Genome and transcriptome analysis to understand the role diversification of cytochrome P450 gene under excess nitrogen treatment
Abstract Background Panax notoginseng (Burk.) F. H. Chen (P. notoginseng) is a medicinal plant. Cytochrome P450 (CYP450) monooxygenase superfamily is involved in the synthesis of a variety of plant hormones. Studies have shown that CYP450 is involved in the synthesis of saponins, which are the main...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-10-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-021-03224-x |
| _version_ | 1819118110591942656 |
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| author | Rui Xiong Ting He Yamei Wang Shifan Liu Yameng Gao Hanwei Yan Yan Xiang |
| author_facet | Rui Xiong Ting He Yamei Wang Shifan Liu Yameng Gao Hanwei Yan Yan Xiang |
| author_sort | Rui Xiong |
| collection | DOAJ |
| description | Abstract Background Panax notoginseng (Burk.) F. H. Chen (P. notoginseng) is a medicinal plant. Cytochrome P450 (CYP450) monooxygenase superfamily is involved in the synthesis of a variety of plant hormones. Studies have shown that CYP450 is involved in the synthesis of saponins, which are the main medicinal component of P. notoginseng. To date, the P. notoginseng CYP450 family has not been systematically studied, and its gene functions remain unclear. Results In this study, a total of 188 PnCYP genes were identified, these genes were divided into 41 subfamilies and clustered into 9 clans. Moreover, we identified 40 paralogous pairs, of which only two had Ka/Ks ratio greater than 1, demonstrating that most PnCYPs underwent purification selection during evolution. In chromosome mapping and gene replication analysis, 8 tandem duplication and 11 segmental duplication events demonstrated that PnCYP genes were continuously replicating during their evolution. Gene ontology (GO) analysis annotated the functions of 188 PnCYPs into 21 functional subclasses, suggesting the functional diversity of these gene families. Functional divergence analyzed the members of the three primitive branches of CYP51, CYP74 and CYP97 at the amino acid level, and found some critical amino acid sites. The expression pattern of PnCYP450 related to nitrogen treatment was studied using transcriptome sequencing data, 10 genes were significantly up-regulated and 37 genes were significantly down-regulated. Combined with transcriptome sequencing analysis, five potential functional genes were screened. Quantitative real-time PCR (qRT-PCR) indicated that these five genes were responded to methyl jasmonate (MEJA) and abscisic acid (ABA) treatment. Conclusions These results provide a valuable basis for comprehending the classification and biological functions of PnCYPs, and offer clues to study their biological functions in response to nitrogen treatment. |
| first_indexed | 2024-12-22T05:43:40Z |
| format | Article |
| id | doaj.art-4b4cd32cf20543cdbc08c1a403aaf3ff |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-22T05:43:40Z |
| publishDate | 2021-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-4b4cd32cf20543cdbc08c1a403aaf3ff2022-12-21T18:37:06ZengBMCBMC Plant Biology1471-22292021-10-0121111610.1186/s12870-021-03224-xGenome and transcriptome analysis to understand the role diversification of cytochrome P450 gene under excess nitrogen treatmentRui Xiong0Ting He1Yamei Wang2Shifan Liu3Yameng Gao4Hanwei Yan5Yan Xiang6Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural UniversityLaboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural UniversityLaboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural UniversityLaboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural UniversityNational Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural UniversityLaboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural UniversityLaboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural UniversityAbstract Background Panax notoginseng (Burk.) F. H. Chen (P. notoginseng) is a medicinal plant. Cytochrome P450 (CYP450) monooxygenase superfamily is involved in the synthesis of a variety of plant hormones. Studies have shown that CYP450 is involved in the synthesis of saponins, which are the main medicinal component of P. notoginseng. To date, the P. notoginseng CYP450 family has not been systematically studied, and its gene functions remain unclear. Results In this study, a total of 188 PnCYP genes were identified, these genes were divided into 41 subfamilies and clustered into 9 clans. Moreover, we identified 40 paralogous pairs, of which only two had Ka/Ks ratio greater than 1, demonstrating that most PnCYPs underwent purification selection during evolution. In chromosome mapping and gene replication analysis, 8 tandem duplication and 11 segmental duplication events demonstrated that PnCYP genes were continuously replicating during their evolution. Gene ontology (GO) analysis annotated the functions of 188 PnCYPs into 21 functional subclasses, suggesting the functional diversity of these gene families. Functional divergence analyzed the members of the three primitive branches of CYP51, CYP74 and CYP97 at the amino acid level, and found some critical amino acid sites. The expression pattern of PnCYP450 related to nitrogen treatment was studied using transcriptome sequencing data, 10 genes were significantly up-regulated and 37 genes were significantly down-regulated. Combined with transcriptome sequencing analysis, five potential functional genes were screened. Quantitative real-time PCR (qRT-PCR) indicated that these five genes were responded to methyl jasmonate (MEJA) and abscisic acid (ABA) treatment. Conclusions These results provide a valuable basis for comprehending the classification and biological functions of PnCYPs, and offer clues to study their biological functions in response to nitrogen treatment.https://doi.org/10.1186/s12870-021-03224-xCytochrome P450Panax notoginsengGene duplicationExpression profileNitrogen treatment |
| spellingShingle | Rui Xiong Ting He Yamei Wang Shifan Liu Yameng Gao Hanwei Yan Yan Xiang Genome and transcriptome analysis to understand the role diversification of cytochrome P450 gene under excess nitrogen treatment BMC Plant Biology Cytochrome P450 Panax notoginseng Gene duplication Expression profile Nitrogen treatment |
| title | Genome and transcriptome analysis to understand the role diversification of cytochrome P450 gene under excess nitrogen treatment |
| title_full | Genome and transcriptome analysis to understand the role diversification of cytochrome P450 gene under excess nitrogen treatment |
| title_fullStr | Genome and transcriptome analysis to understand the role diversification of cytochrome P450 gene under excess nitrogen treatment |
| title_full_unstemmed | Genome and transcriptome analysis to understand the role diversification of cytochrome P450 gene under excess nitrogen treatment |
| title_short | Genome and transcriptome analysis to understand the role diversification of cytochrome P450 gene under excess nitrogen treatment |
| title_sort | genome and transcriptome analysis to understand the role diversification of cytochrome p450 gene under excess nitrogen treatment |
| topic | Cytochrome P450 Panax notoginseng Gene duplication Expression profile Nitrogen treatment |
| url | https://doi.org/10.1186/s12870-021-03224-x |
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