The complete chloroplast genome of Chinese endemic species Abies ferreana (Pinaceae) and its phylogenetic analysis

Abstract Abies ferreana Bordères & Gaussen 1947 is endemic to China, where it is distributed at 3300–4000 meters in the mountains of Southwest Sichuan and Northwest Yunnan. In this study, the complete chloroplast genome of A. ferreana was reconstructed by de novo assembly using whole-genome sequencing data. The complete chloroplast genome of A. ferreana was 120,049 bp in length with a GC content of 37.9%. A total of 113 genes were identified, including 4 rRNA genes, 35 tRNA genes, and 74 protein-coding genes. Among these, 14 genes contain introns. In the phylogenetic tree with 12 other species of Abies, A. ferreana and Abies fanjingshanensis W. L. Huang et al. 1984 were grouped into the same branch, with a bootstrap value of 100%. The complete chloroplast genome of A. ferreana provides potential genetic resources for further Abies evolutionary and genomic studies.

Abies species, commonly known as fir, are a genus comprised of 48-55 species of coniferous evergreen trees in the Pinaceae family (Liu 1971). Abies is distributed mainly in the mountains and less frequently on the plains of the northern hemisphere, where they have important ecological and economic value. However, many species of Abies have been listed as endangered species (Xiang et al. 2015). Therefore, the classification and conservation of Abies has mutual importance for both the ecological and industrial communities. Abies ferreana Bord eres & Gaussen 1947 is in the second largest genus of Pinaceae and endemic to China. It is found in the mountainous regions of northwest Yunnan and southwest Sichuan at altitudes of 3300-4000 meters. However, current projections indicate a decline in the suitable habitats for Abies (Naudiyal et al. 2021). Plant chloroplasts have conserved genomic characteristics and high evolution rates, and are widely used in genetic and evolutionary studies (Rogalski et al. 2015;Yang et al. 2021). We have assembled and characterized the complete chloroplast of A. ferreana, which will provide genetic resources for further conservation and evolutionary studies of A. ferreana.
This article is licensed under a Regulations of Yunnan Province on biodiversity protection and approved by the Chinese Academy of Forestry (Beijing, China). The sample of A. ferreana was collected from Baimaxueshan National Nature Reserve (Yunnan, China; 28 22 0 57.59 00 N, 99 0 0 6.76 00 E). The total DNA was extracted from fresh leaves for whole-genome sequencing on an Illumina Hiseq-PE150 platform. The DNA and specimen were deposited at the State Key Laboratory of Tree Genetics and Breeding (Website: http://skltgb.caf.ac.cn/, Contact: XM HAN, Email: 602405029@qq.com) under the voucher number TGBZH201010016. A total of 2.84 GB as 150 bp paired-end raw reads were retrieved and then qualitytrimmed clean reads were used for the chloroplast genome de novo assembly using GetOrganelle with default parameters (Jin et al. 2020). The chloroplast genome of A. ferreana was annotated with the online programs, CPGAVAS2 and GeSeq (Michael et al. 2017;Shi et al. 2019;Shi et al. 2019 ). The annotated genomic sequence was registered with GenBank using the accession number OM321039.
A maximum likelihood (ML) tree was constructed with P. abies (HF937082.1) and P. sinensis var. wilsoniana (NC _016986.1) as outgroups using IQ-TREE (Nguyen et al. 2015). The phylogenetic tree showed that A. ferreana and Abies fanjingshanensis W. L. Huang et al. 1984 were grouped together with a 100% bootstrap support (Figure 1). The complete chloroplast genome of A. ferreana fills an important gap in current chloroplast genome information for Abies genus of Pinaceae family, providing useful perspectives for further evolutionary and genomic studies in Abies.

Author contributions
Dan Wang analyzed the data, prepared figures, wrote original draft, and approved the final draft; Qingyin Zeng reviewed and edited the draft; Xuemin Han designed the experiments, collected materials, reviewed and edited the draft.

Disclosure statement
No potential conflict of interest was reported by the author(s).