Genome-Wide Identification of the YABBY Gene Family in <i>Dendrobium</i> Orchids and Its Expression Patterns in <i>Dendrobium chrysotoxum</i>
The small plant-specific YABBY gene family plays key roles in diverse developmental processes in plants. <i>Dendrobium chrysotoxum</i>, <i>D. huoshanense</i>, and <i>D. nobile</i> are perennial herbaceous plants belonging to Orchidaceae with a high ornamental valu...
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| Format: | Article |
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MDPI AG
2023-06-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/12/10165 |
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| author | Qinyao Zheng Xuewei Zhao Ye Huang Meng-Meng Zhang Xin He Shijie Ke Yuanyuan Li Cuili Zhang Sagheer Ahmad Siren Lan Minghe Li Zhong-Jian Liu |
| author_facet | Qinyao Zheng Xuewei Zhao Ye Huang Meng-Meng Zhang Xin He Shijie Ke Yuanyuan Li Cuili Zhang Sagheer Ahmad Siren Lan Minghe Li Zhong-Jian Liu |
| author_sort | Qinyao Zheng |
| collection | DOAJ |
| description | The small plant-specific YABBY gene family plays key roles in diverse developmental processes in plants. <i>Dendrobium chrysotoxum</i>, <i>D. huoshanense</i>, and <i>D. nobile</i> are perennial herbaceous plants belonging to Orchidaceae with a high ornamental value. However, the relationships and specific functions of the YABBY genes in the <i>Dendrobium</i> species remain unknown. In this study, six <i>DchYABBY</i>s, nine <i>DhuYABBY</i>s, and nine <i>DnoYABBY</i>s were identified from the genome databases of the three <i>Dendrobium</i> species, which were unevenly distributed on five, eight, and nine chromosomes, respectively. The 24 YABBY genes were classified into four subfamilies (CRC/DL, INO, YAB2, and FIL/YAB3) based on their phylogenetic analysis. A sequence analysis showed that most of the YABBY proteins contained conserved C2C2 zinc-finger and YABBY domains, while a gene structure analysis revealed that 46% of the total YABBY genes contained seven exons and six introns. All the YABBY genes harbored a large number of Methyl Jasmonate responsive elements, as well as anaerobic induction <i>cis</i>-acting elements in the promoter regions. Through a collinearity analysis, one, two, and two segmental duplicated gene pairs were identified in the <i>D. chrysotoxum</i>, <i>D. huoshanense</i>, and <i>D. nobile</i> genomes, respectively. The <i>Ka/Ks</i> values of these five gene pairs were lower than 0.5, indicating that the <i>Dendrobium</i> YABBY genes underwent negative selection. In addition, an expression analysis revealed that <i>DchYABBY2</i> plays a role in ovary and early-stage petal development, while <i>DchYABBY5</i> is essential for lip development and <i>DchYABBY6</i> is crucial for early sepal formation. <i>DchYABBY1</i> primarily regulates sepals during blooming. Furthermore, there is the potential involvement of <i>DchYABBY2</i> and <i>DchYABBY5</i> in gynostemium development. The results of a comprehensive genome-wide study would provide significant clues for future functional investigations and pattern analyses of YABBY genes in different flower parts during flower development in the <i>Dendrobium</i> species. |
| first_indexed | 2024-03-11T02:21:50Z |
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| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T02:21:50Z |
| publishDate | 2023-06-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-ce99099f3bbc4eed9073395d13f7dbea2023-11-18T10:49:36ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-06-0124121016510.3390/ijms241210165Genome-Wide Identification of the YABBY Gene Family in <i>Dendrobium</i> Orchids and Its Expression Patterns in <i>Dendrobium chrysotoxum</i>Qinyao Zheng0Xuewei Zhao1Ye Huang2Meng-Meng Zhang3Xin He4Shijie Ke5Yuanyuan Li6Cuili Zhang7Sagheer Ahmad8Siren Lan9Minghe Li10Zhong-Jian Liu11Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaCollege of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaCollege of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaCollege of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaCollege