Genome-wide identification, evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo (Phyllostachys edulis) shoots
Abstract Background Aspartic proteases (APs) are a class of aspartic peptidases belonging to nine proteolytic enzyme families whose members are widely distributed in biological organisms. APs play essential functions during plant development and environmental adaptation. However, there are few repor...
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| Format: | Article |
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BMC
2021-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-020-07290-7 |
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| author | Xiaqin Wang Xinyang Yan Shubin Li Yun Jing Lianfeng Gu Shuangquan Zou Jin Zhang Bobin Liu |
| author_facet | Xiaqin Wang Xinyang Yan Shubin Li Yun Jing Lianfeng Gu Shuangquan Zou Jin Zhang Bobin Liu |
| author_sort | Xiaqin Wang |
| collection | DOAJ |
| description | Abstract Background Aspartic proteases (APs) are a class of aspartic peptidases belonging to nine proteolytic enzyme families whose members are widely distributed in biological organisms. APs play essential functions during plant development and environmental adaptation. However, there are few reports about APs in fast-growing moso bamboo. Result In this study, we identified a total of 129 AP proteins (PhAPs) encoded by the moso bamboo genome. Phylogenetic and gene structure analyses showed that these 129 PhAPs could be divided into three categories (categories A, B and C). The PhAP gene family in moso bamboo may have undergone gene expansion, especially the members of categories A and B, although homologs of some members in category C have been lost. The chromosomal location of PhAPs suggested that segmental and tandem duplication events were critical for PhAP gene expansion. Promoter analysis revealed that PhAPs in moso bamboo may be involved in plant development and responses to environmental stress. Furthermore, PhAPs showed tissue-specific expression patterns and may play important roles in rapid growth, including programmed cell death, cell division and elongation, by integrating environmental signals such as light and gibberellin signals. Conclusion Comprehensive analysis of the AP gene family in moso bamboo suggests that PhAPs have experienced gene expansion that is distinct from that in rice and may play an important role in moso bamboo organ development and rapid growth. Our results provide a direction and lay a foundation for further analysis of plant AP genes to clarify their function during rapid growth. |
| first_indexed | 2024-12-17T05:04:10Z |
| format | Article |
| id | doaj.art-bc3e80a9d9b0435d86afa5f9c8006a67 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-17T05:04:10Z |
| publishDate | 2021-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-bc3e80a9d9b0435d86afa5f9c8006a672022-12-21T22:02:29ZengBMCBMC Genomics1471-21642021-01-0122112010.1186/s12864-020-07290-7Genome-wide identification, evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo (Phyllostachys edulis) shootsXiaqin Wang0Xinyang Yan1Shubin Li2Yun Jing3Lianfeng Gu4Shuangquan Zou5Jin Zhang6Bobin Liu7College of Forestry, Fujian Agriculture and Forestry UniversityCollege of Forestry, Fujian Agriculture and Forestry UniversityCollege of Forestry, Fujian Agriculture and Forestry UniversityCollege of Forestry, Fujian Agriculture and Forestry UniversityCollege of Forestry, Fujian Agriculture and Forestry UniversityCollege of Forestry, Fujian Agriculture and Forestry UniversityState Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F UniversityCollege of Forestry, Fujian Agriculture and Forestry UniversityAbstract Background Aspartic proteases (APs) are a class of aspartic peptidases belonging to nine proteolytic enzyme families whose members are widely distributed in biological organisms. APs play essential functions during plant development and environmental adaptation. However, there are few reports about APs in fast-growing moso bamboo. Result In this study, we identified a total of 129 AP proteins (PhAPs) encoded by the moso bamboo genome. Phylogenetic and gene structure analyses showed that these 129 PhAPs could be divided into three categories (categories A, B and C). The PhAP gene family in moso bamboo may have undergone gene expansion, especially the members of categories A and B, although homologs of some members in category C have been lost. The chromosomal location of PhAPs suggested that segmental and tandem duplication events were critical for PhAP gene expansion. Promoter analysis revealed that PhAPs in moso bamboo may be involved in plant development and responses to environmental stress. Furthermore, PhAPs showed tissue-specific expression patterns and may play important roles in rapid growth, including programmed cell death, cell division and elongation, by integrating environmental signals such as light and gibberellin signals. Conclusion Comprehensive analysis of the AP gene family in moso bamboo suggests that PhAPs have experienced gene expansion that is distinct from that in rice and may play an important role in moso bamboo organ development and rapid growth. Our results provide a direction and lay a foundation for further analysis of plant AP genes to clarify their function during rapid growth.https://doi.org/10.1186/s12864-020-07290-7Aspartic proteaseMoso bambooProgrammed cell deathRapid growth |
| spellingShingle | Xiaqin Wang Xinyang Yan Shubin Li Yun Jing Lianfeng Gu Shuangquan Zou Jin Zhang Bobin Liu Genome-wide identification, evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo (Phyllostachys edulis) shoots BMC Genomics Aspartic protease Moso bamboo Programmed cell death Rapid growth |
| title | Genome-wide identification, evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo (Phyllostachys edulis) shoots |
| title_full | Genome-wide identification, evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo (Phyllostachys edulis) shoots |
| title_fullStr | Genome-wide identification, evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo (Phyllostachys edulis) shoots |
| title_full_unstemmed | Genome-wide identification, evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo (Phyllostachys edulis) shoots |
| title_short | Genome-wide identification, evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo (Phyllostachys edulis) shoots |
| title_sort | genome wide identification evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo phyllostachys edulis shoots |
| topic | Aspartic protease Moso bamboo Programmed cell death Rapid growth |
| url | https://doi.org/10.1186/s12864-020-07290-7 |
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