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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Main Authors: Yue Xu, Xiaona Li, Xiong Yang, Misganaw Wassie, Haiyan Shi
Format: Article
Language:English
Published: BMC 2023-01-01
Series:BMC Genomics
Subjects:
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.
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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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