The complete chloroplast genome of Phoebe minutiflora (Lauraceae)

Abstract

Phoebe minutiflora H. W. Li, is a member of the Lauraceae family, while its generic relationship has been long-term controversial. The complete chloroplast (cp) genome of P. minutiflora was first reported in this paper. The cp genome was 152,654 bp in length with four typical quadripartite structures, which was consisted of a large single-copy (LSC) region of 93,697 bp, a small single-copy (SSC) region of 18,809 bp, and two inverted repeats (IRs) of 20,074 bp. In addition, there were a total of 112 unique genes, including 79 protein-coding genes, 29 tRNA genes, and four rRNA genes. The phylogenetic analysis indicated that P. minutiflora should be placed into Machilus.

Keywords:

• Chloroplast genome
• Lauraceae
• Phoebe minutiflora
• phylogenetic analysis

Phoebe minutiflora H. W. Li (Phoebe, Lauraceae), a large evergreen tree primarily distributed in Yunnan, China (Li 1996), plays an important role of tropical forest. P. minutiflora was one of the special species within Phoebe in terms of spherical fruit, while the other species in this genus have ellipsoid or ovoid fruit. Li (2010) supported that P. minutiflora belonged to Machilus based on nuclear DNA ITS and LEAFY intronII sequences. In order to further verify the P. minutiflora belong to Phoebe or Machilus, our phylogenetic studies were carried out based on 34 chloroplast (cp) genome sequences of Lauraceae.

We collected fresh leaves of P. minutiflora from Mengla, Yunnan province of China (N21°29′21″, E101°17′44″) and the specimen was deposited at the herbarium of Nanjing University (http://www.cfh.ac.cn/subsite/default.aspx?siteid=N, Shan Lu, [email protected]) under the voucher number YJT190323. Total genomic DNA of P. minutiflora was extracted from approximately 5 mg of the silica-dried leaf tissue using the modified CTAB method (Doyle and Doyle 1987). The high-quality genomic DNA of P. minutiflora was used to construct Illumina paired-end (2 × 150 bp) library and implement the low-coverage shotgun sequencing in a lane of HiSeqXten platform (Illumina, San Diego, CA) at The Beijing Genomics Institute (BGI, Shenzhen, China). Approximately, 3.09 Gb of raw data were generated and then we de novo assembled the complete cp genome of P. minutiflora using GetOrganelle pipeline (Wyman et al. 2004). The cp genome was then automatically annotated using Plastid Genome Annotator (Qu et al. 2019), with manual adjusting and confirming the annotated protein-coding genes (CDS) in Geneious Primer (Kearse et al. 2012). The complete cp genome sequence was submitted to GenBank with an accession number MW367223.

The results showed that the complete cp genome of P. minutiflora (152,654 bp, 39.2% GC content) possessed quadripartite structure, containing a large single-copy (LSC) region (93,697 bp, 37.9% GC content), a small single-copy (SSC) region (18,809 bp, 34% GC content), and a pair of inverted repeats (IRs) (20,074 bp, 44.4% GC content). In total, 79 protein-coding genes, 29 tRNA genes, and four rRNA genes were identified, and there were 14 genes (atpF, petB, petD, ndhA, ndhB, rpl2, rps16, rpoC1, trnA-UGC, trnG-UCC, trnI-GAU, trnK-UUU, trnL-UAA, and trnV-UAC) with one intron and three genes (clpP, rps12, and ycf3) with two introns among the 112 unique genes.

The maximum-likelihood (ML) phylogenetic tree of 34 Lauraceae species was constructed using IQ-TREE v1.6.12 (Nguyen et al. 2015) under the best model of GTR + F+R10 with 1000 bootstrap replicates (Figure 1). The tree was visualized using the iTOL online tool (Letunic and Bork 2019). According to the results, nine Phoebe species formed a large clade and were sister to Machilus, which indicated that Phoebe was monophyletic, similar as Song et al.’s results (Song et al. 2017). The Machilus clade was also evidently monophyletic, adjacent to Persea americana and Phoebe clade. Particularly, P. minutiflora was closely related to Machilus thunbergia, M. yunnanensis, and M. pauhoi, which supported P. minutiflora belonged to Machilus, same as Li (2010) and Li et al. (2011)’s results. Therefore, this systematic classification results of P. minutiflora emphasized the importance of combining morphology with molecular systematics, which also became the future directions of Lauraceae systematic researches.

Figure 1. Maximum-likelihood (ML) tree of 34 Lauraceae species based on chloroplast genome. Numbers near the nodes are ML bootstrap values.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

The data that support the findings of this study are openly available in National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/genbank/), GenBank accession number: MW367223. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA717114, SRR14066842, and SAMN18477996, respectively.

Additional information

Funding

This research was supported by the National Natural Science Foundation of China [Grant No. 30970512].