Genome-wide identification and expression profile of Dof transcription factor gene family in pepper (Capsicum annuum L.)
Dof (DNA-binding One Zinc Finger) transcription factor family is unique to plants and has diverse roles associated with plant-specific phenomena, such as light responses, phytohormone and defense responses, and seed development and germination. Although genome-wide analysis of this family has been p...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2016-04-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.00574/full |
| _version_ | 1817971359731417088 |
|---|---|
| author | Cheng eQin Cheng eQin Zhiming eWu Jiaowen eChen Junjie eCui Xiaowan eXu Guansheng eLiang Xirong eLuo Xiaocui eChen Xiangqun eTang Kailin eHu |
| author_facet | Cheng eQin Cheng eQin Zhiming eWu Jiaowen eChen Junjie eCui Xiaowan eXu Guansheng eLiang Xirong eLuo Xiaocui eChen Xiangqun eTang Kailin eHu |
| author_sort | Cheng eQin |
| collection | DOAJ |
| description | Dof (DNA-binding One Zinc Finger) transcription factor family is unique to plants and has diverse roles associated with plant-specific phenomena, such as light responses, phytohormone and defense responses, and seed development and germination. Although genome-wide analysis of this family has been performed in many species, information regarding Dof genes in the pepper, Capsicum annuum L., is extremely limited. In this study, exhaustive searches of pepper genome revealed 33 potential CaDofs that were phylogenetically clustered into four subgroups. Twenty-nine of the 33 Dof genes could be mapped on 11 chromosomes, except for chromosome 7, at different densities. The intron/exon organizations and conserved motif compositions of these genes were also analyzed. Additionally, phylogenetic analysis and classification of the Dof transcription factor family in eight plant species revealed that S. lycopersicum and C. annuum, and O. sativa and S. bicolor Dof proteins may have evolved conservatively. Moreover, comprehensive expression analysis of CaDofs using a RNA-seq atlas and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that these genes exhibit a variety of expression patterns. Most of the CaDofs were expressed in at least one of the tissues tested, whereas several genes were identified as being highly responsive to heat and salt stresses. Overall, this study described the first genome-wide analysis of the pepper Dof family, and these genes exhibited different expression patterns in all primary fruit developmental stages and tissue types, and response to abiotic stress. In particular, some Dof genes might be used as biomarkers for heat and salt stress. The results could expand our understanding of the roles of Dof genes in pepper. Key words: Pepper; DNA-binding one zinc finger; Phylogenetic analysis; Expression analysis; Heat stress; Salinity stress |
| first_indexed | 2024-04-13T20:45:43Z |
| format | Article |
| id | doaj.art-d6bc0f0dc6bb46d79e4af3594d9e89ac |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-13T20:45:43Z |
| publishDate | 2016-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-d6bc0f0dc6bb46d79e4af3594d9e89ac2022-12-22T02:30:41ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2016-04-01710.3389/fpls.2016.00574185464Genome-wide identification and expression profile of Dof transcription factor gene family in pepper (Capsicum annuum L.)Cheng eQin0Cheng eQin1Zhiming eWu2Jiaowen eChen3Junjie eCui4Xiaowan eXu5Guansheng eLiang6Xirong eLuo7Xiaocui eChen8Xiangqun eTang9Kailin eHu10Pepper Institute, Zunyi Academy of Agricultural SciencesGuizhou Provincial College-based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines, Zunyi Medical UniversityCollege of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and EngineeringSouth China Agricultural UniversitySouth China Agricultural UniversityGuangdong Academy of Agricultural SciencesCollege of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and EngineeringPepper Institute, Zunyi Academy of Agricultural SciencesPepper Institute, Zunyi Academy of Agricultural SciencesPepper Institute, Zunyi Academy of Agricultural SciencesSouth China Agricultural UniversityDof (DNA-binding One Zinc Finger) transcription factor family is unique to plants and has diverse roles associated with plant-specific phenomena, such as light responses, phytohormone and defense responses, and seed development and germination. Although genome-wide analysis of this family has been performed in