of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaThe small plant-specific YABBY gene family plays key roles in diverse developmental processes in plants. <i>Dendrobium chrysotoxum</i>, <i>D. huoshanense</i>, and <i>D. nobile</i> are perennial herbaceous plants belonging to Orchidaceae with a high ornamental value. However, the relationships and specific functions of the YABBY genes in the <i>Dendrobium</i> species remain unknown. In this study, six <i>DchYABBY</i>s, nine <i>DhuYABBY</i>s, and nine <i>DnoYABBY</i>s were identified from the genome databases of the three <i>Dendrobium</i> species, which were unevenly distributed on five, eight, and nine chromosomes, respectively. The 24 YABBY genes were classified into four subfamilies (CRC/DL, INO, YAB2, and FIL/YAB3) based on their phylogenetic analysis. A sequence analysis showed that most of the YABBY proteins contained conserved C2C2 zinc-finger and YABBY domains, while a gene structure analysis revealed that 46% of the total YABBY genes contained seven exons and six introns. All the YABBY genes harbored a large number of Methyl Jasmonate responsive elements, as well as anaerobic induction <i>cis</i>-acting elements in the promoter regions. Through a collinearity analysis, one, two, and two segmental duplicated gene pairs were identified in the <i>D. chrysotoxum</i>, <i>D. huoshanense</i>, and <i>D. nobile</i> genomes, respectively. The <i>Ka/Ks</i> values of these five gene pairs were lower than 0.5, indicating that the <i>Dendrobium</i> YABBY genes underwent negative selection. In addition, an expression analysis revealed that <i>DchYABBY2</i> plays a role in ovary and early-stage petal development, while <i>DchYABBY5</i> is essential for lip development and <i>DchYABBY6</i> is crucial for early sepal formation. <i>DchYABBY1</i> primarily regulates sepals during blooming. Furthermore, there is the potential involvement of <i>DchYABBY2</i> and <i>DchYABBY5</i> in gynostemium development. The results of a comprehensive genome-wide study would provide significant clues for future functional investigations and pattern analyses of YABBY genes in different flower parts during flower development in the <i>Dendrobium</i> species.https://www.mdpi.com/1422-0067/24/12/10165YABBY transcription factor<i>Dendrobium</i> orchidexpression pattern<i>D. chrysotoxum</i><i>D. huoshanense</i><i>D. nobile</i> |
| spellingShingle | Qinyao Zheng Xuewei Zhao Ye Huang Meng-Meng Zhang Xin He Shijie Ke Yuanyuan Li Cuili Zhang Sagheer Ahmad Siren Lan Minghe Li Zhong-Jian Liu Genome-Wide Identification of the YABBY Gene Family in <i>Dendrobium</i> Orchids and Its Expression Patterns in <i>Dendrobium chrysotoxum</i> International Journal of Molecular Sciences YABBY transcription factor <i>Dendrobium</i> orchid expression pattern <i>D. chrysotoxum</i> <i>D. huoshanense</i> <i>D. nobile</i> |
| title | Genome-Wide Identification of the YABBY Gene Family in <i>Dendrobium</i> Orchids and Its Expression Patterns in <i>Dendrobium chrysotoxum</i> |
| title_full | Genome-Wide Identification of the YABBY Gene Family in <i>Dendrobium</i> Orchids and Its Expression Patterns in <i>Dendrobium chrysotoxum</i> |
| title_fullStr | Genome-Wide Identification of the YABBY Gene Family in <i>Dendrobium</i> Orchids and Its Expression Patterns in <i>Dendrobium chrysotoxum</i> |
| title_full_unstemmed | Genome-Wide Identification of the YABBY Gene Family in <i>Dendrobium</i> Orchids and Its Expression Patterns in <i>Dendrobium chrysotoxum</i> |
| title_short | Genome-Wide Identification of the YABBY Gene Family in <i>Dendrobium</i> Orchids and Its Expression Patterns in <i>Dendrobium chrysotoxum</i> |
| title_sort | genome wide identification of the yabby gene family in i dendrobium i orchids and its expression patterns in i dendrobium chrysotoxum i |
| topic | YABBY transcription factor <i>Dendrobium</i> orchid expression pattern <i>D. chrysotoxum</i> <i>D. huoshanense</i> <i>D. nobile</i> |
| url | https://www.mdpi.com/1422-0067/24/12/10165 |
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