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De novo transcriptome assembly for the basal angiosperm Illicium anisatum provides insights into the biosynthesis of shikimate and neurotoxin anisatin

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Abstract

Illicium anisatum, an ancient angiosperm belonging to the ANITA grade, contains abundant plant metabolites with antimicrobial activity, including shikimate and sesquiterpene lactones (STLs) such as anisatin. The aim of this study was to generate a full-length transcriptome resource for identifying genes related to the shikimate and STL biosynthetic pathways in I. anisatum and for studying the evolution of Illicium species. We performed RNA isoform sequencing of I. anisatum leaf, stem, flower, and floral bud samples and annotated the assembled transcripts based on a homology search. A total of 148,593 transcripts with an average length of 2.2 kb and high assembly completeness were generated. Functional pathway analysis revealed the evolutionary conservation of the shikimate and aromatic amino acid (AAA) biosynthetic pathways in I. anisatum and the upregulation of genes that encode chorismite synthase, which is highly associated with the production of shikimate and serve as a precursor for the biosynthesis of AAAs, in floral organs. I. anisatum germacrene A oxidase (IaGAO) and germacrene D synthase (IaGDS), which participate in STL biosynthesis, showed evolutionary divergence from their homologs in the plants of the family Asteraceae, and their genes were mainly expressed in flower organs. Interestingly, alternative splicing isoforms of IaGDS transcripts were found, probably resulting in differential expression in flower and floral bud. We also constructed a map of the I. anisatum chloroplast genome. Isoform sequencing provided a high level of transcriptome assembly completeness and gene annotation and enabled effective prediction of protein domains. The reported long-read sequencing-based de novo assembly of the I. anisatum transcriptome should aid in exploring genes related to the shikimate and STL biosynthesis pathways and associated molecular mechanisms in Illicium species.

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Data availability

Sequencing data generated during the current study are available in the National Agricultural Biotechnology Center (NABIC) and the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database under the following accession numbers: SRX11660706–SRX11660709 (PacBio Iso-Seq data), SRX11660710–SRX11660713 (Illumina RNA-Seq data), and SRX11660714 (Illumina WGS data). The data on unigene, coding, and protein sequences are available from our website http://ianisatum.transcriptome.theragenbio.com/IaU_1.0.

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Acknowledgements

This work was supported by the Research Program for Agricultural Science & Technology Development (Project No. PJ01427601) and the Cooperative Research Program for National Agricultural Genome Program (Project No. PJ01349002), Rural Development Administration (RDA), Republic of Korea.

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Authors and Affiliations

  1. Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea

    Dong-Jun Lee & **-Hyun Kim

  2. Theragen Bio Co., Ltd, Seongnam, 13488, Republic of Korea

    Boram Choi, Eonji Noh, Seung-il Yoo, Solbi Kweon, SeonJu Choi & Chang Pyo Hong

  3. Green Plant Institute, Yongin, 16954, Republic of Korea

    Minjee Lee & Jungho Lee

  4. Department of Industrial Plant Science & Technology, Chungbuk National University, Cheongju, 28644, Republic of Korea

    Yi Lee

  5. Nakdonggang National Institute of Biological Resources, Sangju, 37242, Republic of Korea

    ** Hee Park

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Contributions

CPH, JL, and DJL conceived this study. JL, JHP, and ML prepared the samples and extracted genomic DNA and total RNA. EN performed WGS and RNA-Seq. CPH, DJL, JHK BC, SY, SK, SJC, ML, JL, and YL performed bioinformatics analyses. CPH, JL, and DJL wrote the manuscript. All authors have read and approved the final manuscript.

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Correspondence to Jungho Lee or Chang Pyo Hong.

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CPH, EN, SY, SK, BC, and SJC are employees of Theragen Bio Co., Ltd. The other authors declare that they have no conflict of interest.

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Communicated by Inhwa Yeam.

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Lee, DJ., Choi, B., Noh, E. et al. De novo transcriptome assembly for the basal angiosperm Illicium anisatum provides insights into the biosynthesis of shikimate and neurotoxin anisatin. Hortic. Environ. Biotechnol. 64, 449–460 (2023). https://doi.org/10.1007/s13580-022-00483-x

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