The complete chloroplast genome of Silvianthus bracteatus (Carlemanniaceae) and phylogenic analysis of Lamiales

Abstract

We assembled and characterized the complete chloroplast genome sequence of Silvianthus bracteatus to investigate its phylogenetic position. With a total length of 155,125 bp, the plastome comprised of a large single-copy (LSC) region of 86,054 bp, a small single-copy (SSC) region of 17,625 bp, and two inverted repeat (IR) regions of 25,723 bp. The overall percentage of GC content was 37.9. The new sequence comprised of total 136 genes, including 88 protein-coding genes, 8 ribosomal RNA genes, and 40 tRNA genes. In these genes, eight genes contained one intron and two genes contained two introns. Phylogenetic analysis showed that S. bracteatus was close to the Oleaceae.

Keywords:

• Chloroplast
• Silvianthus bracteatus
• phylogenetic analysis

The Carlemanniaceae is a family of shrub to herbaceous perennial flowering plants, including only two genera (Carlemannia and Silvianthus) and four species. Taxonomists had put the two genera into the Caprifoliaceae or the Rubiaceae (Chen and Anthony 2011). The Angiosperm Phylogeny Group placed the group in the Lamiales and as a sister group to the Oleaceae and the systematic position of Carlemanniaceae is still largely unknown (Stevens 2017). Here, we report and characterize the first complete plastome of Silvianthus bracteatus, an endemic shrub in the northern Indochina peninsula to investigate its phylogenetic position (GenBank accession number: MN908147).

The leaves of S. bracteatus was sampled from Xishuangbanna, China (21.9658°N, 101.2181°E) and we deposited the voucher specimen at the Herbarium of Guizhou Normal University (Accession number: Zhu201905004). Total genomic DNA was extracted with the Qiagen DNeasy Plant Mini Kit (Qiagen, Carlsbad, CA, USA). The genomic paired-end (PE150) sequencing was performed on an Illumina Hiseq 2500 instrument. The cp genome was assembled using the program GetOrganelle v1.6.2e (Jin et al. 2018). Annotation was performed using PGA (Qu et al. 2019) and manually corrected.

A typical quadripartite structure as most angiosperms was displayed by the plastome of S. bracteatus, containing two inverted repeat regions of 25,723 bp, a large single-copy region of 86,054 bp, and a small single-copy region of 17,625 bp. The new sequence comprised total 136 genes, including 88 protein-coding genes, 8 ribosomal RNA genes, and 40 tRNA genes. In these genes, eight protein-coding genes (atpF, ndhA, ndhB, petD, rpl16, rpl2, rps12, rps16) contained one intron and two genes (clpP and ycf3) contained two introns. The overall percentage of GC content was 37.9 and the corresponding value of the LSC, SSC, and IR region were 35.9, 32.4, and 43.1, respectively.

Fifteen complete chloroplast genome sequences of Lamiales and one complete chloroplast genome sequences of Boraginales were downloaded from NCBI to further investigate the phylogenetic position of S. bracteatus. We constructed a maximum likelihood tree using RAxML (Stamatakis 2014) after the sequences were aligned using MAFFT v7.307 (Katoh and Standley 2013). Our results showed that S. bracteatus was close to the Oleaceae (Figure 1). This published S. bracteatus chloroplast genome will provide useful information for phylogenetic and evolutionary studies in Carlemanniaceae and Lamiales.

Figure 1. ML phylogenetic tree of 16 species within Lamiales based on 15 chloroplast genome sequences in GenBank, plus the chloroplast sequence of Silvianthus bracteatus. The tree is rooted with the Boraginales (Tiquilia plicata). Bootstraps (100,000 replicates) are shown at the nodes.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by the Doctoral Foundation of Guizhou Normal University [GZNUD[2018] No. 2].