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Comprehensive Analysis of the Complete Chloroplast Genome of Cinnamomum daphnoides (Lauraceae), An Endangered Island Endemic Plant

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Abstract

Cinnamomum daphnoides (Siebold & Zucc 1846) is a rare and endangered island species with a unique Sino-Japanese distribution pattern. However, inormation regarding the species’ chloroplast (cp) genome, structural features, and the phylogenetic relationship is still lacking. We utilized high-throughput sequencing technology to assemble and annotate the first cp genome of C. daphnoides (GenBank OR654104), followed by genomic characterization and phylogenetic analysis to fill the gaps in this species’ cp genome. Our analysis showed that the cp genome has a quadripartite structure spanning 152,765 bp with a GC content of 39.15%. The genome encodes 126 genes, which include 36 tRNA genes, 8 rRNA genes, and 82 mRNA genes. Specifically, 44 genes are related to photosynthesis, 59 are associated with self-replication, six are other genes, and four have unknown functionality. The Codon usage bias in the genome exhibits a preference for A/U bases. We identified 29 interspaced repeat sequences that belonging to three types of repeat sequences. A total of 217 cpSSR loci were detected with single nucleotide repeats (59.91%) being the most frequent loci, mainly composed of A/T repeats. Our selection pressure analysis revealed that the ycf2 gene experienced strong positive selection (Ka/Ks = 1.81, P > 0.844). Further, we identified three highly variable fragments (psbM, psbT, and ycf1) that can be utilized as specific DNA barcoding markers for species definition and population genetic studies. We conducted boundary analysis, which showed that the structure and gene sequence of the two species were highly conserved. Finally, our phylogenetic analysis supports that C. daphnoides is close to C. cassia in the Cinnamomum genes, indicating that the two species share a common ancestry. Overall, providing genomic information on C. daphnoides will be beneficial for the conservation and utilization of endangered plant genetic resources. It will also serve as a reference for the identification of species and the phylogenetic analysis of Cinnamomum. This information will be useful in future research.

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Data Availability

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov under accession no. OR654104.

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Acknowledgements

The authors are very grateful for comments and suggestions from two anonymous reviewers who helped improve the original manuscript.

Funding

This study was funded by the Zhejiang Provincial Scientific Research Institution special project (Grant Nos. 2022F1068-3 and 2021F1065-6), and the “Pioneer” and “Leading Goose” R&D Program of Zhejiang (2022C02038).

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Authors and Affiliations

  1. Zhejiang Academy of Forestry, Hangzhou, 310023, China

    Hong Zhu & Hepeng Li

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  1. Hong Zhu
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Contributions

All authors contributed to the study conception and design. Material preparation, data collection, and analysis were performed by HZ. The first draft of the manuscript was written by HZ, and HL commented on previous versions of the manuscript and revised the manuscript. All authors read and approved the final manuscript.

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Correspondence to Hong Zhu.

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No potential conflict of interest was reported by the authors.

Ethical Approval

This article does not contain any studies with animals performed by any of the authors. The plant materials used in this study were collected from the arboretum of Zhejiang Academy of Forestry, and the collection process was in accordance with the regulations of the academy and relevant local laws and regulations.

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Zhu, H., Li, H. Comprehensive Analysis of the Complete Chloroplast Genome of Cinnamomum daphnoides (Lauraceae), An Endangered Island Endemic Plant. Mol Biotechnol (2023). https://doi.org/10.1007/s12033-023-00950-5

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