Triticeae-BGC: a Web-based platform for detecting, annotating and evolutionary analysis of biosynthetic gene clusters in Triticeae

Mingxv Li; Haoyu Wang; Shilong Tian; Yan Zhu; Yijing Zhang

doi:10.1016/j.jgg.2023.09.014

Triticeae-BGC: a Web-based platform for detecting, annotating and evolutionary analysis of biosynthetic gene clusters in Triticeae

doi: 10.1016/j.jgg.2023.09.014

a State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China;
b National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China;
c State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, College of Agriculture, Henan University, Kaifeng, Henan 457004, China

基金项目:

This study was supported by State Key Laboratory of Crop Gene Exploration and Utilization in Southwest (SKL-KF202305) and State Key Laboratory of Genetic Engineering (SKLGE-2312).

详细信息

通讯作者:
Yan Zhu,E-mail:zhu_yan@fudan.edu.cn

Yijing Zhang,E-mail:zhangyijing@fudan.edu.cn

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- 文章访问数: 210
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出版历程
- 收稿日期: 2023-08-23
- 录用日期: 2023-09-23
- 修回日期: 2023-09-21
- 网络出版日期: 2023-10-06

Triticeae-BGC: a Web-based platform for detecting, annotating and evolutionary analysis of biosynthetic gene clusters in Triticeae

Mingxv Li^a,
Haoyu Wang^b,c,
Shilong Tian^b,
Yan Zhu^{a
, ,},
Yijing Zhang^{a
, ,}

a State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China;
b National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China;
c State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, College of Agriculture, Henan University, Kaifeng, Henan 457004, China

Funds:

This study was supported by State Key Laboratory of Crop Gene Exploration and Utilization in Southwest (SKL-KF202305) and State Key Laboratory of Genetic Engineering (SKLGE-2312).

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参考文献(16)

Boycheva, S., Daviet, L., Wolfender, J.-L., Fitzpatrick, T.B., 2014. The rise of operon-like gene clusters in plants. Trends Plant Sci. 19, 447-459.

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Cimermancic, P., Medema, M.H., Claesen, J., Kurita, K., Wieland Brown, L.C., Mavrommatis, K., Pati, A., Godfrey, P.A., Koehrsen, M., Clardy, J., et al., 2014. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell 158, 412-421.

Doroghazi, J.R., Albright, J.C., Goering, A.W., Ju, K.-S., Haines, R.R., Tchalukov, K.A., Labeda, D.P., Kelleher, N.L., Metcalf, W.W., 2014. A roadmap for natural product discovery based on large-scale genomics and metabolomics. Nat. Chem. Biol. 10, 963-968.

Field, B., Osbourn, A.E., 2008. Metabolic diversification——independent assembly of operon-like gene clusters in different plants. Science 320, 543-547.

Frey, M., Schullehner, K., Dick, R., Fiesselmann, A., Gierl, A., 2009. Benzoxazinoid biosynthesis, a model for evolution of secondary metabolic pathways in plants.Phytochemistry, Evolution of Metabolic Diversity 70, 1645-1651.

International Wheat Genome Sequencing Consortium (IWGSC), 2018. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361, eaar7191.

Kautsar, S.A., Suarez Duran, H.G., Blin, K., Osbourn, A., Medema, M.H., 2017.plantiSMASH:automated identification, annotation and expression analysis of plant biosynthetic gene clusters. Nucleic Acids Res. 45, W55-W63.

Liu, J., Yao, Y., Xin, M., Peng, H., Ni, Z., Sun, Q., 2021. Shaping polyploid wheat for success:Origins, domestication, and the genetic improvement of agronomic traits. J.Integr. Plant Biol. jipb.13210.

Medema, M.H., Cimermancic, P., Sali, A., Takano, E., Fischbach, M.A., 2014. A systematic computational analysis of biosynthetic gene cluster evolution:lessons for engineering biosynthesis. PLoS Comput. Biol. 10, e1004016.

Polturak, G., Dippe, M., Stephenson, M.J., Chandra Misra, R., Owen, C., Ramirez-Gonzalez, R.H., Haidoulis, J.F., Schoonbeek, H.-J., Chartrain, L., Borrill, P., et al., 2022.

Pathogen-induced biosynthetic pathways encode defense-related molecules in bread wheat. Proc. Natl. Acad. Sci. U. S. A. 119, e2123299119.

van der Lee, T.A.J., Medema, M.H., 2016. Computational strategies for genome-based natural product discovery and engineering in fungi. Fungal Genet. Biol. FG B 89, 29-36.

Wang, Y., Tang, H., Debarry, J.D., Tan, X., Li, J., Wang, X., Lee, T., Jin, H., Marler, B., Guo, H., et al., 2012. MCScanX:a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49.

Zhang, D., Bai, G., Zhu, C., Yu, J., Carver, B.F., 2010. Genetic Diversity, Population Structure, and Linkage Disequilibrium in U.S. Elite Winter Wheat. Plant Genome 3.

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Triticeae-BGC: a Web-based platform for detecting, annotating and evolutionary analysis of biosynthetic gene clusters in Triticeae

doi: 10.1016/j.jgg.2023.09.014

通讯作者:
Yan Zhu,E-mail:zhu_yan@fudan.edu.cn

Yijing Zhang,E-mail:zhangyijing@fudan.edu.cn

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Triticeae-BGC: a Web-based platform for detecting, annotating and evolutionary analysis of biosynthetic gene clusters in Triticeae

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留言板

Triticeae-BGC: a Web-based platform for detecting, annotating and evolutionary analysis of biosynthetic gene clusters in Triticeae

doi: 10.1016/j.jgg.2023.09.014

通讯作者: Yan Zhu,E-mail:zhu_yan@fudan.edu.cn Yijing Zhang,E-mail:zhangyijing@fudan.edu.cn

计量

出版历程

Triticeae-BGC: a Web-based platform for detecting, annotating and evolutionary analysis of biosynthetic gene clusters in Triticeae

计量

出版历程

目录

通讯作者:
Yan Zhu,E-mail:zhu_yan@fudan.edu.cn

Yijing Zhang,E-mail:zhangyijing@fudan.edu.cn