Alternative splicing of the PECTINESTERASE gene encoding a cell wall-degrading enzyme affects postharvest softening in grape
The firmness of table grape berries is a crucial quality parameter. Despite extensive research on postharvest fruit softening, its precise molecular mechanisms remain elusive. To enhance our comprehension of the underlying molecular factors, we initially identified differentially expressed genes (DE...
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| Format: | Article |
| Language: | English |
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Elsevier
2024-03-01
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| Series: | Journal of Integrative Agriculture |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2095311923004203 |
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| author | Hainan Liu Maosong Pei Charles Ampomah-Dwamena Yaxin Shang Yihe Yu Tonglu Wei Qiaofang Shi Dalong Guo |
| author_facet | Hainan Liu Maosong Pei Charles Ampomah-Dwamena Yaxin Shang Yihe Yu Tonglu Wei Qiaofang Shi Dalong Guo |
| author_sort | Hainan Liu |
| collection | DOAJ |
| description | The firmness of table grape berries is a crucial quality parameter. Despite extensive research on postharvest fruit softening, its precise molecular mechanisms remain elusive. To enhance our comprehension of the underlying molecular factors, we initially identified differentially expressed genes (DEGs) by comparing the transcriptomes of folic acid (FA)-treated and water-treated (CK) berries at different time points. We then analyzed the sequences to detect alternatively spliced (AS) genes associated with postharvest softening. A total of 2,559 DEGs were identified and categorized into four subclusters based on their expression patterns, with subcluster-4 genes exhibiting higher expression in the CK group compared with the FA treatment group. There were 1,045 AS-associated genes specific to FA-treated berries and 1,042 in the CK-treated berries, respectively. Gene Ontology (GO) annotation indicated that the AS-associated genes in CK-treated berries were predominantly enriched in cell wall metabolic processes, particularly cell wall degradation processes. Through a comparison between treatment-associated AS genes and subcluster-4 DEGs, we identified eight genes, including Pectinesterase 2 (VvPE2, Vitvi15g00704), which encodes a cell wall-degrading enzyme and was predicted to undergo an A3SS event. The reverse transcription polymerase chain reaction further confirmed the presence of a truncated transcript variant of VvPE2 in the FA-treated berries. Our study provides a comprehensive analysis of AS events in postharvest grape berries using transcriptome sequencing and underscores the pivotal role of VvPE2 during the postharvest storage of grape berries. |
| first_indexed | 2024-04-24T23:48:07Z |
| format | Article |
| id | doaj.art-decfea1c8744411e978fc58493569ce3 |
| institution | Directory Open Access Journal |
| issn | 2095-3119 |
| language | English |
| last_indexed | 2024-04-24T23:48:07Z |
| publishDate | 2024-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Integrative Agriculture |
| spelling | doaj.art-decfea1c8744411e978fc58493569ce32024-03-15T04:43:12ZengElsevierJournal of Integrative Agriculture2095-31192024-03-01233863875Alternative splicing of the PECTINESTERASE gene encoding a cell wall-degrading enzyme affects postharvest softening in grapeHainan Liu0Maosong Pei1Charles Ampomah-Dwamena2Yaxin Shang3Yihe Yu4Tonglu Wei5Qiaofang Shi6Dalong Guo7College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471000, China; Henan Engineering Technology Research Center of Quality Regulation and Control of Horticultural Plants, Luoyang 471000, ChinaCollege of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471000, China; Henan Engineering Technology Research Center of Quality Regulation and Control of Horticultural Plants, Luoyang 471000, ChinaThe New Zealand Institute for Plant & Food Research Limited (PFR), Auckland 1010, New ZealandCollege of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471000, China; Henan Engineering Technology Research Center of Quality Regulation and Control of Horticultural Plants, Luoyang 471000, ChinaCollege of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471000, China; Henan Engineering Technology Research Center of Quality Regulation and Control of Horticultural Plants, Luoyang 471000, ChinaCollege of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471000, China; Henan Engineering Technology Research Center of Quality Regulation and Control of Horticultural Plants, Luoyang 471000, ChinaCollege of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471000, China; Henan Engineering Technology Research Center of Quality Regulation and Control of Horticultural Plants, Luoyang 471000, ChinaCollege of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471000, China; Henan Engineering Technology Research Center of Quality Regulation and Control of Horticultural Plants, Luoyang 471000, China; Correspondence Dalong GuoThe firmness of table grape berries is a crucial quality parameter. Despite extensive research on postharvest fruit softening, its precise molecular mechanisms remain elusive. To enhance our comprehension of the underlying molecular factors, we initially identified differentially expressed genes (DEGs) by comparing the transcriptomes of folic acid (FA)-treated and water-treated (CK) berries at different time points. We then analyzed the sequences to detect alternatively spliced (AS) genes associated with postharvest softening. A total of 2,559 DEGs were identified and categorized into four subclusters based on their expression patterns, with subcluster-4 genes exhibiting higher expression in the CK group compared with the FA treatment group. There were 1,045 AS-associated genes specific to FA-treated berries and 1,042 in the CK-treated berries, respectively. Gene Ontology (GO) annotation indicated that the AS-associated genes in CK-treated berries were predominantly enriched in cell wall metabolic processes, particularly cell wall degradation processes. Through a comparison between treatment-associated AS genes and subcluster-4 DEGs, we identified eight genes, including Pectinesterase 2 (VvPE2, Vitvi15g00704), which encodes a cell wall-degrading enzyme and was predicted to undergo an A3SS event. The reverse transcription polymerase chain reaction further confirmed the presence of a truncated transcript variant of VvPE2 in the FA-treated berries. Our study provides a comprehensive analysis of AS events in postharvest grape berries using transcriptome sequencing and underscores the pivotal role of VvPE2 during the postharvest storage of grape berries.http://www.sciencedirect.com/science/article/pii/S2095311923004203grapepostharvest softeningfolic acidalternative splicingPectinesterase 2alternative 3´ splice site (A3SS) |
| spellingShingle | Hainan Liu Maosong Pei Charles Ampomah-Dwamena Yaxin Shang Yihe Yu Tonglu Wei Qiaofang Shi Dalong Guo Alternative splicing of the PECTINESTERASE gene encoding a cell wall-degrading enzyme affects postharvest softening in grape Journal of Integrative Agriculture grape postharvest softening folic acid alternative splicing Pectinesterase 2 alternative 3´ splice site (A3SS) |
| title | Alternative splicing of the PECTINESTERASE gene encoding a cell wall-degrading enzyme affects postharvest softening in grape |
| title_full | Alternative splicing of the PECTINESTERASE gene encoding a cell wall-degrading enzyme affects postharvest softening in grape |
| title_fullStr | Alternative splicing of the PECTINESTERASE gene encoding a cell wall-degrading enzyme affects postharvest softening in grape |
| title_full_unstemmed | Alternative splicing of the PECTINESTERASE gene encoding a cell wall-degrading enzyme affects postharvest softening in grape |
| title_short | Alternative splicing of the PECTINESTERASE gene encoding a cell wall-degrading enzyme affects postharvest softening in grape |
| title_sort | alternative splicing of the pectinesterase gene encoding a cell wall degrading enzyme affects postharvest softening in grape |
| topic | grape postharvest softening folic acid alternative splicing Pectinesterase 2 alternative 3´ splice site (A3SS) |
| url | http://www.sciencedirect.com/science/article/pii/S2095311923004203 |
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