Genome-wide identification and expression analysis of the plant-specific PLATZ gene family in Tartary buckwheat (Fagopyrum tataricum)
Abstract Background Plant AT-rich sequence and zinc-binding (PLATZ) proteins belong to a novel class of plant-specific zinc-finger-dependent DNA-binding proteins that play essential roles in plant growth and development. Although the PLATZ gene family has been identified in several species, systemat...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2022-04-01
|
| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-022-03546-4 |
| _version_ | 1819052446553473024 |
|---|---|
| author | Jing Li Shan Feng Yuchuan Zhang Lei Xu Yan Luo Yuhao Yuan Qinghua Yang Baili Feng |
| author_facet | Jing Li Shan Feng Yuchuan Zhang Lei Xu Yan Luo Yuhao Yuan Qinghua Yang Baili Feng |
| author_sort | Jing Li |
| collection | DOAJ |
| description | Abstract Background Plant AT-rich sequence and zinc-binding (PLATZ) proteins belong to a novel class of plant-specific zinc-finger-dependent DNA-binding proteins that play essential roles in plant growth and development. Although the PLATZ gene family has been identified in several species, systematic identification and characterization of this gene family has not yet been carried out for Tartary buckwheat, which is an important medicinal and edible crop with high nutritional value. The recent completion of Tartary buckwheat genome sequencing has laid the foundation for this study. Results A total of 14 FtPLATZ proteins were identified in Tartary buckwheat and were classified into four phylogenetic groups. The gene structure and motif composition were similar within the same group, and evident distinctions among different groups were detected. Gene duplication, particularly segmental duplication, was the main driving force in the evolution of FtPLATZs. Synteny analysis revealed that Tartary buckwheat shares more orthologous PLATZ genes with dicotyledons, particularly soybean. In addition, the expression of FtPLATZs in different tissues and developmental stages of grains showed evident specificity and preference. FtPLATZ3 may be involved in the regulation of grain size, and FtPLATZ4 and FtPLATZ11 may participate in root development. Abundant and variable hormone-responsive cis-acting elements were distributed in the promoter regions of FtPLATZs, and almost all FtPLATZs were significantly regulated after exogenous hormone treatments, particularly methyl jasmonate treatment. Moreover, FtPLATZ6 was significantly upregulated under all exogenous hormone treatments, which may indicate that this gene plays a critical role in the hormone response of Tartary buckwheat. Conclusions This study lays a foundation for further exploration of the function of FtPLATZ proteins and their roles in the growth and development of Tartary buckwheat and contributes to the genetic improvement of Tartary buckwheat. |
| first_indexed | 2024-12-21T12:19:58Z |
| format | Article |
| id | doaj.art-ff29607220f7411dbfddb92c59402563 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-21T12:19:58Z |
| publishDate | 2022-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-ff29607220f7411dbfddb92c594025632022-12-21T19:04:21ZengBMCBMC Plant Biology1471-22292022-04-0122111510.1186/s12870-022-03546-4Genome-wide identification and expression analysis of the plant-specific PLATZ gene family in Tartary buckwheat (Fagopyrum tataricum)Jing Li0Shan Feng1Yuchuan Zhang2Lei Xu3Yan Luo4Yuhao Yuan5Qinghua Yang6Baili Feng7State Key Laboratory of Crop Stress Biology for Arid Areas / College of Agronomy, Northwest A & F UniversitySchool of Mathematics and Statistics, Northwestern Polytechnical UniversityState Key Laboratory of Crop Stress Biology for Arid Areas / College of Agronomy, Northwest A & F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas / College of Agronomy, Northwest A & F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas / College of Agronomy, Northwest A & F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas / College of Agronomy, Northwest A & F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas / College of Agronomy, Northwest A & F UniversityState Key Laboratory of Crop Stress Biology for Arid Areas / College of Agronomy, Northwest A & F UniversityAbstract Background Plant AT-rich sequence and zinc-binding (PLATZ) proteins belong to a novel class of plant-specific zinc-finger-dependent DNA-binding proteins that play essential roles in plant growth and