The complete chloroplast genome of Abies ernestii Rehder (Pinaceae) and its phylogenetic implications

Abstract

Abies ernestii Rehder is endemic to the montane regions of Southwest China. Till now, phylogenetic relationships between A. ernestii and other closely related species remain unclear. In this study, we first characterized the complete chloroplast (cp) genome of A. ernestii. The whole cp genome was 121,841 bp in size, including one hundred and thirteen genes. Results of comparative cp genome revealed that only ycf1 and ycf2 was characterized by a considerable variation. Our phylogenetic analyses supported the monophyly of the genus Abies and revealed a clear separation between A. ernestii and A. chensiensis Tiegh. This study highlights the significance of using cp genomes to examine species boundaries among closely related fir species.

Keywords: Abies ernestii; SSR analysis; chloroplast genome; comparative genome analysis; phylogenetic analyses.

Figure 1.

The chloroplast genome map of Abies ernestii. Genes shown outside the circle are transcribed clockwise, and genes inside are transcribed counter-clockwise. Genes belonging to different functional groups are color-coded. The darker grey in the inner corresponds to the GC content and the lighter grey to the AT content.

Figure 2.

Comparison of four chloroplast genomes using the mVista alignment program, with Abies chensiensis (MH706706) as a reference. The x-axis means the midpoint of the window, and the y-axis means nucleotide diversity (Pi). Genome regions are color-coded as protein-coding, rRNA coding, tRNA coding, or conserved noncoding sequences.

Figure 3.

The best maximum-likelihood (ML) phylogram inferred from 17 chloroplast genomes in Abies, with Juniperus squamata as an outgroup (bootstrap values are indicated on the branches). The following sequences were used: A. nukiangensis MH706711 (Shao et al. 2020), A. fanjingshanensis MH706717 (Guo et al. 2019), A. delavayi subsp. fansipanensis MH706720 (Shao et al. 2020), A. forrestii MH706715 (Dong et al. 2021), A. delavayi MH706709 (Shao et al. 2020), A. fabri MH706710 (Shao et al. 2020), A. georgei var. smithii NC_054152 (Li et al. 2020), A. yuanbaoshanensis MH706718 (Zhang et al. 2020), A. beshanzuensis var. ziyuanensis MH706705 (Fu et al. 2019), A. koreana KP742350 (Yi et al. 2015), A. nephrolepis KT834974 (Yi et al. 2016), A. kawakamii MH706726 (Shao et al. 2019 ), A. chensiensis MH 706706 (Su et al. 2019), A. fargesii MH706716 (Guo and Xu 2019), A. beshanzuensis MH 476330 (Shao et al. ; Shao et al., 2020), A. balsamea MH 706725 (Wu et al. 2019), and Juniperus squamata MK085509 (www.ncbi.nlm.nih.gov/).