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.
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No competing interests reported.
This is a list of supplementary files associated with this preprint. Click to download.
Additional file1: Table S1: List of the 163 ZoAP2ERF genes identified in this study
Additional file2: Fig S1: Schematic representations for the chromosomal distribution of ginger AP2ERF genes.
Additional file3: Fig S2: Alignment of multiple ZoAP2ERF and selected AP2 domain amino acid sequences
Additional file4: Fig S3: Analysis and distribution of conserved motifs in ginger AP2ERF proteins.
Additional file5: Table S2: List of the tandem repeat gene pairs of AP2ERF in ginger.
Additional file6: Fig S4: Analysis and distributio of conserved motif in AP2 subgroup of ginger and other species.
Additional file7: Fig S5: Analysis and distributio of conserved motif in ERF subgroup of ginger and other species.
Additional file8: Fig S6: Analysis and distributio of conserved motif in RAV subgroup of ginger and other species.
Additional file9: Table S3: Ginger and other species AP2ERF synteny gene pairs list.
Additional file10: Table S4: Ka/Ks ratio.
Additional file11: Table S5: The primer sequences of qRT-PCR.
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Posted 24 Mar, 2021
On 14 Apr, 2021
Received 07 Apr, 2021
Received 07 Apr, 2021
Received 07 Apr, 2021
Received 07 Apr, 2021
Received 07 Apr, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
Invitations sent on 22 Mar, 2021
On 22 Mar, 2021
On 22 Mar, 2021
On 22 Mar, 2021
On 23 Feb, 2021
Posted 24 Mar, 2021
On 14 Apr, 2021
Received 07 Apr, 2021
Received 07 Apr, 2021
Received 07 Apr, 2021
Received 07 Apr, 2021
Received 07 Apr, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
On 24 Mar, 2021
Invitations sent on 22 Mar, 2021
On 22 Mar, 2021
On 22 Mar, 2021
On 22 Mar, 2021
On 23 Feb, 2021
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
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