The complete chloroplast genome of the white-berry yew Pseudotaxus chienii (Cupressales: Taxaceae), a rare and endangered relict plant endemic to southern China

Abstract

The white-berry yew (Pseudotaxus chienii) is a rare relict conifer endemic to southern China. Here, we assembled its chloroplast genome using Illumina sequencing technology. The circular genome is 126,925 bp long with an asymmetric base composition. It encodes a total of 115 genes, including 82 protein-coding genes (PCGs), 30 tRNAs and three rRNAs. Gene duplication was detected for a couple of tRNA genes. Nine genes have a single intron, and another gene possesses a couple of introns. Phylogenetic analysis suggested that P. chienii is closely related to three taxa of the genus Taxus (T. baccata, T. mairei, and T. wallichiana).

Keywords:

• Genomics
• high-throughput sequencing
• NOVOPlasty
• plastid genome
• Pseudotaxus chienii

The white-berry yew Pseudotaxus chienii, the only representative of the monotypic genus Pseudotaxus (Taxaceae), is a rare relict conifer endemic to southern China (Fu et al. 1999; Deng et al. 2013). Due to anthropogenic disturbances and its extremely weak natural regeneration, this plant has experienced a continuous population decline during the past century (Fu and Jin 1992; Hu et al. 2003; Yang et al. 2005; Su et al. 2009; Thomas and Yang 2013). It is currently categorized as a rare and endangered plant in China (Fu and Jin 1992), and as ‘Vulnerable A2cd’ (VU) by the International Union for Conservation of Nature (IUCN) (Thomas and Yang 2013). Here, its chloroplast (cp) genome was assembled using high-throughput sequencing technology. The annotated genomic sequence is currently available from GenBank with the accession number MH023407.

Genomic DNA was extracted from fresh leaves (29°32′57.44ʺN, 115°59′2.40ʺE; Lushan Botanical Garden, Jiangxi Province, China; voucher specimen: PCHIE20171209) using the DNeasy Plant Mini Kit (Qiagen, CA). The shotgun library preparation and the high-throughput DNA sequencing were carried out by Beijing Novogene Bioinformatics Technology Co., Ltd (Beijing, China) following the manufacturer's protocol for the Illumina HiSeq X Ten Sequencing System (Illumina, CA). In all, 6.80 M of 150-bp raw paired reads were obtained, and were employed to assemble the cp genome using NOVOPlasty v2.63 (Dierckxsens et al. 2017) with that of Taxus wallichiana (KX431996) (Jia and Liu 2017) as the seed reference. Genome annotation was conducted in GENEIOUS R11 (Biomatters Ltd., Auckland, New Zealand) by comparing with those of related taxa, e.g. Amentotaxus argotaenia (KR780582) (Li et al. 2016), Taxus mairei (KJ123824) (Zhang et al. 2014) and Taxus wallichiana (KX431996) (Jia and Liu 2017). A schematic map of the genome was automatically generated using the web-based tool OGDRAW v1.2 (Lohse et al. 2013).

The cp genome of P chienii was 126,925 bp in size. The base composition is asymmetric (32.1% A, 17.9% C, 17.3% G, and 32.7% T) with an overall A + T content of 64.8% (light strand). A total of 115 genes are encoded, including 82 protein-coding genes (PCGs), 30 tRNAs, and three rRNAs. A couple of genes (trnI-CAU and trnQ-UUG) are duplicated, while the others occur as a single copy. Out of these 115 genes, nine genes (atpF, ndhA, ndhB, ropC1, rpl2, rps12, trnA-UGC, trnK-UUU, and trnL-UAA) harbor a single intron, and another gene (ycf3) possesses a couple of introns.

To ascertain its taxonomic position within the order Cupressales, phylogenetic analysis was conducted based on the maximum-likelihood (ML) analysis of concatenated cp PCG sequences for 26 species with sequenced cp genomes (Figure 1). The ML phylogenetic tree was reconstructed using PhyML v3.1 (Guindon et al. 2010) with 200 bootstrap replicates and with ‘GTR + G+I’ as the best-fit nucleotide substitution model. Pseudotaxus chienii was found to be closely related to three taxa of the genus Taxus (T. baccata, T. mairei, and T. wallichiana), which consists with the widely held close relationship between the two genera Pseudotaxus and Taxus (Deng et al. 2013).

Figure 1. Phylogenetic relationships of 26 species within the order Cupressales based on the maximum-likelihood (ML) analysis of the concatenated coding sequences of 17 chloroplast PCGs. The bootstrap values were based on 200 replicates, and are shown next to the branches.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by the Natural Science Foundation of Shanxi Province [201701D221166], the Funding Project for ‘131’ Pioneering Talents in Yuncheng University [XK-2015034], the Transverse Project in Yuncheng University, the Disciplinary Research Project in Yuncheng University [XK-2018015] and the Fund for Shanxi Key Subjects Construction (FSKSC).