The complete chloroplast genome sequence of Podocarpus imbricatus (Podocarpaceae) and its phylogenetic analysis

Abstract

In this study, the complete chloroplast genome sequence of Podocarpus imbricatus (Podocarpaceae) was determined. Like other chloroplast genomes in conifers, the Podocarpus imbricatus genome did not have typical quadripartite structure. The genome was 133,816 bp in length, containing 118 unique genes (82 protein-coding genes, 32 tRNA genes and four rRNA genes). The overall GC content of the genome is 37.23%. A phylogenetic tree based on 56 chloroplast genes showed that Podocarpaceae was clustered with Araucariaceae. In addition, all the Podocarpaceae species analyzed in this study formed a monophyletic clade.

Keywords:

• Podocarpus imbricatus
• Podocarpaceae
• chloroplast genome
• phylogeny

Podocarpus imbricatus, belongs to the Podocarpaceae family, is mainly distributed in Southern China, Myanmar, Vietnam and Indonesia. The timber of P. imbricatus is used for construction and making furniture. The 20-Hydroxyecdysone isolated from P. imbricatus bark can inhibit the proliferation of acute myeloid leukaemia cells (Thuy et al. 2017). However, in the past years, P. imbricatus has experienced indiscriminate felling and then was listed as threatened plant in the China Plant Red Data Book (Fu and Jin 1992). The Podocarpaceae is the largest family in cupressophytes, comprising about 19 genera with 180 species (Christenhusz et al. 2011). To date, the complete chloroplast genome from 13 species covering 12 genera in this family has been reported (Vieira et al. 2014; Wu and Chaw 2014, 2016; Sudianto et al. 2018). In order to have a deep insight into the evolution of Podocarpaceae, the complete chloroplast genome sequence of P. imbricatus was sequenced in this study.

The fresh leaves of P. imbricatus used in this study were collected from South China Botanical Garden, Chinese Academy of Sciences. The voucher specimens of P. imbricatus were deposited in Shaanxi Xueqian Normal University. Total genomic DNA was extracted using the modified CTAB method (Gawel and Jarret 1991) and sequenced by the Illumina HiseqTM 2500 platform (Illumina Inc., San Diego, CA). The complete chloroplast genome sequence of P. imbricatus was assembled by NOVOPlasty software (Dierckxsens et al. 2017). Annotations were originally performed by DOGMA (Wyman et al. 2004) and tRNAscan-SE (Schattner et al. 2005). The exact boundaries of each gene were verified by alignment with other conifers chloroplast gene.

The gene order and structure of P. imbricatus chloroplast genome are similar to other conifer species, which did not have the typical inverted repeat sequence. The complete chloroplast genome sequence of P. imbricatus is 133,816 bp in length (GenBank accession no. MH979330). In total, 118 unique genes were identified, including 82 protein-coding genes, 32 tRNA genes and four rRNA genes. Fourteen genes contain one intron and ycf3 has two introns. In addition, rps16 gene was lost and two copies of trnN-GUU gene were found in P. imbricatus chloroplast genome. The overall GC content of the chloroplast genome is 37.23% (protein-coding genes, 38.18%; tRNA genes, 53.01%; rRNA genes, 54.03%; introns, 37.84%; intergenic spacers, 33.70%). The percentage of the coding region is 55.40% and the gene density is 0.89 genes/kb.

Maximum likelihood phylogenetic tree was constructed by 52 protein-coding and four rRNA genes from 24 gymnosperm taxa, using Cycas taitungensis and Ginkgo biloba as the outgroup. The dataset was implemented in RAxML v8.1.x (Stamatakis 2014). The ML tree strongly supported the sister relationship between P. imbricatus and a clade containing Podocarpus totara, Podocarpus lambertii, Nageia nagi and Retrophyllum piresii. In addition, Podocarpaceae was clustered with Wollemia nobills (Araucariaceae) by 100% bootstrap (Figure 1). The complete chloroplast genome sequence of P. imbricatus facilitates a better understanding of population and phylogenetic studies for Podocarpaceae.

Figure 1. Maximum likelihood phylogenetic tree based on 52 protein-coding and four rRNA genes from 24 taxa. Numbers above the branch indicate the bootstrap values.

Disclosure statement

The author declares no conflicts of interest. The author alone is responsible for the content and writing the manuscript.

Additional information

Funding

This work was supported by the Doctoral Scientific Research Foundation of Shaanxi Xueqian Normal University (2016DS04); the Scientific Research Foundation of Shaanxi Xueqian Normal University (2018YBKJ52) and Provincial Experimental Teaching Demonstration Center of Biology (2016).