The complete chloroplast genome sequence of Castanopsis fordii Hance (Fagaceae)

Abstract Castanopsis fordii Hance 1884 is a typical evergreen broad-leaved forest plant in the south subtropical and middle subtropical regions of China. It has high utilization value in wood production and soil erosion protection. Here, we first reported and characterized the complete chloroplast (cp) genome sequence of C. fordii based on Illumina paired-end sequencing data. The complete cp genome sequence of C. fordii was 160,853 base pairs (bp) in length which contained two inverted repeats (IRs) of 25,699 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 90,474 bp and 18,981 bp, respectively. The cpDNA contained 129 genes, comprising 85 protein-coding genes, 36 tRNA genes, 8 rRNA genes. The overall GC content of the plastome was 36.8%. Phylogenetic analysis base on 14 chloroplast genomes indicated that C. fordii was closely related to the species C. tibetana and C. concinna in Fagaceae.


Introduction
Castanopsis fordii belongs to the genus Castanopsis of Fagaceae family is naturally distributed in southeastern China with the Nanling Mountains as the distribution center, and is often the main tree species constituting the local evergreen broad-leaved forest (Lian Bei et al. 2018). C. fordii with straight trunk, fast growth and reddish-brown heartwood is a common wood species in southern China and has high economic value (Xu et al. 2010). In this study, we reported the complete chloroplast (cp) genome of C. fordii based on Illumina pair-end sequencing data, which was helpful for well understanding its characteristics and the origin in evolution.

Results
The complete cp genome sequence of C. fordii was 160,853 base pairs (bp) (Figure 2) in length which contained two inverted repeats (IRs) of 25,699 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 90,474 bp and 18,981 bp, respectively. The cpDNA contained 129 genes, comprising 85 protein-coding genes, 36 tRNA genes, 8 rRNA genes. Most of the genes occurred in a single copy; however, six protein-coding genes (ndhB, rpl2, rpl23, rps12, rps7 and ycf2), seven tRNA genes (trnl-CAU, trnV-GAC, trnR-ACG, trnL-CAA, trnl-GAU, trnN-GUU and trnA-UGC), and four rRNA genes (4.5S, 5S, 16S and 23S) were totally duplicated. The over all GC content of the plastome was 36.8%, and the corresponding values in LSC was 35.07%. No gene has not been predicted. The annotated chloroplast genome of C. fordii has been deposited in GenBank with accession number ON710841.
In order to reveal the phylogenetic position of C. fordii with other members of Fagaceae, a phylogenetic analysis was performed by MAFFT v7.158b (Katoh and Standley 2013) based on 11 complete cp genomes of Fagaceae, and Lithocarpus hancei, Lithocarpus balansae as outgroups. Then, the phylogenetic tree with 1000 ultrafast bootstrap (UFBoot) replicates (Minh et al. 2013) was constructed by RAxML. As shown in the ML phylogenetic tree (Figure 3), the genus Castanea and Lithocarpus formed a monophyletic clade with high bootstrap value, respectively. C. fordii was closely related to C. concinna and C. tibetana. These results based on complete cp genome reported here will lay a basis for the study of phylogeny, phylogeography and population genetic diversity of C. fordii.

Discussion and conclusion
The chloroplast genome structures of the Fagaceae species that have been studied all contain one LSC region one SSC region and two IR regions, which is consistent with the basic structural characteristics of angiosperm chloroplast genomes. At the same time, it was found that the variation in the LSC region accounted for the vast majority of the variation in the whole genome, and the difference in the length of the whole genome was mainly caused by the difference in the length of the LSC. In this study, a phylogenetic tree was constructed based on the complete cp genomes sequences of 14 Fagaceae species. The classification of each species was basically consistent with the traditional taxonomy. This study lays the foundation for further studies on the evolution of Fagaceae genomes.

Author contributions
Ya-feng Wang, Yonglin Huang and Rui-jie He were involved in the conception and design. Ya-feng Wang was involved in the drafting of the paper. Yonglin Huang Zhang-bin Liu and Bing-yuan Yang make critical revisions to intellectual content. Yonglin Huang and Zhang-bin Liu were involved in the final approval of the version to be published; and that all authors agree to be accountable for all aspects of the work.

Disclosure statement
No potential conflict of interest was reported by the authors. The collection of plant material was carried out in accordance with national or international regulations.

Funding
This work was supported by Basic research fund of Guangxi Academy of Sciences [CQZ-C-1901]

Sampling statement
Our materials are not listed in the Wild Plants Under State Protection in China, so we need not any permission or license to collect them; and we only sampled a few leaf materials for molecular experiment and didn't damage any plant.