2/ERF transcription factors perform indispensable functions in various biological processes, such as plant growth, development, biotic and abiotic stresses responses. The AP2/ERF transcription factor family has been identified in many plants, and several AP2/ERF transcription factors from Arabidopsis (Arabidopsis thaliana) have been functionally characterized. However, little research has been conducted on the AP2/ERF genes of ginger (Zingiber officinale), which is an important edible and medicinal horticultural plant. The recently published whole genome sequence of ginger allowed us to study the tissue and expression profiles of AP2/ERF genes in ginger on a genome-wide basis.
Results:
In this study, 163 AP2/ERF genes of ginger (ZoAP2/ERF) were identified and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. According to the number conserved domains and gene structure, the AP2/ERF genes were divided into three subfamilies by phylogenetic analysis, namely, AP2 (35 members), ERF (125 members) and RAV (3 members). A total of 10 motifs were detected in ginger AP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes.
Conclusion:
A comprehensive analysis of AP2/ERF gene expression patterns in different tissues and rhizome development stages by transcriptom sequence and quantitative real-time PCR (qRT-PCR) showed that they played an important role in the growth and development of ginger, and genes that might regulate rhizome and flower development were preliminarily identified. This systematic analysis establishes a foundation for further studies of the functional characteristics of ZoAP2/ERF genes and improvement of ginger.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9
No competing interests reported.
This is a list of supplementary files associated with this preprint. Click to download.
- Additionalfile1FigS1SchematicrepresentationsforthechromosomaldistributionofgingerAP2ERFgenes.jpg
Additional file1: Table S1: List of the 163 ZoAP2ERF genes identified in this study
- Additionalfile2TableS1Listofthe163ZoAP2ERFgenesidentifiedinthisstudy.xls
Additional file2: Fig S1: Schematic representations for the chromosomal distribution of ginger AP2ERF genes.
- Additionalfile3FigS2AlignmentofmultipleZoAP2ERFandselectedAP2domainaminoacidsequences.jpg
Additional file3: Fig S2: Alignment of multiple ZoAP2ERF and selected AP2 domain amino acid sequences
- Additionalfile4FigS3AnalysisanddistributionofconservedmotifsingingerAP2ERFproteins..png
Additional file4: Fig S3: Analysis and distribution of conserved motifs in ginger AP2ERF proteins.
- Additionalfile5TableS2ListofthetandemrepeatgenepairsofAP2ERFinginger.xls
Additional file5: Table S2: List of the tandem repeat gene pairs of AP2ERF in ginger.
- Additionalfile6FigS4.AnalysisanddistributioofconservedmotifinAP2subgroupofgingerandotherspecies.png
Additional file6: Fig S4: Analysis and distributio of conserved motif in AP2 subgroup of ginger and other species.
- Additionalfile7FigS5AnalysisanddistributioofconservedmotifinERFsubgroupofgingerandotherspecies.png
Additional file7: Fig S5: Analysis and distributio of conserved motif in ERF subgroup of ginger and other species.
- Additionalfile8FigS6AnalysisanddistributioofconservedmotifinRAVsubgroupofgingerandotherspecies.png
Additional file8: Fig S6: Analysis and distributio of conserved motif in RAV subgroup of ginger and other species.
- Additionalfile9TableS3GingerandotherspeciesAP2ERFsyntenygenepairslist.xls
Additional file9: Table S3: Ginger and other species AP2ERF synteny gene pairs list.
- Additionalfile10TableS4KaKsratio.xls
Additional file10: Table S4: Ka/Ks ratio.
- Additionalfile11TableS5TheprimersequencesofqRTPCR.xls
Additional file11: Table S5: The primer sequences of qRT-PCR.
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