development. Although the PLATZ gene family has been identified in several species, systematic identification and characterization of this gene family has not yet been carried out for Tartary buckwheat, which is an important medicinal and edible crop with high nutritional value. The recent completion of Tartary buckwheat genome sequencing has laid the foundation for this study. Results A total of 14 FtPLATZ proteins were identified in Tartary buckwheat and were classified into four phylogenetic groups. The gene structure and motif composition were similar within the same group, and evident distinctions among different groups were detected. Gene duplication, particularly segmental duplication, was the main driving force in the evolution of FtPLATZs. Synteny analysis revealed that Tartary buckwheat shares more orthologous PLATZ genes with dicotyledons, particularly soybean. In addition, the expression of FtPLATZs in different tissues and developmental stages of grains showed evident specificity and preference. FtPLATZ3 may be involved in the regulation of grain size, and FtPLATZ4 and FtPLATZ11 may participate in root development. Abundant and variable hormone-responsive cis-acting elements were distributed in the promoter regions of FtPLATZs, and almost all FtPLATZs were significantly regulated after exogenous hormone treatments, particularly methyl jasmonate treatment. Moreover, FtPLATZ6 was significantly upregulated under all exogenous hormone treatments, which may indicate that this gene plays a critical role in the hormone response of Tartary buckwheat. Conclusions This study lays a foundation for further exploration of the function of FtPLATZ proteins and their roles in the growth and development of Tartary buckwheat and contributes to the genetic improvement of Tartary buckwheat.https://doi.org/10.1186/s12870-022-03546-4Phylogenetic analysisTandem duplicationSegmental duplicationSynteny analysiscis-acting elementExogenous hormones |
| spellingShingle | Jing Li Shan Feng Yuchuan Zhang Lei Xu Yan Luo Yuhao Yuan Qinghua Yang Baili Feng Genome-wide identification and expression analysis of the plant-specific PLATZ gene family in Tartary buckwheat (Fagopyrum tataricum) BMC Plant Biology Phylogenetic analysis Tandem duplication Segmental duplication Synteny analysis cis-acting element Exogenous hormones |
| title | Genome-wide identification and expression analysis of the plant-specific PLATZ gene family in Tartary buckwheat (Fagopyrum tataricum) |
| title_full | Genome-wide identification and expression analysis of the plant-specific PLATZ gene family in Tartary buckwheat (Fagopyrum tataricum) |
| title_fullStr | Genome-wide identification and expression analysis of the plant-specific PLATZ gene family in Tartary buckwheat (Fagopyrum tataricum) |
| title_full_unstemmed | Genome-wide identification and expression analysis of the plant-specific PLATZ gene family in Tartary buckwheat (Fagopyrum tataricum) |
| title_short | Genome-wide identification and expression analysis of the plant-specific PLATZ gene family in Tartary buckwheat (Fagopyrum tataricum) |
| title_sort | genome wide identification and expression analysis of the plant specific platz gene family in tartary buckwheat fagopyrum tataricum |
| topic | Phylogenetic analysis Tandem duplication Segmental duplication Synteny analysis cis-acting element Exogenous hormones |
| url | https://doi.org/10.1186/s12870-022-03546-4 |
| work_keys_str_mv | AT jingli genomewideidentificationandexpressionanalysisoftheplantspecificplatzgenefamilyintartarybuckwheatfagopyrumtataricum AT shanfeng genomewideidentificationandexpressionanalysisoftheplantspecificplatzgenefamilyintartarybuckwheatfagopyrumtataricum AT yuchuanzhang genomewideidentificationandexpressionanalysisoftheplantspecificplatzgenefamilyintartarybuckwheatfagopyrumtataricum AT leixu genomewideidentificationandexpressionanalysisoftheplantspecificplatzgenefamilyintartarybuckwheatfagopyrumtataricum AT yanluo genomewideidentificationandexpressionanalysisoftheplantspecificplatzgenefamilyintartarybuckwheatfagopyrumtataricum AT yuhaoyuan genomewideidentificationandexpressionanalysisoftheplantspecificplatzgenefamilyintartarybuckwheatfagopyrumtataricum AT qinghuayang genomewideidentificationandexpressionanalysisoftheplantspecificplatzgenefamilyintartarybuckwheatfagopyrumtataricum AT bailifeng genomewideidentificationandexpressionanalysisoftheplantspecificplatzgenefamilyintartarybuckwheatfagopyrumtataricum |