Genomic Architecture of <i>AP2</i>/<i>ERF</i> Superfamily Genes in Marigold (<i>Tagetes erecta</i>) and Insights into the Differential Expression Patterns of <i>AP2</i> Family Genes During Floral Organ Specification
The APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily is one of the largest transcription factor families in plants, playing diverse roles in development, stress response, and metabolic regulation. Despite their ecological and economic importance, <i>AP2</i>/<i>ERF</i>...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-05-01
|
| Series: | Agronomy |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4395/15/5/1231 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850254863273820160 |
|---|---|
| author | Hang Li Guoqing Chen Shirui Hu Cuicui Liu Manzhu Bao Yanhong He |
| author_facet | Hang Li Guoqing Chen Shirui Hu Cuicui Liu Manzhu Bao Yanhong He |
| author_sort | Hang Li |
| collection | DOAJ |
| description | The APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily is one of the largest transcription factor families in plants, playing diverse roles in development, stress response, and metabolic regulation. Despite their ecological and economic importance, <i>AP2</i>/<i>ERF</i> genes remain uncharacterized in marigold (<i>Tagetes erecta</i>), a valuable ornamental and medicinal plant in the Asteraceae family known for its unique capitulum-type inflorescence with distinct ray and disc florets. Here, we conducted a comprehensive genome-wide analysis of the AP2/ERF superfamily in marigold and identified 177 <i>AP2</i>/<i>ERF</i> genes distributed across 11 of the 12 chromosomes. Phylogenetic analysis revealed their classification into the AP2 (28 genes), ERF (143 genes), RAV (4 genes), and Soloist (2 genes) families based on domain architecture. Gene structure and motif composition analyses demonstrated group-specific patterns that correlated with their evolutionary relationships. Chromosome mapping and synteny analyses revealed that segmental duplications significantly contributed to <i>AP2</i>/<i>ERF</i> superfamily gene expansion in marigold, with extensive collinearity observed between marigold and other species. Expression profiling across different tissues and developmental stages indicated distinct spatio-temporal expression patterns, with several genes exhibiting tissue-specific expression in Asteraceae-specific structures. In floral organs, <i>TeAP2</i>/<i>ERF145</i> exhibited significantly higher expression in ray floret corollas compared to disc florets, while <i>TeAP2</i>/<i>ERF103</i> showed stamen-specific expression in disc florets. Protein interaction network analysis revealed AP2 as a central hub with extensive predicted interactions with MADS-box and TCP family proteins. These findings suggest that <i>AP2</i> family genes may collaborate with <i>MADS-box</i> and <i>CYC2</i> genes in regulating the characteristic floral architecture of marigold, establishing a foundation for future functional studies and molecular breeding efforts to enhance ornamental and agricultural traits in this economically important plant. |
| format | Article |
| id | doaj-art-474342fd0bde41d6a14a2cccfe8e3840 |
| institution | OA Journals |
| issn | 2073-4395 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agronomy |
| spelling | doaj-art-474342fd0bde41d6a14a2cccfe8e38402025-08-20T01:57:01ZengMDPI AGAgronomy2073-43952025-05-01155123110.3390/agronomy15051231Genomic Architecture of <i>AP2</i>/<i>ERF</i> Superfamily Genes in Marigold (<i>Tagetes erecta</i>) and Insights into the Differential Expression Patterns of <i>AP2</i> Family Genes During Floral Organ SpecificationHang Li0Guoqing Chen1Shirui Hu2Cuicui Liu3Manzhu Bao4Yanhong He5National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, ChinaNational Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, ChinaNational Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, ChinaNational Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, ChinaNational Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, ChinaNational Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, ChinaThe APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily is one of the largest transcription factor families in plants, playing diverse roles in development, stress response, and metabolic regulation. Despite their ecological and economic importance, <i>AP2</i>/<i>ERF</i> genes remain uncharacterized in marigold (<i>Tagetes erecta</i>), a valuable ornamental and medicinal plant in the Asteraceae family known for its unique capitulum-type inflorescence with distinct ray and disc florets. Here, we conducted a comprehensive genome-wide analysis of the AP2/ERF superfamily in marigold and identified 177 <i>AP2</i>/<i>ERF</i> genes distributed across 