Genome-wide identification and expression analysis of the NRT genes in Ginkgo biloba under nitrate treatment reveal the potential roles during calluses browning
Abstract Nitrate is a primary nitrogen source for plant growth, and previous studies have indicated a correlation between nitrogen and browning. Nitrate transporters (NRTs) are crucial in nitrate allocation. Here, we utilized a genome-wide approach to identify and analyze the expression pattern of 7...
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| Format: | Article |
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BMC
2023-10-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09732-4 |
| _version_ | 1797577976633622528 |
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| author | Jin Feng Can Zhu Jiaqi Cao Chen Liu Jiaqi Zhang Fuliang Cao Xiaohong Zhou |
| author_facet | Jin Feng Can Zhu Jiaqi Cao Chen Liu Jiaqi Zhang Fuliang Cao Xiaohong Zhou |
| author_sort | Jin Feng |
| collection | DOAJ |
| description | Abstract Nitrate is a primary nitrogen source for plant growth, and previous studies have indicated a correlation between nitrogen and browning. Nitrate transporters (NRTs) are crucial in nitrate allocation. Here, we utilized a genome-wide approach to identify and analyze the expression pattern of 74 potential GbNRTs under nitrate treatments during calluses browning in Ginkgo, including 68 NITRATE TRANSPORTER 1 (NRT1)/PEPTIDE TRANSPORTER (PTR) (NPF), 4 NRT2 and 2 NRT3. Conserved domains, motifs, phylogeny, and cis-acting elements (CREs) were analyzed to demonstrate the evolutionary conservation and functional diversity of GbNRTs. Our analysis showed that the NPF family was divided into eight branches, with the GbNPF2 and GbNPF6 subfamilies split into three groups. Each GbNRT contained 108–214 CREs of 19–36 types, especially with binding sites of auxin and transcription factors v-myb avian myeloblastosis viral oncogene homolog (MYB) and basic helix-loop-helix (bHLH). The E1X1X2E2R motif had significant variations in GbNPFs, indicating changes in the potential dynamic proton transporting ability. The expression profiles of GbNRTs indicated that they may function in regulating nitrate uptake and modulating the signaling of auxin and polyphenols biosynthesis, thereby affecting browning in Ginkgo callus induction. These findings provide a better understanding of the role of NRTs during NO3 − uptake and utilization in vitro culture, which is crucial to prevent browning and develop an efficient regeneration and suspension production system in Ginkgo. |
| first_indexed | 2024-03-10T22:15:45Z |
| format | Article |
| id | doaj.art-c7451c76c9f24aa8a834dc508ea47229 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-10T22:15:45Z |
| publishDate | 2023-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-c7451c76c9f24aa8a834dc508ea472292023-11-19T12:27:57ZengBMCBMC Genomics1471-21642023-10-0124111510.1186/s12864-023-09732-4Genome-wide identification and expression analysis of the NRT genes in Ginkgo biloba under nitrate treatment reveal the potential roles during calluses browningJin Feng0Can Zhu1Jiaqi Cao2Chen Liu3Jiaqi Zhang4Fuliang Cao5Xiaohong Zhou6State Key Laboratory of Subtropical Silviculture, Zhejiang A&F UniversityState Key Laboratory of Subtropical Silviculture, Zhejiang A&F UniversityState Key Laboratory of Subtropical Silviculture, Zhejiang A&F UniversityState Key Laboratory of Subtropical Silviculture, Zhejiang A&F UniversityState Key Laboratory of Subtropical Silviculture, Zhejiang A&F UniversityState Key Laboratory of Subtropical Silviculture, Zhejiang A&F UniversityState Key Laboratory of Subtropical Silviculture, Zhejiang A&F UniversityAbstract Nitrate is a primary nitrogen source for plant growth, and previous studies have indicated a correlation between nitrogen and browning. Nitrate transporters (NRTs) are crucial in nitrate allocation. Here, we utilized a genome-wide approach to identify and analyze the expression pattern of 74 potential GbNRTs under nitrate treatments during calluses browning in Ginkgo, including 68 NITRATE TRANSPORTER 1 (NRT1)/PEPTIDE TRANSPORTER (PTR) (NPF), 4 NRT2 and 2 NRT3. Conserved domains, motifs, phylogeny, and cis-acting elements (CREs) were analyzed to demonstrate the evolutionary conservation and functional diversity of GbNRTs. Our analysis showed that the NPF family was divided into eight branches, with the GbNPF2 and GbNPF6 subfamilies split into three groups. Each GbNRT contained 108–214 CREs of 19–36 types, especially with binding sites of auxin and transcription factors v-myb avian myeloblastosis viral oncogene homolog (MYB) and basic helix-loop-helix (bHLH). The E1X1X2E2R motif had significant variations in GbNPFs, indicating changes in the potential dynamic proton transporting ability. The expression profiles of GbNRTs indicated that they may function in regulating nitrate uptake and modulating the signaling of auxin and polyphenols biosynthesis, thereby affecting browning in Ginkgo callus induction. These findings provide a better understanding of the role of NRTs during NO3 − uptake and utilization in vitro culture, which is crucial to prevent browning and develop an efficient regeneration and suspension production system in Ginkgo.https://doi.org/10.1186/s12864-023-09732-4Ginkgo bilobaNRT genesCallus browningAuxinIn vitro culture |
| spellingShingle | Jin Feng Can Zhu Jiaqi Cao Chen Liu Jiaqi Zhang Fuliang Cao Xiaohong Zhou Genome-wide identification and expression analysis of the NRT genes in Ginkgo biloba under nitrate treatment reveal the potential roles during calluses browning BMC Genomics Ginkgo biloba NRT genes Callus browning Auxin In vitro culture |
| title | Genome-wide identification and expression analysis of the NRT genes in Ginkgo biloba under nitrate treatment reveal the potential roles during calluses browning |
| title_full | Genome-wide identification and expression analysis of the NRT genes in Ginkgo biloba under nitrate treatment reveal the potential roles during calluses browning |
| title_fullStr | Genome-wide identification and expression analysis of the NRT genes in Ginkgo biloba under nitrate treatment reveal the potential roles during calluses browning |
| title_full_unstemmed | Genome-wide identification and expression analysis of the NRT genes in Ginkgo biloba under nitrate treatment reveal the potential roles during calluses browning |
| title_short | Genome-wide identification and expression analysis of the NRT genes in Ginkgo biloba under nitrate treatment reveal the potential roles during calluses browning |
| title_sort | genome wide identification and expression analysis of the nrt genes in ginkgo biloba under nitrate treatment reveal the potential roles during calluses browning |
| topic | Ginkgo biloba NRT genes Callus browning Auxin In vitro culture |
| url | https://doi.org/10.1186/s12864-023-09732-4 |
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