Genome-wide identification and molecular characterization of the AP2/ERF superfamily members in sand pear (Pyrus pyrifolia)
Abstract Background ‘Whangkeumbae’ (Pyrus pyrifolia) is a typical climacteric fruit variety of sand pear with excellent taste. However, the rapid postharvest ethylene production limits the shelf life of ‘Whangkeumbae’ fruit. AP2/ERF superfamily is a large family of transcription factors involved in...
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Format: | Article |
Language: | English |
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BMC
2023-01-01
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Series: | BMC Genomics |
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Online Access: | https://doi.org/10.1186/s12864-022-09104-4 |
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author | Yue Xu Xiaona Li Xiong Yang Misganaw Wassie Haiyan Shi |
author_facet | Yue Xu Xiaona Li Xiong Yang Misganaw Wassie Haiyan Shi |
author_sort | Yue Xu |
collection | DOAJ |
description | Abstract Background ‘Whangkeumbae’ (Pyrus pyrifolia) is a typical climacteric fruit variety of sand pear with excellent taste. However, the rapid postharvest ethylene production limits the shelf life of ‘Whangkeumbae’ fruit. AP2/ERF superfamily is a large family of transcription factors involved in plant growth and development, including fruit ripening and senescence through the ethylene signaling pathway. The numbers and functions of AP2/ERF superfamily members in sand pear remain largely unknown. Results In this study, a total of 234 AP2/ERF family members were identified through the transcriptome of Pyrus pyrifolia ‘Whangkeumbae’ (17 genes) and Pyrus pyrifolia genome (223 genes) analyses. Six genes (Accession: EVM0023062.1, EVM0034833.1, EVM0027049.1, EVM0034047.1, EVM0028755.1, EVM0015862.1) identified via genome analysis shared 100% identity with PpERF14-L, PpERF5-L, PpERF3a, PpERF3, PpERF017 and PpERF098, respectively, which were identified from transcriptome sequencing. Further, the AP2/ERF superfamily members were divided into AP2, ERF, and RAV subfamilies, each comprising 38, 188, and 8 members, respectively. Tissue-specific expression analysis showed that PpERF061, PpERF113, PpERF51L-B, PpERF5-L, and PpERF017 were predominantly expressed in fruits than in other tissues. Additionally, PpERF5-L and PpERF017 showed higher expressions at the early stage of fruit development. While, PpERF51B-L exhibited higher expression during the fruit ripening stage. Besides, PpERF061 and PpERF113 had pronounced expressions during fruit senescence. Conclusion These results indicate that PpERF061, PpERF113, PpERF51L-B, PpERF5-L, and PpERF017 could play crucial roles in sand pear fruit development, ripening, and senescence. Overall, this study provides valuable information for further functional analysis of the AP2/ERF genes during fruit ripening and senescence in sand pear. |
first_indexed | 2024-04-10T21:03:50Z |
format | Article |
id | doaj.art-03852843b9564ec491ae908bb9ce2c13 |
institution | Directory Open Access Journal |
issn | 1471-2164 |
language | English |
last_indexed | 2024-04-10T21:03:50Z |
publishDate | 2023-01-01 |
publisher | BMC |
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series | BMC Genomics |
spelling | doaj.art-03852843b9564ec491ae908bb9ce2c132023-01-22T12:05:29ZengBMCBMC Genomics1471-21642023-01-0124111210.1186/s12864-022-09104-4Genome-wide identification and molecular characterization of the AP2/ERF superfamily members in sand pear (Pyrus pyrifolia)Yue Xu0Xiaona Li1Xiong Yang2Misganaw Wassie3Haiyan Shi4College of Horticulture, Hebei Agricultural UniversityCollege of Horticulture, Hebei Agricultural UniversityCollege of Horticulture, Hebei Agricultural UniversityWuhan Botanical Garden, Chinese Academy of SciencesCollege of Horticulture, Hebei Agricultural UniversityAbstract Background ‘Whangkeumbae’ (Pyrus pyrifolia) is a typical climacteric fruit variety of sand pear with excellent taste. However, the rapid postharvest ethylene production limits the shelf life of ‘Whangkeumbae’ fruit. AP2/ERF superfamily is a large family of transcription factors involved in plant growth and development, including fruit ripening and senescence through the ethylene signaling pathway. The numbers and functions of AP2/ERF superfamily members in sand pear remain largely unknown. Results In this study, a total of 234 AP2/ERF family members were identified through the transcriptome of Pyrus pyrifolia ‘Whangkeumbae’ (17 genes) and Pyrus pyrifolia genome (223 genes) analyses. Six genes (Accession: EVM0023062.1, EVM0034833.1, EVM0027049.1, EVM0034047.1, EVM0028755.1, EVM0015862.1) identified via genome analysis shared 100% identity with PpERF14-L, PpERF5-L, PpERF3a, PpERF3, PpERF017 and PpERF098, respectively, which were identified from transcriptome sequencing. Further, the AP2/ERF superfamily members were divided into AP2, ERF, and RAV subfamilies, each comprising 38, 188, and 8 members, respectively. Tissue-specific expression analysis showed that PpERF061, PpERF113, PpERF51L-B, PpERF5-L, and PpERF017 were predominantly expressed in fruits than in other tissues. Additionally, PpERF5-L and PpERF017 showed higher expressions at the early stage of fruit development. While, PpERF51B-L exhibited higher expression during the fruit ripening stage. Besides, PpERF061 and PpERF113 had pronounced expressions during fruit senescence. Conclusion These results indicate that PpERF061, PpERF113, PpERF51L-B, PpERF5-L, and PpERF017 could play crucial roles in sand pear fruit development, ripening, and senescence. Overall, this study provides valuable information for further functional analysis of the AP2/ERF genes during fruit ripening and senescence in sand pear.https://doi.org/10.1186/s12864-022-09104-4Pyrus pyrifoliaAP2/ERF genesRipening and senescenceMolecular characterizationExpression introduction |
spellingShingle | Yue Xu Xiaona Li Xiong Yang Misganaw Wassie Haiyan Shi Genome-wide identification and molecular characterization of the AP2/ERF superfamily members in sand pear (Pyrus pyrifolia) BMC Genomics Pyrus pyrifolia AP2/ERF genes Ripening and senescence Molecular characterization Expression introduction |
title | Genome-wide identification and molecular characterization of the AP2/ERF superfamily members in sand pear (Pyrus pyrifolia) |
title_full | Genome-wide identification and molecular characterization of the AP2/ERF superfamily members in sand pear (Pyrus pyrifolia) |
title_fullStr | Genome-wide identification and molecular characterization of the AP2/ERF superfamily members in sand pear (Pyrus pyrifolia) |
title_full_unstemmed | Genome-wide identification and molecular characterization of the AP2/ERF superfamily members in sand pear (Pyrus pyrifolia) |
title_short | Genome-wide identification and molecular characterization of the AP2/ERF superfamily members in sand pear (Pyrus pyrifolia) |
title_sort | genome wide identification and molecular characterization of the ap2 erf superfamily members in sand pear pyrus pyrifolia |
topic | Pyrus pyrifolia AP2/ERF genes Ripening and senescence Molecular characterization Expression introduction |
url | https://doi.org/10.1186/s12864-022-09104-4 |
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