11 of the 12 chromosomes. Phylogenetic analysis revealed their classification into the AP2 (28 genes), ERF (143 genes), RAV (4 genes), and Soloist (2 genes) families based on domain architecture. Gene structure and motif composition analyses demonstrated group-specific patterns that correlated with their evolutionary relationships. Chromosome mapping and synteny analyses revealed that segmental duplications significantly contributed to <i>AP2</i>/<i>ERF</i> superfamily gene expansion in marigold, with extensive collinearity observed between marigold and other species. Expression profiling across different tissues and developmental stages indicated distinct spatio-temporal expression patterns, with several genes exhibiting tissue-specific expression in Asteraceae-specific structures. In floral organs, <i>TeAP2</i>/<i>ERF145</i> exhibited significantly higher expression in ray floret corollas compared to disc florets, while <i>TeAP2</i>/<i>ERF103</i> showed stamen-specific expression in disc florets. Protein interaction network analysis revealed AP2 as a central hub with extensive predicted interactions with MADS-box and TCP family proteins. These findings suggest that <i>AP2</i> family genes may collaborate with <i>MADS-box</i> and <i>CYC2</i> genes in regulating the characteristic floral architecture of marigold, establishing a foundation for future functional studies and molecular breeding efforts to enhance ornamental and agricultural traits in this economically important plant.https://www.mdpi.com/2073-4395/15/5/1231AP2/ERF transcription factorsmarigold (<i>Tagetes erecta</i>)floral developmentphylogenetic analysisexpression pattern |
| spellingShingle | Hang Li Guoqing Chen Shirui Hu Cuicui Liu Manzhu Bao Yanhong He Genomic Architecture of <i>AP2</i>/<i>ERF</i> Superfamily Genes in Marigold (<i>Tagetes erecta</i>) and Insights into the Differential Expression Patterns of <i>AP2</i> Family Genes During Floral Organ Specification Agronomy AP2/ERF transcription factors marigold (<i>Tagetes erecta</i>) floral development phylogenetic analysis expression pattern |
| title | Genomic Architecture of <i>AP2</i>/<i>ERF</i> Superfamily Genes in Marigold (<i>Tagetes erecta</i>) and Insights into the Differential Expression Patterns of <i>AP2</i> Family Genes During Floral Organ Specification |
| title_full | Genomic Architecture of <i>AP2</i>/<i>ERF</i> Superfamily Genes in Marigold (<i>Tagetes erecta</i>) and Insights into the Differential Expression Patterns of <i>AP2</i> Family Genes During Floral Organ Specification |
| title_fullStr | Genomic Architecture of <i>AP2</i>/<i>ERF</i> Superfamily Genes in Marigold (<i>Tagetes erecta</i>) and Insights into the Differential Expression Patterns of <i>AP2</i> Family Genes During Floral Organ Specification |
| title_full_unstemmed | Genomic Architecture of <i>AP2</i>/<i>ERF</i> Superfamily Genes in Marigold (<i>Tagetes erecta</i>) and Insights into the Differential Expression Patterns of <i>AP2</i> Family Genes During Floral Organ Specification |
| title_short | Genomic Architecture of <i>AP2</i>/<i>ERF</i> Superfamily Genes in Marigold (<i>Tagetes erecta</i>) and Insights into the Differential Expression Patterns of <i>AP2</i> Family Genes During Floral Organ Specification |
| title_sort | genomic architecture of i ap2 i i erf i superfamily genes in marigold i tagetes erecta i and insights into the differential expression patterns of i ap2 i family genes during floral organ specification |
| topic | AP2/ERF transcription factors marigold (<i>Tagetes erecta</i>) floral development phylogenetic analysis expression pattern |
| url | https://www.mdpi.com/2073-4395/15/5/1231 |
| work_keys_str_mv | AT hangli genomicarchitectureofiap2iierfisuperfamilygenesinmarigolditageteserectaiandinsightsintothedifferentialexpressionpatternsofiap2ifamilygenesduringfloralorganspecification AT guoqingchen genomicarchitectureofiap2iierfisuperfamilygenesinmarigolditageteserectaiandinsightsintothedifferentialexpressionpatternsofiap2ifamilygenesduringfloralorganspecification AT shiruihu genomicarchitectureofiap2iierfisuperfamilygenesinmarigolditageteserectaiandinsightsintothedifferentialexpressionpatternsofiap2ifamilygenesduringfloralorganspecification AT cuicuiliu genomicarchitectureofiap2iierfisuperfamilygenesinmarigolditageteserectaiandinsightsintothedifferentialexpressionpatternsofiap2ifamilygenesduringfloralorganspecification AT manzhubao genomicarchitectureofiap2iierfisuperfamilygenesinmarigolditageteserectaiandinsightsintothedifferentialexpressionpatternsofiap2ifamilygenesduringfloralorganspecification AT yanhonghe genomicarchitectureofiap2iierfisuperfamilygenesinmarigolditageteserectaiandinsightsintothedifferentialexpressionpatternsofiap2ifamilygenesduringfloralorganspecification |