The complete chloroplast genome of Phoebe zhennan

Abstract

Phoebe zhennan is a large tree with straight trunk and grey-brown or grey-yellowish villous as rare wood. In the study, the complete chloroplastid genome was assembled and annotated, its full length of 152,831 bp, include large single-copy (LSC) region of 93,753 bp, small single-copy (SSC) region of 18,928 bp, a pair of invert repeats (IR) regions of 20,075 bp. Plastid genome contains 127 genes, 81 protein-coding genes, 36 tRNA genes and 8 rRNA genes. Phylogenetic analysis suggested P. zhennan is sister to Phoebe sheareri and embed in Lauraceae.

Keywords:

• Phoebe zhennan
• plastid genome
• phylogeny

Phoebe zhennan is megaphanerophyte, which is evergreen, it is known for fine timber, greening and essential oil extraction material. Phoebe zhennan belongs to Phoebe genus which contains 69 species, mainly distributed in western of Hubei province, northwestern of Guizhou province and Sichuan province of China, and it is a second-class national protection species in China (eFloras 2008). Present study assembled and characterized the plastid genome of P. zhennan as a resource for evolution and breeding research.

Fresh leaf sample of P. zhennan was acquired from Mount Emei (29°25′N,103°18′E), Leshan City, Sichuan Province of China, and voucher specimen deposited at Herbarium of College of Forestry, Fujian Agriculture and Forestry University (specimen code FJFC 0008180). DNA extraction from fresh leaf tissue, with 400 bp randomly interrupted by the Covaris ultrasonic breaker for library construction. The constructed library was sequenced PE150 by Illumina Hiseq X Ten platform (Shanghai, China), approximately 2 GB data generated. Raw data quality trimmed by CLC Genomics Workbench v10 (CLC Bio, Aarhus, Denmark) with default parameters. Complete plastid genome of P. sheareri as a reference (Song et al. 2016), plastid genome of P. zhennan was assembled by MITObim v1.8 (omicX) (Hahn et al. 2013) with default parameters. Assembled chloroplast genome annotation based on comparison with P. sheareri by GENEIOUS R10 (Biomatters Ltd., Auckland, New Zealand) (Kearse et al. 2012). The annotation result was drawn with the online tool OGDRAW (http://ogdraw.mpimp-golm.mpg.de/) (Lohse et al. 2013).

The complete plastid genome sequence of P. zhennan (GenBank accession MF 315089) was 152,831 bp in length, with a large single-copy (LSC) region of 93,753 bp, a small single-copy (SSC) region of 18,928 bp, and a pair of inverted repeats (IR) regions of 20,075 bp. Complete chloroplastid genome contains 127 genes, there were 81 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The complete genome GC content was 39.10%. To study the phylogenetic relationship of P. zhenna with other members of Lauraceae, eight species (Cinnamomum micranthum, Machilus yunnanensis, Machilus balansae, Litsea glutinosa, Persea americana, P. omeiensis, P. sheareri, Laurus nobilis) of Lauraceae, one species (Calycanthus fertilis) from Calycanthaceae as outgroup, them all downloaded from NCBI GenBank. The sequences were aligned by MAFFT v7.307 (Katoh and Standley 2013), and the phylogenetic tree constructed by RAxML (Stamatakis 2014) (Figure 1). Phoebe zhennan sister to P. sheareri, and genus Phoebe is monophyletic group embed in Lauraceae with strong bootstrap support.

Figure 1. Phylogenetic analysis of nine species of Lauraceae and Calycanthus fertilis (Calycanthaceae) as outgroup based on plastid genome sequences by RAxML, bootstrap support value near the branch.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by Science and Technology Department guiding project of Fujian Province – Phoebe bournei seedling cultivation and afforestation technology [2016N0001]; The fifth project of forest and seedling Science and Technology of Fujian Province Forestry Department - research on the breeding and rapid propagation of fine germplasm materials in Phoebe bournei [Minlin [2016]No. 9].