The complete chloroplast genome of the Abies yuanbaoshanensis, an endangered Pinaceae species in Southern China.

Abies yuanbaoshanensis is critically endangered and endemic to Guangxi province of China, with no more than 900 surviving individuals. In this study, we reported the complete chloroplast (cp) genome of A. yuanbaoshanensis. The complete chloroplast genome is 121897 bp in size. In total, 112 genes were identified, including 74 protein-coding genes, 34tRNA genes, and four rRNA genes. In phylogenetic analysis, the tree supported the monophyly of the genus Abies. The complete plastome of A. yuanbaoshanensis will provide potential genetic resources for further conservation and evolutionary studies of this highly endangered species.

Abies consists of around 50 species, which are widely distributed in the Northern Hemisphere with major centres of distribution in North America and eastern Asia. (Liu 1971; Farjon 2001). Abies are ecologically crucial for water and soil restoration in areas where they occur (Liu 1971). However, many fir species have been listed as endangered species (Xiang et al. 2015). Abies yuanbaoshanensis is listed as highly endangered species in the Red List (IUCN 2018). Now A. yuanbaoshanensis is endemic to Guangxi province of China with less than 900 surviving individuals (Li et al. 2002). Here, we assembled and characterized the complete plastome of A. yuanbaoshanensis. It will provide potential genetic resources for further conservation and evolutionary studies of A. yuanbaoshanensis.

The plant material of A. yuanbaoshanensis was collected from a single individual that lives in the natural forest habitat of Mt. Yuanbaoshan (Guangxi, China; 25.43°N, 109.18°E). Voucher specimen (YBS20190711) and DNA sample were deposited in the herbarium of Institute of Botany, CAS (PE). In total, 6 G high-quality clean reads (150 bp PE read length) were generated with adaptors trimmed. The GetOrganelle (Jin et al. 2018), Bandage (Wick et al. 2015), Geneious R11 (Biomatters Ltd., Auckland, New Zealand), were used to align, assemble, and annotate the plastome.

The full length of A. yuanbaoshanensis chloroplast genome (GenBank Accession No. MN399749) was 121897 bp and comprised of a large single copy region (LSC with 67152 bp), a small single copy region (SSC with 54467 bp), and two inverted repeat regions (IR with 139 bp). The overall GC content of the A. yuanbaoshanensis cp genome was 38.30%. A total of 112 genes were contained in the cp genome (74 protein-coding genes, 34 tRNA genes, and four rRNA genes). Only one tRNA gene (trnI-CAU) is duplicated and located on the IR regions.

Fourteen chloroplast genomes were selected to infer the phylogenetic relationships among the main representative species of Pinaceae with Ginkgo biloba (Ginkgoaceae) as the outgroup. All of these 14 complete chloroplast sequences were aligned by the MAFFT version 7 software (Katoh and Standley 2013). A maximum-likelihood (ML) tree was inferred by Ultrafast bootstrapping with 1000 replicates through IQ-TREE 1.5.5 (Nguyen et al. 2015) based on the GTR + F+R3 nucleotide substitution model, which was selected by Model Finder (Kalyaanamoorthy et al. 2017). The result revealed that the five Abies species (A. yuanbaoshanensis, A. koreana, A. kawakami, A. fargesii, A. chensiensis, and A. ziyuanensis) are strongly supported as monophyletic (Figure 1).

Figure 1.

The ML phylogeny result from 14 complete plastome sequences by IQ-TREE. Accession numbers: Abies chensiensis NC_041464, A. fargesii NC_042775, A. kawakamii NC_042776, A. yuanbaoshanensis MN399749, A. koreana NC_026892, A. ziyuanensis MH706705, Keteleeria davidiana NC_011930, Cedrus deodara NC_014575, Picea sitchensis NC_011152, Pinus lambertiana NC_011156, Cathaya argyrophylla NC_014589, Larix decidua NC_016058, Pseudotsuga sinensis NC_016064, and Ginkgo biloba NC_016986.