Genome-wide identification and analysis of the EIN3/EIL gene family in allotetraploid Brassica napus reveal its potential advantages during polyploidization
Abstract Background Polyploidization is a common event in the evolutionary history of angiosperms, and there will be some changes in the genomes of plants other than a simple genomic doubling after polyploidization. Allotetraploid Brassica napus and its diploid progenitors (B. rapa and B. oleracea)...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-03-01
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| Series: | BMC Plant Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s12870-019-1716-z |
| _version_ | 1818334703143354368 |
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| author | Mengdi Li Ruihua Wang Ziwei Liang Xiaoming Wu Jianbo Wang |
| author_facet | Mengdi Li Ruihua Wang Ziwei Liang Xiaoming Wu Jianbo Wang |
| author_sort | Mengdi Li |
| collection | DOAJ |
| description | Abstract Background Polyploidization is a common event in the evolutionary history of angiosperms, and there will be some changes in the genomes of plants other than a simple genomic doubling after polyploidization. Allotetraploid Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are a good group for studying the problems associated with polyploidization. On the other hand, the EIN3/EIL gene family is an important gene family in plants, all members of which are key genes in the ethylene signaling pathway. Until now, the EIN3/EIL gene family in B. napus and its diploid progenitors have been largely unknown, so it is necessary to comprehensively identify and analyze this gene family. Results In this study, 13, 7 and 7 EIN3/EIL genes were identified in B. napus (2n = 4x = 38, AnCn), B. rapa (2n = 2x = 20, Ar) and B. oleracea (2n = 2x = 18, Co). All of the identified EIN3/EIL proteins were divided into 3 clades and further divided into 8 sub-clades. Ka/Ks analysis showed that all identified EIN3/EIL genes underwent purifying selection after the duplication events. Moreover, gene structure analysis showed that some EIN3/EIL genes in B. napus acquired introns during polyploidization, and homolog expression bias analysis showed that B. napus was biased towards its diploid progenitor B. rapa. The promoters of the EIN3/EIL genes in B. napus contained more cis-acting elements, which were mainly involved in endosperm gene expression and light responsiveness, than its diploid progenitors. Thus, B. napus might have potential advantages in some biological aspects. Conclusions The results indicated allotetraploid B. napus might have potential advantages in some biological aspects. Moreover, our results can increase the understanding of the evolution of the EIN3/EIL gene family in B. napus, and provided more reference for future research about polyploidization. |
| first_indexed | 2024-12-13T14:11:44Z |
| format | Article |
| id | doaj.art-e5b77096fa704a27ba2fb7704a15aafb |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-13T14:11:44Z |
| publishDate | 2019-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-e5b77096fa704a27ba2fb7704a15aafb2022-12-21T23:42:27ZengBMCBMC Plant Biology1471-22292019-03-0119111610.1186/s12870-019-1716-zGenome-wide identification and analysis of the EIN3/EIL gene family in allotetraploid Brassica napus reveal its potential advantages during polyploidizationMengdi Li0Ruihua Wang1Ziwei Liang2Xiaoming Wu3Jianbo Wang4State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityKey Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of CAASState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityAbstract Background Polyploidization is a common event in the evolutionary history of angiosperms, and there will be some changes in the genomes of plants other than a simple genomic doubling after polyploidization. Allotetraploid Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are a good group for studying the problems associated with polyploidization. On the other hand, the EIN3/EIL gene family is an important gene family in plants, all members of which are key genes in the ethylene signaling pathway. Until now, the EIN3/EIL gene family in B. napus and its diploid progenitors have been largely unknown, so it is necessary to comprehensively identify and analyze this gene family. Results In this study, 13, 7 and 7 EIN3/EIL genes were identified in B. napus (2n = 4x = 38, AnCn), B. rapa (2n = 2x = 20, Ar) and B. oleracea (2n = 2x = 18, Co). All of the identified EIN3/EIL proteins were divided into 3 clades and further divided into 8 sub-clades. Ka/Ks analysis showed that all identified EIN3/EIL genes underwent purifying selection after the duplication events. Moreover, gene structure analysis showed that some EIN3/EIL genes in B. napus acquired introns during polyploidization, and homolog expression bias analysis showed that B. napus was biased towards its diploid progenitor B. rapa. The promoters of the EIN3/EIL genes in B. napus contained more cis-acting elements, which were mainly involved in endosperm gene expression and light responsiveness, than its diploid progenitors. Thus, B. napus might have potential advantages in some biological aspects. Conclusions The results indicated allotetraploid B. napus might have potential advantages in some biological aspects. Moreover, our results can increase the understanding of the evolution of the EIN3/EIL gene family in B. napus, and provided more reference for future research about polyploidization.http://link.springer.com/article/10.1186/s12870-019-1716-zEIN3/EIL gene familyCis-elementIntronsAllotetraploidBrassica napusPolyploidization |
| spellingShingle | Mengdi Li Ruihua Wang Ziwei Liang Xiaoming Wu Jianbo Wang Genome-wide identification and analysis of the EIN3/EIL gene family in allotetraploid Brassica napus reveal its potential advantages during polyploidization BMC Plant Biology EIN3/EIL gene family Cis-element Introns Allotetraploid Brassica napus Polyploidization |
| title | Genome-wide identification and analysis of the EIN3/EIL gene family in allotetraploid Brassica napus reveal its potential advantages during polyploidization |
| title_full | Genome-wide identification and analysis of the EIN3/EIL gene family in allotetraploid Brassica napus reveal its potential advantages during polyploidization |
| title_fullStr | Genome-wide identification and analysis of the EIN3/EIL gene family in allotetraploid Brassica napus reveal its potential advantages during polyploidization |
| title_full_unstemmed | Genome-wide identification and analysis of the EIN3/EIL gene family in allotetraploid Brassica napus reveal its potential advantages during polyploidization |
| title_short | Genome-wide identification and analysis of the EIN3/EIL gene family in allotetraploid Brassica napus reveal its potential advantages during polyploidization |
| title_sort | genome wide identification and analysis of the ein3 eil gene family in allotetraploid brassica napus reveal its potential advantages during polyploidization |
| topic | EIN3/EIL gene family Cis-element Introns Allotetraploid Brassica napus Polyploidization |
| url | http://link.springer.com/article/10.1186/s12870-019-1716-z |
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