The complete chloroplast genome of Torreya parvifolia, a species with extremely small population in China

Abstract

Torreya parvifolia (Torreya, Taxaceae) is endemic in Sichuan, China. It consisted of an extremely small population with less than 100 wild individuals. In this study, the complete chloroplast genome of T. parvifolia was assembled using the Illumina data. The complete chloroplast genome of T. parvifolia is 137,106 bp in length. The genome consists of 119 genes in total, including 82 protein-coding genes (PCGs), 4 ribosomal RNA (rRNA) genes, and 33 transfer RNA (tRNA) genes. Phylogenetic analysis indicated that T. parvifolia was closely related to T. fargesii, T. nucifera, and T. fargesii var. yunnanensis with strong support.

Keywords:

• Torreya parvifolia
• chloroplast genome
• phylogenetic analysis

Torreya parvifolia T.P. Yi, Lin Yang & T.L. Long, belonging to Torreya in Taxaceae family, is a species with extremely small population (Yi et al. 2006). It is reported that there are less than 100 individuals surviving in the wild (Pan et al. 2014). In this study, we reported the complete chloroplast genome of T. parvifolia for the first time and performed a phylogenetic analysis with 11 other species based on their complete chloroplast genomes.

We collected the fresh leaves of a wild T. parvifolia individual from Liangshan Yi Autonomous Prefectu, Sichuan Province, China (27°30′N, 102°56′E). Voucher specimen of the species was deposited in the Ecological Security and Protection Key Laboratory of Sichuan Province, China under the accession number: MNU-PHO-0160. The total DNA was extracted with the CTAB method (Doyle and Doyle 1987). We performed the whole-genome sequencing with HiSeq2500 Platform (Illumina, San Diego, CA) and obtained ∼10 Gb high-quality clean data. The complete chloroplast genome of T. parvifolia was de novo assembled with NOVOPlasty (Dierckxsens et al. 2017). The gene prediction was carried out by Plann (Huang and Cronk 2015) and Sequin (NCBI website). Finally, we obtained a chloroplast genome of T. parvifolia. The genome has been submitted to the GenBank under the accession number of NC_043866.1.

The complete chloroplast genome of T. parvifolia is 137,106 bp in length, with a GC content of 35.47% in total. The genome structure is similar to other Taxaceae species (Miu et al. 2018; Ge et al. 2019; Shin et al. 2019), with the loss of one copy of the inverted repeats (IRs). The chloroplast genome of T. parvifolia contains 119 genes, including 82 protein-coding genes (PCGs), 4 ribosomal RNA (rRNA) genes, and 33 transfer RNA (tRNA) genes.

To infer the phylogenetic position of T. parvifolia, we reconstructed a phylogenetic tree using the concatenated 64 PCGs sequences of T. parvifolia and 11 other species. The sequences of each gene were aligned by PRANK (Löytynoja 2014). RAxML (Stamatakis 2014) was performed to construct the phylogenetic relationships with 100 bootstrap replicates under the GTRGAMMA model. The maximum likelihood (ML) tree revealed T. parvifolia was closely related to T. fargesii, T. nucifera, and T. fargesii var. yunnanensis with strong support (Figure 1). Within the concatenated 64 PCGs sequences, T. parvifolia had 50, 187, and 162 varied sites with T. fargesii, T. nucifera, and T. fargesii var. yunnanensis, respectively. The genetic relationships of other Torreya species were identical with the previous study (Zhang et al. 2019) (Figure 1). Furthermore, we found T. fargesii did not cluster with T. fargesii var. yunnanensis. T. grandis and T. grandis var. jiulongshanensis were also not clustered together. It was possible because of the mis-identification of materials for sequencing, or the inaccurate published new varieties, which were only based on the characteristics of morphology in past years. In summary, the chloroplast genome of T. parvifolia could help us facilitate the identification and protection for T. parvifolia.

Figure 1. Maximum likelihood (ML) tree based on the concatenated data of 64 PCGs sequences of Torreya parvifolia and 11 other species. Numbers at the nodes indicate bootstrap values.

Disclosure statement

No potential competing interest was reported by the authors.

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/) under the accession no. NC_043866.1. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA683944, SRR13235763, and SAMN17048565, respectively. The voucher specimen of the species is free accessible at Ecological Security and Protection Key Laboratory of Sichuan Province, China with the no. MNU-PHO-0160.

Additional information

Funding

This work was financially supported by Scientific Research Project of Department of Sichuan Education [14ZB0268] and Scientific Research Project of Mianyang Normal University [2012A05].