Isolation of ripening-related genes from ethylene/1-MCP treated papaya through RNA-seq
Abstract Background Since papaya is a typical climacteric fruit, exogenous ethylene (ETH) applications can induce premature and quicker ripening, while 1-methylcyclopropene (1-MCP) slows down the ripening processes. Differential gene expression in ETH or 1-MCP-treated papaya fruits accounts for the...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2017-08-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-017-4072-0 |
| _version_ | 1831841384072478720 |
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| author | Yan Hong Shen Bing Guo Lu Li Feng Fei Ying Yang Jiao Jiao Geng Ray Ming Xiao Jing Chen |
| author_facet | Yan Hong Shen Bing Guo Lu Li Feng Fei Ying Yang Jiao Jiao Geng Ray Ming Xiao Jing Chen |
| author_sort | Yan Hong Shen |
| collection | DOAJ |
| description | Abstract Background Since papaya is a typical climacteric fruit, exogenous ethylene (ETH) applications can induce premature and quicker ripening, while 1-methylcyclopropene (1-MCP) slows down the ripening processes. Differential gene expression in ETH or 1-MCP-treated papaya fruits accounts for the ripening processes. To isolate the key ripening-related genes and better understand fruit ripening mechanisms, transcriptomes of ETH or 1-MCP-treated, and non-treated (Control Group, CG) papaya fruits were sequenced using Illumina Hiseq2500. Results A total of 18,648 (1-MCP), 19,093 (CG), and 15,321 (ETH) genes were detected, with the genes detected in the ETH-treatment being the least. This suggests that ETH may inhibit the expression of some genes. Based on the differential gene expression (DGE) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, 53 fruit ripening-related genes were selected: 20 cell wall-related genes, 18 chlorophyll and carotenoid metabolism-related genes, four proteinases and their inhibitors, six plant hormone signal transduction pathway genes, four transcription factors, and one senescence-associated gene. Reverse transcription quantitative PCR (RT-qPCR) analyses confirmed the results of RNA-seq and verified that the expression pattern of six genes is consistent with the fruit senescence process. Based on the expression profiling of genes in carbohydrate metabolic process, chlorophyll metabolism pathway, and carotenoid metabolism pathway, the mechanism of pulp softening and coloration of papaya was deduced and discussed. We illustrate that papaya fruit softening is a complex process with significant cell wall hydrolases, such as pectinases, cellulases, and hemicellulases involved in the process. Exogenous ethylene accelerates the coloration of papaya changing from green to yellow. This is likely due to the inhibition of chlorophyll biosynthesis and the α-branch of carotenoid metabolism. Chy-b may play an important role in the yellow color of papaya fruit. Conclusions Comparing the differential gene expression in ETH/1-MCP-treated papaya using RNA-seq is a sound approach to isolate ripening-related genes. The results of this study can improve our understanding of papaya fruit ripening molecular mechanism and reveal candidate fruit ripening-related genes for further research. |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-23T06:27:36Z |
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| spelling | doaj.art-5bde72d4a75f42fdb4f2d0d6ccf225de2022-12-21T17:57:00ZengBMCBMC Genomics1471-21642017-08-0118111310.1186/s12864-017-4072-0Isolation of ripening-related genes from ethylene/1-MCP treated papaya through RNA-seqYan Hong Shen0Bing Guo Lu1Li Feng2Fei Ying Yang3Jiao Jiao Geng4Ray Ming5Xiao Jing Chen6College of Horticulture, Fijian Agriculture and Forestry UniversityCollege of Life Sciences, Fujian Normal UniversityCollege of Horticulture, Fijian Agriculture and Forestry UniversityCollege of Horticulture, Fijian Agriculture and Forestry UniversityCollege of Horticulture, Fijian Agriculture and Forestry UniversityFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry UniversityCollege of Horticulture, Fijian Agriculture and Forestry UniversityAbstract Background Since papaya is a typical climacteric fruit, exogenous ethylene (ETH) applications can induce premature and quicker ripening, while 1-methylcyclopropene (1-MCP) slows down the ripening processes. Differential gene expression in ETH or 1-MCP-treated papaya fruits accounts for the ripening processes. To isolate the key ripening-related genes and better understand fruit ripening mechanisms, transcriptomes of ETH or 1-MCP-treated, and non-treated (Control Group, CG) papaya fruits were sequenced using Illumina Hiseq2500. Results A total of 18,648 (1-MCP), 19,093 (CG), and 15,321 (ETH) genes were detected, with the genes detected in the ETH-treatment being the least. This suggests that ETH may inhibit the expression of some genes. Based on the differential gene expression (DGE) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, 53 fruit ripening-related genes were selected: 20 cell wall-related genes, 18 chlorophyll and carotenoid metabolism-related genes, four proteinases and their inhibitors, six plant hormone signal transduction pathway genes, four transcription factors, and one senescence-associated gene. Reverse transcription quantitative PCR (RT-qPCR) analyses confirmed the results of RNA-seq and verified that the expression pattern of six genes is consistent with the fruit senescence process. Based on the expression profiling of genes in carbohydrate metabolic process, chlorophyll metabolism pathway, and carotenoid metabolism pathway, the mechanism of pulp softening and coloration of papaya was deduced and discussed. We illustrate that papaya fruit softening is a complex process with significant cell wall hydrolases, such as pectinases, cellulases, and hemicellulases involved in the process. Exogenous ethylene accelerates the coloration of papaya changing from green to yellow. This is likely due to the inhibition of chlorophyll biosynthesis and the α-branch of carotenoid metabolism. Chy-b may play an important role in the yellow color of papaya fruit. Conclusions Comparing the differential gene expression in ETH/1-MCP-treated papaya using RNA-seq is a sound approach to isolate ripening-related genes. The results of this study can improve our understanding of papaya fruit ripening molecular mechanism and reveal candidate fruit ripening-related genes for further research.http://link.springer.com/article/10.1186/s12864-017-4072-0Carica papaya L.FirmnessColorationTranscriptomeEthylene1-MCP |
| spellingShingle | Yan Hong Shen Bing Guo Lu Li Feng Fei Ying Yang Jiao Jiao Geng Ray Ming Xiao Jing Chen Isolation of ripening-related genes from ethylene/1-MCP treated papaya through RNA-seq BMC Genomics Carica papaya L. Firmness Coloration Transcriptome Ethylene 1-MCP |
| title | Isolation of ripening-related genes from ethylene/1-MCP treated papaya through RNA-seq |
| title_full | Isolation of ripening-related genes from ethylene/1-MCP treated papaya through RNA-seq |
| title_fullStr | Isolation of ripening-related genes from ethylene/1-MCP treated papaya through RNA-seq |
| title_full_unstemmed | Isolation of ripening-related genes from ethylene/1-MCP treated papaya through RNA-seq |
| title_short | Isolation of ripening-related genes from ethylene/1-MCP treated papaya through RNA-seq |
| title_sort | isolation of ripening related genes from ethylene 1 mcp treated papaya through rna seq |
| topic | Carica papaya L. Firmness Coloration Transcriptome Ethylene 1-MCP |
| url | http://link.springer.com/article/10.1186/s12864-017-4072-0 |
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