Next-generation sequencing yields the complete chloroplast genome of Abies fanjingshanensis, an Endangered species from South China

Abstract

Abies fansipanensis is an Endangered species in South China with less than 2500 mature trees. In this study, we reported the complete chloroplast genome of A. fansipanensis. The complete chloroplast genome is 120,057 bp in length, comprising a large single copy (LSC) region of 65,355 bp, a small single copy (SSC) region of 54,174 bp, and two inverted repeat regions (IRa and IRb) of 264 bp each. The genome contains 114 genes and there were 68 peptide-encoding genes, 35 tRNA genes, four rRNA genes, 6 open reading frames, and 1 pseudogene. Loss of ndh genes and inverted repeat sequences were identified in this genome. The phylogenetic analysis confirms that the Abies species are supported as monophyletic, with high bootstrap values.

Keywords:

• Abies fansipanensis
• chloroplast genome
• Threatened
• phylogenetic

Abies are ecologically crucial for water and soil restoration in areas where they occur (Liu 1971). However, many firs have been listed as Endangered species (Shao et al. 2017). Abies fansipanensis Q. P. Xiang, L. K. Fu & Nan Li is endemic to Fanjingshan Mountain (Guizhou province, China) (Farjon 2001). Its population size is estimated to about 10,000 trees, but the number of mature trees is probably less than 2500 and all of the mature trees are scattered in one population, which is undergoing a continuing decline. Due to its critically rare and narrow distribution, it is listed as a Threatened species in the Red List (IUCN 2018) and categorized as key protected wild plants in China. In this study, we assembled and characterized the complete plastome of A. fansipanensis for a better understanding of its conservation and management strategies.

The plant material was collected from the Fanjingshan Mountain of China (108°42′E, 27°55′N). Specimens were given identification numbers and registered in the herbarium of Institute of Botany, CAS (PE), with Voucher no. 0134. The complete chloroplast (cp) genome was sequenced by HiSeq4000 of Illumina (San Diego, California, USA) and finally, 10.3 million high-quality clean reads (150 bp PE read length) were obtained. In total, ca. 10.1 million high-quality clean reads (150 bp PE read length) were generated with adaptors trimmed. The CLC de novo assembler (CLC Bio, Aarhus, Denmark), BLAST, GeSeq (Tillich et al. 2017), and tRNAscan-SE v1.3.1 (Schattner et al. 2005) were used to align, assemble, and annotate the plastome.

The complete chloroplast genome consists of 120,057 bp for Abies fansipanensis (GenBank: MH706717). The circle genome was comprised of a large single copy (LSC) region of 65,355 bp, a small single copy (SSC) region of 54,174 bp, and two inverted repeat regions (IRa and IRb) of 264 bp each. The GC content is 38.3% with the SSC region having higher GC content (39.3%) than the LSC (37.4%) and IR (39.0%) regions. The genome contains 114 genes and there were 68 peptide-encoding genes, 35 tRNA genes, 4 rRNA genes, 6 open reading frames, and 1 pseudogene. All ndh genes have been lost in the genome. Short inverted repeat sequences were detected in 52 kb inversion points of the cp genome, which consists of trnS-psaM-ycf12-trnG and trnG-ycf12-psaM-trnS (1183 bp). Interestingly, such missing of ndh genes and inverted repeats had been reported in several members of the genus Abies (A. beshanzuensis, A. koreana) (Yi et al. 2015; Shao et al. 2018).

To investigate the phylogenetic position of Abies fansipanensis, nine chloroplast genomes were selected in Pinaceae with Ginkgo biloba (Ginkgoaceae) as the outgroup. These genomes were fully aligned with MAFFT v7.3 (Suita, Osaka, Japan) (Katoh and Standley 2013) and the maximum likelihood (ML) inference was performed using GTRþIþC model with RAxML v.8.2.1 (Karlsruhe, Germany) (Stamatakis 2014) on the CIPRES cluster service (Miller et al. 2010). The ML tree revealed that A. fansipanensis and A. beshanzuensis formed a monophyletic group with bootstrap support values of 100% (Figure 1).

Figure 1. The best maximum likelihood (ML) phylogram inferred from 10 chloroplast genomes in Pinaceae and Ginkgoaceae (bootstrap value are indicated on the branches).

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China [81803425].