Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida
Abstract Background The basic leucine zipper (bZIP) transcription factor is one of the most abundant and conserved transcription factor families. In addition to being involved in growth and development, bZIP transcription factors also play an important role in plant adaption to abiotic stresses. Res...
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BMC
2019-04-01
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| Series: | BMC Genetics |
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| Online Access: | http://link.springer.com/article/10.1186/s12863-019-0743-y |
| _version_ | 1818040155645149184 |
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| author | Zhengmei Yang Jian Sun Yao Chen Panpan Zhu Lei Zhang Shaoyuan Wu Daifu Ma Qinghe Cao Zongyun Li Tao Xu |
| author_facet | Zhengmei Yang Jian Sun Yao Chen Panpan Zhu Lei Zhang Shaoyuan Wu Daifu Ma Qinghe Cao Zongyun Li Tao Xu |
| author_sort | Zhengmei Yang |
| collection | DOAJ |
| description | Abstract Background The basic leucine zipper (bZIP) transcription factor is one of the most abundant and conserved transcription factor families. In addition to being involved in growth and development, bZIP transcription factors also play an important role in plant adaption to abiotic stresses. Results A total of 41 bZIP genes that encode 66 proteins were identified in Ipomoea trifida. They were distributed on 14 chromosomes of Ipomoea trifida. Segmental and tandem duplication analysis showed that segmental duplication played an important role in the ItfbZIP gene amplification. ItfbZIPs were divided into ten groups (A, B, C, D, E, F, G, H, I and S groups) according to their phylogenetic relationships with Solanum lycopersicum and Arabidopsis thaliana. The regularity of the exon/intron numbers and distributions is consistent with the group classification in evolutionary tree. Prediction of the cis-acting elements found that promoter regions of ItfbZIPs harbored several stress responsive cis-acting elements. Protein three-dimensional structural analysis indicated that ItfbZIP proteins mainly consisted of α-helices and random coils. The gene expression pattern from transcriptome data and qRT-PCR analysis showed that ItfbZIP genes expressed with a tissue-specific manner and differently expressed under various abiotic stresses, suggesting that the ItfbZIPs were involved in stress response and adaption in Ipomoea trifida. Conclusions Genome-wide identification, gene structure, phylogeny and expression analysis of bZIP gene in Ipomoea trifida supplied a solid theoretical foundation for the functional study of bZIP gene family and further facilitated the molecular breeding of sweet potato. |
| first_indexed | 2024-12-10T08:10:02Z |
| format | Article |
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| language | English |
| last_indexed | 2024-12-10T08:10:02Z |
| publishDate | 2019-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genetics |
| spelling | doaj.art-52b340d9ddd14016bdddad05aaf026dd2022-12-22T01:56:36ZengBMCBMC Genetics1471-21562019-04-0120111810.1186/s12863-019-0743-yGenome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifidaZhengmei Yang0Jian Sun1Yao Chen2Panpan Zhu3Lei Zhang4Shaoyuan Wu5Daifu Ma6Qinghe Cao7Zongyun Li8Tao Xu9Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal UniversityInstitute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal UniversityInstitute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal UniversityDepartment of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National UniversityInstitute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal UniversityInstitute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal UniversityXuzhou Academy of Agricultural Sciences/Sweet Potato Research Institute, CAASXuzhou Academy of Agricultural Sciences/Sweet Potato Research Institute, CAASInstitute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal UniversityInstitute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal UniversityAbstract Background The basic leucine zipper (bZIP) transcription factor is one of the most abundant and conserved transcription factor families. In addition to being involved in growth and development, bZIP transcription factors also play an important role in plant adaption to abiotic stresses. Results A total of 41 bZIP genes that encode 66 proteins were identified in Ipomoea trifida. They were distributed on 14 chromosomes of Ipomoea trifida. Segmental and tandem duplication analysis showed that segmental duplication played an important role in the ItfbZIP gene amplification. ItfbZIPs were divided into ten groups (A, B, C, D, E, F, G, H, I and S groups) according to their phylogenetic relationships with Solanum lycopersicum and Arabidopsis thaliana. The regularity of the exon/intron numbers and distributions is consistent with the group classification in evolutionary tree. Prediction of the cis-acting elements found that promoter regions of ItfbZIPs harbored several stress responsive cis-acting elements. Protein three-dimensional structural analysis indicated that ItfbZIP proteins mainly consisted of α-helices and random coils. The gene expression pattern from transcriptome data and qRT-PCR analysis showed that ItfbZIP genes expressed with a tissue-specific manner and differently expressed under various abiotic stresses, suggesting that the ItfbZIPs were involved in stress response and adaption in Ipomoea trifida. Conclusions Genome-wide identification, gene structure, phylogeny and expression analysis of bZIP gene in Ipomoea trifida supplied a solid theoretical foundation for the functional study of bZIP gene family and further facilitated the molecular breeding of sweet potato.http://link.springer.com/article/10.1186/s12863-019-0743-yIpomoea trifidaSweet potatobZIP transcription factorPhylogenetic analysisGene expression |
| spellingShingle | Zhengmei Yang Jian Sun Yao Chen Panpan Zhu Lei Zhang Shaoyuan Wu Daifu Ma Qinghe Cao Zongyun Li Tao Xu Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida BMC Genetics Ipomoea trifida Sweet potato bZIP transcription factor Phylogenetic analysis Gene expression |
| title | Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida |
| title_full | Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida |
| title_fullStr | Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida |
| title_full_unstemmed | Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida |
| title_short | Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida |
| title_sort | genome wide identification structural and gene expression analysis of the bzip transcription factor family in sweet potato wild relative ipomoea trifida |
| topic | Ipomoea trifida Sweet potato bZIP transcription factor Phylogenetic analysis Gene expression |
| url | http://link.springer.com/article/10.1186/s12863-019-0743-y |
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