The complete chloroplast genome of Castanopsis sieboldii (Makino) Hatus (Fagaceae)

Abstract Castanopsis sieboldii (Makino) Hatus is an evergreen tree that distributes in Eastern Asia including Islands of Korea and Japan. The chloroplast genome of C. sieboldii was successfully sequenced. Its length is 160,705 bp long (GC ratio is 36.8%) and has four subregions: 90,821 bp of large single copy (34.6%) and 19,014 bp of small single copy (30.8%) regions are separated by 25,075 bp of inverted repeat (42.8%) regions including 134 genes (89 protein-coding genes, eight rRNAs, and 37 tRNAs). Interspecific variations of Castanopsis are at a moderate level in comparison to those of the other genera. Phylogenetic trees show that C. sieboldii chloroplast genome was clustered with the other two Castanopsis species.

Castanopsis sieboldii (Makino) Hatus, belonging to Fagaceae, is a species of an evergreen tree that distributes in subtropical Eastern Asia, including Islands in Western and Southern Korea  and Honshu, Shikoku, and Kyushu Islands in Japan (Yamazaki 1987). This species is considered as a climax species in an evergreen forest (Yamanaka 1966). The genetic diversity of C. sieboldii in Japan is relatively high (Aoki et al. 2014): one of the major reasons is that they have been isolated in islands. It is one of hot topics to understand the origin of the island species based on chloroplast genomes, such as founder effects (Del Valle et al. 2019), multiple introductions in the islands (Nock et al. 2019), or the origin of endemic species in the islands (Yang et al. 2018;Park, Bae, et al. 2021). To understand its genetic diversity of C. sieboldii in Korea, as the first step, we completed the first chloroplast genome of C. sibboldii from the sample isolated in one of the islands in Korea, Oenalodo Island.
Based on pair-wise alignments against chloroplast genomes of C. fargesii and C. concinna, distributed in Southern China (Sun et al. 2014 Oh et al. 2019aOh et al. , 2019bPark, Kim, Xi, Oh, et al. 2019;Park, Suh, et al. 2020;Heo et al. 2020;Oh and Park 2020). These results indicate that the numbers of interspecific variations identified from the three Castanopsis species are at a moderate level.
Thirteen Fagaceae chloroplast genomes including one outgroup species, Betula platyphylla, were used for constructing bootstrapped Maximum-Likelihood (ML), Neighbor-joining (NJ), and Bayesian Inference (BI) phylogenic trees using MEGA X (Kumar et al. 2018) and MrBayes v3.2.6 (Ronquist et al. 2012), respectively, after aligning whole chloroplast genomes by MAFFT v7.450 (Katoh and Standley 2013). A heuristic search was used with nearest-neighbor interchange branch swapping, the Tamura-Nei model, and uniform rates among sites to construct ML and NJ phylogenetic trees with default values for other options using MEGA X. Bootstrap analyses with 1000 and 10,000 pseudoreplicates were conducted for ML and NJ trees, respectively. The GTR model with gamma rates was used as a molecular model and Markov-chain Monte Carlo algorithm was employed for 1,100,000 generations, sampling trees every 200 generations, with four chains running simultaneously for BI tree. Three phylogenetic trees display that three Castanopsis species are clustered in one clade and are congruent to each other with high supportive values of ML, NJ, and BI (Figure 1). In addition, the topology of Castanopsis, Castanea, Quercus, and Fagus genera in the phylogenetic tree is congruent to the previous phylogenetic and morphological study (Manos et al. 2008). Taken together, our chloroplast genome is useful to investigate phylogenetic relationships of C. sieboldii as well as its genetic diversities along with geographical distribution.

Disclosure statement
The authors declare that they have no competing interests.

Funding
This study was carried out with the support of R&D Program for Forest Science Technology [Project No. 2020206A00-2022-BA01]