many species, information regarding Dof genes in the pepper, Capsicum annuum L., is extremely limited. In this study, exhaustive searches of pepper genome revealed 33 potential CaDofs that were phylogenetically clustered into four subgroups. Twenty-nine of the 33 Dof genes could be mapped on 11 chromosomes, except for chromosome 7, at different densities. The intron/exon organizations and conserved motif compositions of these genes were also analyzed. Additionally, phylogenetic analysis and classification of the Dof transcription factor family in eight plant species revealed that S. lycopersicum and C. annuum, and O. sativa and S. bicolor Dof proteins may have evolved conservatively. Moreover, comprehensive expression analysis of CaDofs using a RNA-seq atlas and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that these genes exhibit a variety of expression patterns. Most of the CaDofs were expressed in at least one of the tissues tested, whereas several genes were identified as being highly responsive to heat and salt stresses. Overall, this study described the first genome-wide analysis of the pepper Dof family, and these genes exhibited different expression patterns in all primary fruit developmental stages and tissue types, and response to abiotic stress. In particular, some Dof genes might be used as biomarkers for heat and salt stress. The results could expand our understanding of the roles of Dof genes in pepper. Key words: Pepper; DNA-binding one zinc finger; Phylogenetic analysis; Expression analysis; Heat stress; Salinity stresshttp://journal.frontiersin.org/Journal/10.3389/fpls.2016.00574/fullpepperphylogenetic analysissalinity stressexpression analysisHeat stressDNA-binding One Zinc Finger |
| spellingShingle | Cheng eQin Cheng eQin Zhiming eWu Jiaowen eChen Junjie eCui Xiaowan eXu Guansheng eLiang Xirong eLuo Xiaocui eChen Xiangqun eTang Kailin eHu Genome-wide identification and expression profile of Dof transcription factor gene family in pepper (Capsicum annuum L.) Frontiers in Plant Science pepper phylogenetic analysis salinity stress expression analysis Heat stress DNA-binding One Zinc Finger |
| title | Genome-wide identification and expression profile of Dof transcription factor gene family in pepper (Capsicum annuum L.) |
| title_full | Genome-wide identification and expression profile of Dof transcription factor gene family in pepper (Capsicum annuum L.) |
| title_fullStr | Genome-wide identification and expression profile of Dof transcription factor gene family in pepper (Capsicum annuum L.) |
| title_full_unstemmed | Genome-wide identification and expression profile of Dof transcription factor gene family in pepper (Capsicum annuum L.) |
| title_short | Genome-wide identification and expression profile of Dof transcription factor gene family in pepper (Capsicum annuum L.) |
| title_sort | genome wide identification and expression profile of dof transcription factor gene family in pepper capsicum annuum l |
| topic | pepper phylogenetic analysis salinity stress expression analysis Heat stress DNA-binding One Zinc Finger |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.00574/full |
| work_keys_str_mv | AT chengeqin genomewideidentificationandexpressionprofileofdoftranscriptionfactorgenefamilyinpeppercapsicumannuuml AT chengeqin genomewideidentificationandexpressionprofileofdoftranscriptionfactorgenefamilyinpeppercapsicumannuuml AT zhimingewu genomewideidentificationandexpressionprofileofdoftranscriptionfactorgenefamilyinpeppercapsicumannuuml AT jiaowenechen genomewideidentificationandexpressionprofileofdoftranscriptionfactorgenefamilyinpeppercapsicumannuuml AT junjieecui genomewideidentificationandexpressionprofileofdoftranscriptionfactorgenefamilyinpeppercapsicumannuuml AT xiaowanexu genomewideidentificationandexpressionprofileofdoftranscriptionfactorgenefamilyinpeppercapsicumannuuml AT guanshengeliang genomewideidentificationandexpressionprofileofdoftranscriptionfactorgenefamilyinpeppercapsicumannuuml AT xirongeluo genomewideidentificationandexpressionprofileofdoftranscriptionfactorgenefamilyinpeppercapsicumannuuml AT xiaocuiechen genomewideidentificationandexpressionprofileofdoftranscriptionfactorgenefamilyinpeppercapsicumannuuml AT xiangqunetang genomewideidentificationandexpressionprofileofdoftranscriptionfactorgenefamilyinpeppercapsicumannuuml AT kailinehu genomewideidentificationandexpressionprofileofdoftranscriptionfactorgenefamilyinpeppercapsicumannuuml |