Abstract
Abies fargesii is endemic to central China and ecologically and economically important. In the present study, we reported the complete chloroplast genome of A. fargesii. The chloroplast genome is 121,799 bp in size, comprising a large single copy (LSC) region of 67,122 bp, a small single copy (SSC) region of 54,149 bp, and 2 inverted repeat regions (IRa and IRb) of 264 bp each. It composed of 114 genes and there were 68 peptide-encoding genes, 35 tRNA genes, 4 rRNA genes, 6 open reading frames, and 1 pseudogene. The phylogenetic analysis confirms that the Abies species are strongly supported as monophyletic in both ML and BI tree. This study provided important genetic resources for the ecologically and economically important fir species.
The fir species are ecologically and economically crucial for water and soil restoration in areas where they occur (Liu Citation1971; Farjon Citation1990, Citation2001). Abies fargesii Franch. is a dominant member of the coniferous forests found at elevations between 1500 and 3900 m (Fu et al. Citation1999). Abies fargesii is endemic to central China, including North Yunnan, Northwest Sichuan, Northwest Hubei, South Gansu, and Southwest Shaanxi (Farjon Citation2001). It is adapted to a cold, humid environment at high elevations and typically occurs in sheltered to windswept sites (Liu Citation1971). In the present study, we assembled and characterized the complete plastome of A. fargesii. It will be fundamental to a better understanding of this ecologically and economically important species.
We collected the plant material from the Huanglongshan Mountain of Sichuan, China. The voucher specimen (Wu C., No. 62063) was deposited at the herbarium of Institute of Botany, CAS (PE). Complete chloroplast (cp) genome of Abies fargesii was sequenced by HiSeq4000 systems of Illumina. Totally, 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. Citation2017), and tRNAscan-SE v1.3.1 (Schattner et al. Citation2005) were used to align, assemble, and annotate the plastome.
The complete chloroplast genome consists of 121,799 bp for Abies fargesii (GenBank: MH706716). The circle genome comprised of a large single copy region (LSC with 67,122 bp), a small single copy region (SSC with 54,149 bp), and two inverted repeat regions (IR with 264 bp). The overall GC content of the A. fargesii cp genome was 38.3%. It composed of 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 of A. fargesii. 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 inverted repeats had been reported in several members of the genus Abies (A. koreana and A. ziyuanensis) (Yi et al. Citation2015; Shao et al. Citation2018).
To infer the phylogenetic position of Abies fargesii, five chloroplast genomes were selected in Pinaceae with Ginkgo biloba (Ginkgoaceae) as an outgroup. These sequences were fully aligned with MAFFT v7.3 (Suita, Osaka, Japan) (Katoh and Standley Citation2013) and the maximum likelihood (ML) inference was performed using GTRþIþC model with RAxML v.8.2.1 (Karlsruhe, Germany) (Stamatakis Citation2014) on the CIPRES cluster service (Miller et al. Citation2010). We also used MrBayes v.3.2.2 (Stockholm, Swedish) (Ronquist and Huelsenbeck Citation2003; Ronquist et al. Citation2012) for the Bayesian inference analyses. MrBayes was run for 1,000,000 generations, sampling, and printing every 100 generations. Our phylogenetic analyses yielded largely congruent topologies by the ML and BI analyses. Based on these six cp genome sequences, the three Abies species (A. fargesii, A. koreana, and A. neprolepis) are supported as one monophyletic lineage with extremely high probabilities (BSML = 100, BIPP = 1.0) ().
Figure 1. Phylogram of Abies fargesii obtained from the maximum likelihood analysis of the whole chloroplast genome sequences. Numbers on branches are support values [maximum likelihood bootstrap values (BSML)/Bayesian inference posterior probability values (PPBI)].
![Figure 1. Phylogram of Abies fargesii obtained from the maximum likelihood analysis of the whole chloroplast genome sequences. Numbers on branches are support values [maximum likelihood bootstrap values (BSML)/Bayesian inference posterior probability values (PPBI)].](/cms/asset/a930c8b7-eef2-4441-bdea-832ba221a7a4/tmdn_a_1591230_f0001_b.jpg)
Our study provided important genetic resources for the ecologically and economically important fir species, as well as new resources for further study of Abies chloroplast genome evolution.
Disclosure statement
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
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References
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