Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa)
Abstract The APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) gene family plays vital roles in plants, serving as a key regulator in responses to abiotic stresses. Despite its significance, a comprehensive understanding of this family in lettuce remains incomplete. In this study, we performed a genome-...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-12-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-49245-4 |
| _version_ | 1797388359332528128 |
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| author | Sunchung Park Ainong Shi Lyndel W. Meinhardt Beiquan Mou |
| author_facet | Sunchung Park Ainong Shi Lyndel W. Meinhardt Beiquan Mou |
| author_sort | Sunchung Park |
| collection | DOAJ |
| description | Abstract The APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) gene family plays vital roles in plants, serving as a key regulator in responses to abiotic stresses. Despite its significance, a comprehensive understanding of this family in lettuce remains incomplete. In this study, we performed a genome-wide search for the AP2/ERF family in lettuce and identified a total of 224 members. The duplication patterns provided evidence that both tandem and segmental duplications contributed to the expansion of this family. Ka/Ks ratio analysis demonstrated that, following duplication events, the genes have been subjected to purifying selection pressure, leading to selective constraints on their protein sequence. This selective pressure provides a dosage benefit against stresses in plants. Additionally, a transcriptome analysis indicated that some duplicated genes gained novel functions, emphasizing the contribution of both dosage effect and functional divergence to the family functionalities. Furthermore, an orthologous relationship study showed that 60% of genes descended from a common ancestor of Rosid and Asterid lineages, 28% from the Asterid ancestor, and 12% evolved in the lettuce lineage, suggesting lineage-specific roles in adaptive evolution. These results provide valuable insights into the evolutionary mechanisms of the AP2/ERF gene family in lettuce, with implications for enhancing abiotic stress tolerance, ultimately contributing to the genetic improvement of lettuce crop production. |
| first_indexed | 2024-03-08T22:39:38Z |
| format | Article |
| id | doaj.art-9f0ef82ce1934b95bb200ab7a2eefa6b |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-08T22:39:38Z |
| publishDate | 2023-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-9f0ef82ce1934b95bb200ab7a2eefa6b2023-12-17T12:16:06ZengNature PortfolioScientific Reports2045-23222023-12-0113111610.1038/s41598-023-49245-4Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa)Sunchung Park0Ainong Shi1Lyndel W. Meinhardt2Beiquan Mou3US Department of Agriculture, Agricultural Research ServiceHorticulture Department, University of ArkansasUS Department of Agriculture, Agricultural Research ServiceUS Department of Agriculture, Agricultural Research ServiceAbstract The APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) gene family plays vital roles in plants, serving as a key regulator in responses to abiotic stresses. Despite its significance, a comprehensive understanding of this family in lettuce remains incomplete. In this study, we performed a genome-wide search for the AP2/ERF family in lettuce and identified a total of 224 members. The duplication patterns provided evidence that both tandem and segmental duplications contributed to the expansion of this family. Ka/Ks ratio analysis demonstrated that, following duplication events, the genes have been subjected to purifying selection pressure, leading to selective constraints on their protein sequence. This selective pressure provides a dosage benefit against stresses in plants. Additionally, a transcriptome analysis indicated that some duplicated genes gained novel functions, emphasizing the contribution of both dosage effect and functional divergence to the family functionalities. Furthermore, an orthologous relationship study showed that 60% of genes descended from a common ancestor of Rosid and Asterid lineages, 28% from the Asterid ancestor, and 12% evolved in the lettuce lineage, suggesting lineage-specific roles in adaptive evolution. These results provide valuable insights into the evolutionary mechanisms of the AP2/ERF gene family in lettuce, with implications for enhancing abiotic stress tolerance, ultimately contributing to the genetic improvement of lettuce crop production.https://doi.org/10.1038/s41598-023-49245-4 |
| spellingShingle | Sunchung Park Ainong Shi Lyndel W. Meinhardt Beiquan Mou Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa) Scientific Reports |
| title | Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa) |
| title_full | Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa) |
| title_fullStr | Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa) |
| title_full_unstemmed | Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa) |
| title_short | Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa) |
| title_sort | genome wide characterization and evolutionary analysis of the ap2 erf gene family in lettuce lactuca sativa |
| url | https://doi.org/10.1038/s41598-023-49245-4 |
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