Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.)
Abstract Background Radish (Raphanus sativus L.) belongs to the family Brassicaceae, and is an economically important root crop grown worldwide. Flowering is necessary for plant propagation, but it is also an important agronomic trait influencing R. sativus fleshy taproot yield and quality in the ca...
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| Format: | Article |
| Language: | English |
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BMC
2017-12-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-017-4377-z |
| _version_ | 1818336528591486976 |
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| author | Jinglei Wang Yang Qiu Feng Cheng Xiaohua Chen Xiaohui Zhang Haiping Wang Jiangping Song Mengmeng Duan Haohui Yang Xixiang Li |
| author_facet | Jinglei Wang Yang Qiu Feng Cheng Xiaohua Chen Xiaohui Zhang Haiping Wang Jiangping Song Mengmeng Duan Haohui Yang Xixiang Li |
| author_sort | Jinglei Wang |
| collection | DOAJ |
| description | Abstract Background Radish (Raphanus sativus L.) belongs to the family Brassicaceae, and is an economically important root crop grown worldwide. Flowering is necessary for plant propagation, but it is also an important agronomic trait influencing R. sativus fleshy taproot yield and quality in the case of an imbalance between vegetative and reproductive growth. There is currently a lack of detailed information regarding the pathways regulating the flowering genes or their evolution in R. sativus. The release of the R. sativus genome sequence provides an opportunity to identify and characterize the flowering genes using a comparative genomics approach. Results We identified 254 R. sativus flowering genes based on sequence similarities and analyses of syntenic regions. The genes were unevenly distributed on the various chromosomes. Furthermore, we discovered the existence of R. sativus core function genes in the flowering regulatory network, which revealed that basic flowering pathways are relatively conserved between Arabidopsis thaliana and R. sativus. Additional comparisons with Brassica oleracea and Brassica rapa indicated that the retained flowering genes differed among species after genome triplication events. The R. sativus flowering genes were preferentially retained, especially those associated with gibberellin signaling and metabolism. Moreover, analyses of selection pressures suggested that the genes in vernalization and autonomous pathways were more variable than the genes in other R. sativus flowering pathways. Conclusions Our results revealed that the core flowering genes are conserved between R. sativus and A. thaliana to a certain extent. Moreover, the copy number variation and functional differentiation of the homologous genes in R. sativus increased the complexity of the flowering regulatory networks after genome polyploidization. Our study provides an integrated framework for the R. sativus flowering pathways and insights into the evolutionary relationships between R. sativus flowering genes and the genes from A. thaliana and close relatives. |
| first_indexed | 2024-12-13T14:40:45Z |
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| language | English |
| last_indexed | 2024-12-13T14:40:45Z |
| publishDate | 2017-12-01 |
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| series | BMC Genomics |
| spelling | doaj.art-0ff2f7eacb06484f9a9f3296231416502022-12-21T23:41:36ZengBMCBMC Genomics1471-21642017-12-0118111010.1186/s12864-017-4377-zGenome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.)Jinglei Wang0Yang Qiu1Feng Cheng2Xiaohua Chen3Xiaohui Zhang4Haiping Wang5Jiangping Song6Mengmeng Duan7Haohui Yang8Xixiang Li9Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of AgricultureInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of AgricultureInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of AgricultureInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of AgricultureInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of AgricultureInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of AgricultureInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of AgricultureInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of AgricultureInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of AgricultureInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of AgricultureAbstract Background Radish (Raphanus sativus L.) belongs to the family Brassicaceae, and is an economically important root crop grown worldwide. Flowering is necessary for plant propagation, but it is also an important agronomic trait influencing R. sativus fleshy taproot yield and quality in the case of an imbalance between vegetative and reproductive growth. There is currently a lack of detailed information regarding the pathways regulating the flowering genes or their evolution in R. sativus. The release of the R. sativus genome sequence provides an opportunity to identify and characterize the flowering genes using a comparative genomics approach. Results We identified 254 R. sativus flowering genes based on sequence similarities and analyses of syntenic regions. The genes were unevenly distributed on the various chromosomes. Furthermore, we discovered the existence of R. sativus core function genes in the flowering regulatory network, which revealed that basic flowering pathways are relatively conserved between Arabidopsis thaliana and R. sativus. Additional comparisons with Brassica oleracea and Brassica rapa indicated that the retained flowering genes differed among species after genome triplication events. The R. sativus flowering genes were preferentially retained, especially those associated with gibberellin signaling and metabolism. Moreover, analyses of selection pressures suggested that the genes in vernalization and autonomous pathways were more variable than the genes in other R. sativus flowering pathways. Conclusions Our results revealed that the core flowering genes are conserved between R. sativus and A. thaliana to a certain extent. Moreover, the copy number variation and functional differentiation of the homologous genes in R. sativus increased the complexity of the flowering regulatory networks after genome polyploidization. Our study provides an integrated framework for the R. sativus flowering pathways and insights into the evolutionary relationships between R. sativus flowering genes and the genes from A. thaliana and close relatives.http://link.springer.com/article/10.1186/s12864-017-4377-zRaphanus sativus L.Genome-wideFlowering genesRegulatory pathway networksEvolution |
| spellingShingle | Jinglei Wang Yang Qiu Feng Cheng Xiaohua Chen Xiaohui Zhang Haiping Wang Jiangping Song Mengmeng Duan Haohui Yang Xixiang Li Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.) BMC Genomics Raphanus sativus L. Genome-wide Flowering genes Regulatory pathway networks Evolution |
| title | Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.) |
| title_full | Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.) |
| title_fullStr | Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.) |
| title_full_unstemmed | Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.) |
| title_short | Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.) |
| title_sort | genome wide identification characterization and evolutionary analysis of flowering genes in radish raphanus sativus l |
| topic | Raphanus sativus L. Genome-wide Flowering genes Regulatory pathway networks Evolution |
| url | http://link.springer.com/article/10.1186/s12864-017-4377-z |
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