Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stresses
Abstract Background AP2/ERF transcription factors (TFs) constitute one of the largest TF families in plants, which play crucial roles in plant metabolism, growth, and development as well as biotic and abiotic stresses responses. Although the AP2/ERF family has been thoroughly identified in many plan...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2021-11-01
|
| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-021-03329-3 |
| _version_ | 1818343065253838848 |
|---|---|
| author | Haitao Xing Yusong Jiang Yong Zou Xiaoling Long Xiaoli Wu Yun Ren Yuan Li Hong-Lei Li |
| author_facet | Haitao Xing Yusong Jiang Yong Zou Xiaoling Long Xiaoli Wu Yun Ren Yuan Li Hong-Lei Li |
| author_sort | Haitao Xing |
| collection | DOAJ |
| description | Abstract Background AP2/ERF transcription factors (TFs) constitute one of the largest TF families in plants, which play crucial roles in plant metabolism, growth, and development as well as biotic and abiotic stresses responses. Although the AP2/ERF family has been thoroughly identified in many plant species and several AP2/ERF TFs have been functionally characterized, little is known about this family in ginger (Zingiber officinale Roscoe), an important affinal drug and diet vegetable. Recent completion of the ginger genome sequencing provides an opportunity to investigate the expression profiles of AP2/ERF genes in ginger on a genome-wide basis. Results A total of 163 AP2/ERF genes were obtained in the Z.officinale genome and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. Phylogenetic analysis divided them into three subfamilies, of which 35 belonged to the AP2 subfamily, 120 to ERF, three to RAV, and five to Sololist, respectively, which is in accordance with the number of conserved domains and gene structure analysis. A total of 10 motifs were detected in ZoAP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes. The chromosomal localization, gene structure, and conserved protein motif analyses, as well as the characterization of gene duplication events provided deep insight into the evolutionary features of these ZoAP2/ERF genes. The expression profiles derived from the RNA-seq data and quantitative reserve transcription (qRT-PCR) analysis of ZoAP2/ERFs during development and responses to abiotic stresses were investigated in ginger. Conclusion A comprehensive analysis of the AP2/ERF gene expression patterns in various tissues by RNA-seq and 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 preliminary identified. In additionally, the ZoAP2/ERF family genes that responded to abiotic stresses were also identified. This study is the first time to identify the ZoAP2/ERF family, which contributes to research on evolutionary characteristics and better understanding the molecular basis for development and abiotic stress response, as well as further functional characterization of ZoAP2/ERF genes with an aim of ginger crop improvement. |
| first_indexed | 2024-12-13T16:24:39Z |
| format | Article |
| id | doaj.art-59cffc6fc7e94a5d9cb4c944f7115ded |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-13T16:24:39Z |
| publishDate | 2021-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-59cffc6fc7e94a5d9cb4c944f7115ded2022-12-21T23:38:38ZengBMCBMC Plant Biology1471-22292021-11-0121112110.1186/s12870-021-03329-3Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stressesHaitao Xing0Yusong Jiang1Yong Zou2Xiaoling Long3Xiaoli Wu4Yun Ren5Yuan Li6Hong-Lei Li7College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and SciencesCollege of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and SciencesCollege of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and SciencesCollege of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and SciencesCollege of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and SciencesCollege of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and SciencesCollege of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and SciencesCollege of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and SciencesAbstract Background AP2/ERF transcription factors (TFs) constitute one of the largest TF families in plants, which play crucial roles in plant metabolism, growth, and development as well as biotic and abiotic stresses responses. Although the AP2/ERF family has been thoroughly identified in many plant species and several AP2/ERF TFs have been functionally characterized, little is known about this family in ginger (Zingiber officinale Roscoe), an important affinal drug and diet vegetable. Recent completion of the ginger genome sequencing provides an opportunity to investigate the expression profiles of AP2/ERF genes in ginger on a genome-wide basis. Results A total of 163 AP2/ERF genes were obtained in the Z.officinale genome and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. Phylogenetic analysis divided them into three subfamilies, of which 35 belonged to the AP2 subfamily, 120 to ERF, three to RAV, and five to Sololist, respectively, which is in accordance with the number of conserved domains and gene structure analysis. A total of 10 motifs were detected in ZoAP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes. The chromosomal localization, gene structure, and conserved protein motif analyses, as well as the characterization of gene duplication events provided deep insight into the evolutionary features of these ZoAP2/ERF genes. The expression profiles derived from the RNA-seq data and quantitative reserve transcription (qRT-PCR) analysis of ZoAP2/ERFs during development and responses to abiotic stresses were investigated in ginger. Conclusion A comprehensive analysis of the AP2/ERF gene expression patterns in various tissues by RNA-seq and 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 preliminary identified. In additionally, the ZoAP2/ERF family genes that responded to abiotic stresses were also identified. This study is the first time to identify the ZoAP2/ERF family, which contributes to research on evolutionary characteristics and better understanding the molecular basis for development and abiotic stress response, as well as further functional characterization of ZoAP2/ERF genes with an aim of ginger crop improvement.https://doi.org/10.1186/s12870-021-03329-3GingerZoAP2/ERFInflorescence/rhizome developmentAbiotic stressExpression patterns |
| spellingShingle | Haitao Xing Yusong Jiang Yong Zou Xiaoling Long Xiaoli Wu Yun Ren Yuan Li Hong-Lei Li Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stresses BMC Plant Biology Ginger ZoAP2/ERF Inflorescence/rhizome development Abiotic stress Expression patterns |
| title | Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stresses |
| title_full | Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stresses |
| title_fullStr | Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stresses |
| title_full_unstemmed | Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stresses |
| title_short | Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stresses |
| title_sort | genome wide investigation of the ap2 erf gene family in ginger evolution and expression profiling during development and abiotic stresses |
| topic | Ginger ZoAP2/ERF Inflorescence/rhizome development Abiotic stress Expression patterns |
| url | https://doi.org/10.1186/s12870-021-03329-3 |
| work_keys_str_mv | AT haitaoxing genomewideinvestigationoftheap2erfgenefamilyingingerevolutionandexpressionprofilingduringdevelopmentandabioticstresses AT yusongjiang genomewideinvestigationoftheap2erfgenefamilyingingerevolutionandexpressionprofilingduringdevelopmentandabioticstresses AT yongzou genomewideinvestigationoftheap2erfgenefamilyingingerevolutionandexpressionprofilingduringdevelopmentandabioticstresses AT xiaolinglong genomewideinvestigationoftheap2erfgenefamilyingingerevolutionandexpressionprofilingduringdevelopmentandabioticstresses AT xiaoliwu genomewideinvestigationoftheap2erfgenefamilyingingerevolutionandexpressionprofilingduringdevelopmentandabioticstresses AT yunren genomewideinvestigationoftheap2erfgenefamilyingingerevolutionandexpressionprofilingduringdevelopmentandabioticstresses AT yuanli genomewideinvestigationoftheap2erfgenefamilyingingerevolutionandexpressionprofilingduringdevelopmentandabioticstresses AT hongleili genomewideinvestigationoftheap2erfgenefamilyingingerevolutionandexpressionprofilingduringdevelopmentandabioticstresses |