Genome-wide identification and expression analysis of the polygalacturonase gene family in sweetpotato
Abstract Background Polygalacturonase (PG), a crucial enzyme involved in pectin degradation, is associated with various plants’ developmental and physiological processes such as seed germination, fruit ripening, fruit softening and plant organ abscission. However, the members of PG gene family in sw...
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| Format: | Article |
| Language: | English |
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BMC
2023-06-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-023-04272-1 |
| _version_ | 1827933459269550080 |
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| author | Peiwen He Jingzhen Zhang Zunfu Lv Peng Cui Ximing Xu Melvin Sidikie George Guoquan Lu |
| author_facet | Peiwen He Jingzhen Zhang Zunfu Lv Peng Cui Ximing Xu Melvin Sidikie George Guoquan Lu |
| author_sort | Peiwen He |
| collection | DOAJ |
| description | Abstract Background Polygalacturonase (PG), a crucial enzyme involved in pectin degradation, is associated with various plants’ developmental and physiological processes such as seed germination, fruit ripening, fruit softening and plant organ abscission. However, the members of PG gene family in sweetpotato (Ipomoea batatas) have not been extensively identified. Results In this study, there were 103 PG genes identified in sweetpotato genome, which were phylogenetically clustered into divergent six clades. The gene structure characteristics of each clade were basically conserved. Subsequently, we renamed these PGs according to their locations of the chromosomes. The investigation of collinearity between the PGs in sweetpotato and other four species, contained Arabidopsis thaliana, Solanum lycopersicum, Malus domestica and Ziziphus jujuba, revealed important clues about the potential evolution of the PG family in sweetpotato. Gene duplication analysis showed that IbPGs with collinearity relationships were all derived from segmental duplications, and these genes were under purifying selection. In addition, each promoter region of IbPG proteins contained cis-acting elements related to plant growth and development processes, environmental stress responses and hormone responses. Furthermore, the 103 IbPGs were differentially expressed in various tissues (leaf, stem, proximal end, distal end, root body, root stalk, initiative storage root and fibrous root) and under different abiotic stresses (salt, drought, cold, SA, MeJa and ABA treatment). IbPG038 and IbPG039 were down-regulated with salt, SA and MeJa treatment. According to the further investigation, we found that IbPG006, IbPG034 and IbPG099 had different patterns under the drought and salt stress in fibrous root of sweetpotato, which provided insights into functional differences among these genes. Conclusion A total of 103 IbPGs were identified and classified into six clades from sweetpotato genome. The results of RNA-Seq and qRT-PCR suggested that IbPG006, IbPG034 and IbPG099 might play a significant role in tissue specificity as well as drought and salt stress responses, which showed valuable information for further functional characterization and application of the IbPGs. |
| first_indexed | 2024-03-13T07:25:02Z |
| format | Article |
| id | doaj.art-1fe50042ae6541c48022c2a07e5d3b49 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-03-13T07:25:02Z |
| publishDate | 2023-06-01 |
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| series | BMC Plant Biology |
| spelling | doaj.art-1fe50042ae6541c48022c2a07e5d3b492023-06-04T11:24:53ZengBMCBMC Plant Biology1471-22292023-06-0123111310.1186/s12870-023-04272-1Genome-wide identification and expression analysis of the polygalacturonase gene family in sweetpotatoPeiwen He0Jingzhen Zhang1Zunfu Lv2Peng Cui3Ximing Xu4Melvin Sidikie George5Guoquan Lu6Institute of Root and Tuber Crops, The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F UniversityInstitute of Root and Tuber Crops, The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F UniversityInstitute of Root and Tuber Crops, The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F UniversityInstitute of Root and Tuber Crops, The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F UniversityInstitute of Root and Tuber Crops, The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F UniversityCrop Science Department, Njala UniversityInstitute of Root and Tuber Crops, The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F UniversityAbstract Background Polygalacturonase (PG), a crucial enzyme involved in pectin degradation, is associated with various plants’ developmental and physiological processes such as seed germination, fruit ripening, fruit softening and plant organ abscission. However, the members of PG gene family in sweetpotato (Ipomoea batatas) have not been extensively identified. Results In this study, there were 103 PG genes identified in sweetpotato genome, which were phylogenetically clustered into divergent six clades. The gene structure characteristics of each clade were basically conserved. Subsequently, we renamed these PGs according to their locations of the chromosomes. The investigation of collinearity between the PGs in sweetpotato and other four species, contained Arabidopsis thaliana, Solanum lycopersicum, Malus domestica and Ziziphus jujuba, revealed important clues about the potential evolution of the PG family in sweetpotato. Gene duplication analysis showed that IbPGs with collinearity relationships were all derived from segmental duplications, and these genes were under purifying selection. In addition, each promoter region of IbPG proteins contained cis-acting elements related to plant growth and development processes, environmental stress responses and hormone responses. Furthermore, the 103 IbPGs were differentially expressed in various tissues (leaf, stem, proximal end, distal end, root body, root stalk, initiative storage root and fibrous root) and under different abiotic stresses (salt, drought, cold, SA, MeJa and ABA treatment). IbPG038 and IbPG039 were down-regulated with salt, SA and MeJa treatment. According to the further investigation, we found that IbPG006, IbPG034 and IbPG099 had different patterns under the drought and salt stress in fibrous root of sweetpotato, which provided insights into functional differences among these genes. Conclusion A total of 103 IbPGs were identified and classified into six clades from sweetpotato genome. The results of RNA-Seq and qRT-PCR suggested that IbPG006, IbPG034 and IbPG099 might play a significant role in tissue specificity as well as drought and salt stress responses, which showed valuable information for further functional characterization and application of the IbPGs.https://doi.org/10.1186/s12870-023-04272-1SweetpotatoPolygalacturonase gene familyGenome-wide identificationGene expression |
| spellingShingle | Peiwen He Jingzhen Zhang Zunfu Lv Peng Cui Ximing Xu Melvin Sidikie George Guoquan Lu Genome-wide identification and expression analysis of the polygalacturonase gene family in sweetpotato BMC Plant Biology Sweetpotato Polygalacturonase gene family Genome-wide identification Gene expression |
| title | Genome-wide identification and expression analysis of the polygalacturonase gene family in sweetpotato |
| title_full | Genome-wide identification and expression analysis of the polygalacturonase gene family in sweetpotato |
| title_fullStr | Genome-wide identification and expression analysis of the polygalacturonase gene family in sweetpotato |
| title_full_unstemmed | Genome-wide identification and expression analysis of the polygalacturonase gene family in sweetpotato |
| title_short | Genome-wide identification and expression analysis of the polygalacturonase gene family in sweetpotato |
| title_sort | genome wide identification and expression analysis of the polygalacturonase gene family in sweetpotato |
| topic | Sweetpotato Polygalacturonase gene family Genome-wide identification Gene expression |
| url | https://doi.org/10.1186/s12870-023-04272-1 |
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