pp 1–16 | Cite as

Characterization and evolution of gene clusters for terpenoid phytoalexin biosynthesis in tobacco

  • Xi Chen
  • Fangjie Liu
  • Lu Liu
  • Jie Qiu
  • Dunhuang Fang
  • Weidi Wang
  • Xingcheng Zhang
  • Chuyu Ye
  • Michael Paul Timko
  • Qian-Hao Zhu
  • Longjiang Fan
  • Bingguang XiaoEmail author
Original Article


Main conclusion

The study performed genome-wide identification, characterization and evolution analysis of gene clusters for phytoalexin terpenoid biosynthesis in tobacco, and specifically illustrated ones for capsidiol, an efficient defensive specialized metabolite.


Terpenoid phytoalexins play an important role in plant self-defense against pest and pathogen attack. Terpenoid biosynthesis involves terpene synthase and cytochrome P450, which always locate and function as cluster(s). In this study, we performed genome-wide investigation of metabolic gene clusters involved in terpenoid production in tobacco (Nicotiana tabacum). Due to the complexity of the tobacco genome, we modified a published prediction pipeline to reduce the influence of the large number of repeats and to improve the annotation of tobacco genes with respect to their metabolic functions. We identified 1181 metabolic gene clusters with 34 of them potentially being involved in terpenoid biosynthesis. Through integration with transcriptome and metabolic pathway annotation analyses, 3 of the 34 terpenoid biosynthesis-related gene clusters were determined to be high-confidence ones, with 2 involved in biosynthesis of capsidiol, a terpenoid recognized as 1 of the effective resistance compounds in the Nicotiana species. The capsidiol-related gene cluster was conserved in N. sylvestris, N. tomentosiformis and N. attenuate. Our findings demonstrate that phytoalexins in tobacco can arise from operon-like gene clusters, a genomic pattern characterized as being beneficial for rapid stress response, gene co-regulation, co-function and co-heredity.


Capsidiol Cytochrome P450 Genome-wide identification Nicotiana tabacum Terpene synthase Transcriptome 



Cytochrome P450


5-Epi-aristolochene dihydroxylase


5-Epi-aristolochene synthase


Metabolic gene cluster


Terpene synthase



This work was supported by the National Natural Science Foundation of China (31860411) to B. Xiao, the Fundamental Research Funds for the Central Universities of China (2017QNA6013) to X. Chen and 111 Project (B17039) to M. Timko.

Supplementary material

425_2019_3255_MOESM1_ESM.pdf (1 mb)
Supplementary material 1 (PDF 1028 kb)
425_2019_3255_MOESM2_ESM.xlsx (18 kb)
Supplementary material 2 (XLSX 18 kb)
425_2019_3255_MOESM3_ESM.xlsx (513 kb)
Dataset S1 Co-expression analysis results of predicted MGCs (XLSX 512 kb)
425_2019_3255_MOESM4_ESM.xlsx (18 kb)
Dataset S2 MGCs predicted by plantiSMASH (XLSX 18 kb)
425_2019_3255_MOESM5_ESM.xlsx (695 kb)
Dataset S3 MGCs predicted by modified PlantClusterfinder pipeline (XLSX 695 kb)
425_2019_3255_MOESM6_ESM.pdf (61 kb)
Dataset S4 TPS sub-class classification results (PDF 61 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Institute of Crop Science and Institute of BioinformaticsZhejiang UniversityHangzhouChina
  2. 2.Research Center for Air Pollution and HealthZhejiang UniversityHangzhouChina
  3. 3.Key Laboratory of Tobacco Biotechnological BreedingYunnan Academy of Tobacco Agricultural SciencesKunmingChina
  4. 4.Department of BiologyUniversity of VirginiaCharlottesvilleUSA
  5. 5.CSIRO Agriculture and FoodCanberraAustralia

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