Characterization of the complete plastome sequence of Torreya grandis var. jiulongshanensis (Taxaceae), a rare and endangered plant species endemic to Zhejiang province, China.

Torreya grandis var. jiulongshanensis (Taxaceae) is an evergreen tree endemic to Zhejiang province, China, and it is listed as a rare plant species with extremely small populations. In our present study, we assembled the chloroplast (CP) genome of T. grandis var. jiulongshanensis using high-throughput sequencing data generated by an Illumina Hiseq X Ten platform. The results indicate that the complete CP genome is 136,705 bp in size with an overall guanine and cytosine content of 35.5%. The plastome has lost its quadripartite structure. In the CP genome, there are a total of 119 genes, including 82 protein-coding genes, 4 ribosomal RNA genes, and 33 transfer RNA genes. Phylogenetic analysis revealed that T. grandis var. jiulongshanensis is a sister species to T. grandis.

Torreya grandis var. jiulongshanensis is an evergreen tree with gray bark and leafy branchlets (Wu et al. 1999). The plant species occurs only in counties of Suichang, Jinyun, Songyang, and Tiantai, Zhejiang province, China. In the wild, T. grandis var. jiulongshanensis has fewer than 100 individuals, and it is described as ‘plant species with extremely small populations’. The chloroplast (CP) genome sequences of three Torreya species, T. grandis, T. parvifolia, and T. fargesii, were assembled. However, the CP genome of T. grandis var. jiulongshanensis has not been reported. Herein, we assembled and annotated the CP chloroplast genome of T. grandis var. jiulongshanensis, a plant species morphologically similar to T. grandis.

Leaves were sampled near Xikengxia Village (28°19.37′N, 118°55.53′E), Jingning She Autonomous County, Zhejiang, China. A voucher specimen coded CHS2017103 was deposited at the Molecular Biology Laboratory at the Taizhou University. Total genomic DNA was extracted according to the CTAB protocol (Doyle and Doyle, 1987). A DNA library was constructed following the manufacturer’s instructions, and was then sequenced to obtain raw data on an Illumina Hiseq X Ten platform (Illumina, CA, USA). Totally, 5.5 Gb of clean data were generated, and the reads were applied to assemble the CP genome by NOVOPlasty (Dierckxsens et al. 2017). The complete plastome was annotated using Dual Organellar GenoMe Annotator (DOGMA), and the gene boundaries were adjusted manually (Wyman et al. 2004). The programs, namely tRNAscan-SE and ARAGORN, were applied to detect tRNAs in the CP genome (Lowe and Eddy 1997; Laslett and Canback 2004). The T. grandis var. jiulongshanensis CP genome (GenBank accession: MN527333) is 136,705 bp long with an overall guanine and cytosine content of 35.5%, and it composes of 32.5% adenine, 17.7% cytosine, 17.9% guanine, and 32.0% thymine.

Typically, the CP genome is a circular molecule with a quadripartite structure, comprising a small single-copy and a large single-copy separated by a pair of inverted repeats (Khan et al. 2017). However, the plastome of T. grandis var. jiulongshanensis has lost its quadripartite structure. The genome consists of 119 genes, including 82 protein-coding genes, 4 ribosomal RNA genes, and 33 transfer RNA genes. Among them, 15 genes (atpF, ndhA, ndhB, petB, petD, rpl2, rpl16, rpoC1, rps12, rps16, trnG-UCC, trnI-GAU, trnK-UUU, trnL-UAA, and trnV-UAC) possess one intron, while another two genes (rps12 and ycf3) contain two introns.

To complete the CP genome sequences of Amentotaxus argotaenia (KR780582), A. formosana (AP014574), Cephalotaxus hainanensis (NC_042392), Taxus brevifolia (NC_041502), T. chinensis (NC_041496), T. floridana (MH390474), T. globose (MH390488), T. fargesii (NC_029398), T. grandis (NC_034806), T. parvifolia (NC_043866), Thuja_occidentalis (NC_042177), five Pinus, as well as six Araucuria species were retrieved from GenBank, and a phylogenetic tree was generated by PhyML 3.1 software under the GTR + G + I model (Guindon et al. 2010). The 27 plants can be divided into 11 different subgroups, namely Amentotaxus subgroup, Pseudotaxus subgroup, Taxus subgroup, and Torreya subgroup, etc. Our results indicated that T. grandis var. jiulongshanensis was sister to the three Torreya species, with a support value of 100% (Figure 1).

Figure 1.

Maximum likelihood tree of 27 plant species based on chloroplast genome sequences, with Ginkgo biloba (JN867585) as the outgroup. The numbers next to nodes indicate bootstrap support values.