The complete chloroplast genome and phylogenetic analysis of Cinnamomum daphnoides (Laurales: Lauraceae)

Abstract

This study presents the complete chloroplast genome of Cinnamomum daphnoides (154,121 bp, GC 39.2%), a newly recorded species in China, revealing a typical quadripartite structure: a large single-copy region (93,688 bp, GC 37.9%), a small single-copy region (18,929 bp, GC 33.9%), and two inverted repeats (20,752 bp each, GC 44.3%). The genome harbors 126 genes (82 protein-coding, 36 tRNA, 8 rRNA). Phylogenetic analysis groups C. daphnoides with C. tamala, differing from prior studies. These findings clarify its systematic position within Cinnamomum and support its potential for coastal greening applications.

Keywords: Cinnamomum daphnoides; Lauraceae; chloroplast genome; phylogeny.

Figure 1.

(A) Whole individual with (B) flowers and (C)fruits of Cinnamomum daphnoides. The leaves of this species are small and dense, densely covered with pale yellow silky hairs underneath, with rounded and blunt tips. The leaf margins curl downwards, and the three main veins unite near the apex, which distinctly differentiates it from other species within the same genus. The image was taken from the Jiushan Archipelago, Xiangshan, Ningbo City, China (122.20° E, 29.43° N) by Jianhong Zhang in April 2024.

Figure 2.

The complete chloroplast genome sequence of Cinnamomum daphnoides. Genes displayed within and beyond the circle undergo transcription in counterclockwise and clockwise directions, respectively. Various hues signify genes possessing distinct functional types. The dashed segment in the inner circle uses dark and light grey to depict GC content and AT content, respectively.

Figure 3.

Phylogenetic tree using maximum-likelihood (ML) based on chloroplast genomes of 15 Cinnamomum species with Sassafras tzumu as an outgroup. Numbers near the nodes represent ML bootstrap values. The Cinnamomum sequences are from Xiao et al. (2022): C. glanduliferum OL943973 (Xiao et al. 2022), C. rufotomentosum NC_065107 (Xiao et al. 2022), C. longepaniculatum NC_065104 (Xiao et al. 2022), C. septentrionale NC_065108 (Xiao et al. 2022), C. chartophyllum NC_065102 (Xiao et al. 2022), C. pingbienense NC_065106 (Xiao et al. 2022), C. cassia OL943970 (Xiao et al. 2022), C. cassia OL943971 (Xiao et al. 2022), Cinnamomum iners NC_065103 (Xiao et al. 2022), C. tenuipile OL943981 (Xiao et al. 2022), C. austrosinense NC_065100 (Xiao et al. 2022), C. burmannii NC_065101 (Xiao et al. 2022), C. appelianum NC_065099 (Xiao et al. 2022), C. pauciflorum NC_065105 (Xiao et al. 2022), C. tamala NC_065109 (Xiao et al. 2022), Sassafras tzumu NC_045268 (Jo et al. 2019).