Characterization of the complete chloroplast genome of Buddleja alternifolia (Buddleiaceae)

Abstract

The complete chloroplast genome sequence of Buddleja alternifolia, a perennial garden plant and common medicinal plant is widely distributed in west China. The plastome is 154,357 bp in length, with one large single copy region of 85,406 bp, one small single copy region of 18,071 bp, and two inverted repeat (IR) regions of 25,440 bp. It contains 130 genes, including 85 protein-coding genes, 8 ribosomal RNA, and 37 transfer RNA. Phylogenetic tree shows that B. alternifolia formed one clade with Buddleja colvilei and Buddleja sessilifolia. The published plastome of B. alternifolia provides significant insight for elucidating the phylogenetic relationship of taxa genus Buddleja.

Buddleja alternifolia Maxim. belongs to genus Buddleja of the Buddleiaceae. Members of this genus are widely distributed in west China, are well known as perennial garden plants (Guan and Chen 2006) and medicinal plants (Cai et al. 2015). The information about B. alternifolia was focussed on tissue culture (Liu et al. 2009), seed germination and the establishment of seedlings (Han et al. 2013) and drought resistance physiology (Yan et al. 2017). In the last decades, the use of B. alternifolia in landscaping has led to a rapid increase in the information available on the tissue rapid propagation of B. alternifolia. However, due to anthropogenic over-exploitation and decreasing distributions, this species needs urgent conservation. Knowledge of the genetic information of this species would contribute to the formulation of protection strategy. In this study, we assembled and characterized the complete chloroplast (cp) genome sequence of B. alternifolia based on high-quality pair-end sequencing data.

Fresh leaves of B. alternifolia were collected from Helanshan mountain (Yichuan, Ningxia, China; coordinate: 105°59′E, 38°40′N). Dried and kept in silica gel for DNA extraction, and then stored in the Herbarium of the College of Life Science, Ningxia University with the accession number of ND190619001. Total genomic DNA was extracted with a modified CTAB method (Doyle and Doyle 1987). First, we obtained 10 million high quality pair-end reads for B. alternifolia, and after removing the adapters, the circular genome was assembled in the toolkit GetOrganelle v1.6.2 (Camacho et al. 2009; Bankevich et al. 2012; Langmead and Salzberg 2012; Wick et al. 2015; Jin et al. 2018). The complete chloroplasts genome sequence of B. colvilei was used as a reference. Plann v1.1 (Huang and Cronk 2015) and Geneious v11.0.3 (Kearse et al. 2012) were used to annotate the chloroplasts genome and correct the annotation. The complete cp genome sequence was deposited in GenBank under accession number MN395662.

The B. alternifolia cp genome is 154,357 bp in length, exhibits a typical quadripartite structural organization, consisting of a large single-copy (LSC) region of 85,406 bp, two inverted repeat (IR) regions of 25,440 bp and a small single-copy (SSC) region of 18,071 bp. The cp genome contains 130 complete genes, including 85 protein-coding genes (85 PCGs), 8 ribosomal RNA genes (8 rRNAs), and 37 tRNA genes (37 tRNAs). Most genes occur in a single copy, while 17 genes occur in double, including 4 rRNAs (4.5S, 5S, 16S, and 23S rRNA), 7 tRNAs (trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, and trnV-GAC), and 6 PCGs (rps7, ndhB, ycf2, ycf15, rpl2 and rpl23). The overall GC content of cp DNA is 40.0%, while the corresponding values of the LSC, SSC, and IR regions are 36.1%, 32.2%, and 42.2%.

In order to further clarify the phylogenetic position of B. alternifolia, plastome of six representative species were obtained from NCBI to construct the plastome phylogeny, with Hemsleya lijiangensis as an outgroup. All the sequences were aligned using MAFFT v.7.313 (Katoh and Standley 2013) and maximum likelihood phylogenetic analyses were conducted using RAxML v.8.2.11 (Stamatakis 2014). The phylogenetic tree shows that Buddleja colvilei clustered together with Buddleja sessilifolia. and then formed one clade with B. alternifolia (Figure 1).

Figure 1.

Phylogenetic relationships of B. alternifolia using whole chloroplast genome. GenBank accession numbers: Buddleja colvilei (NC_042766); Buddleja sessilifolia (NC_042767); Catharanthus roseus (KC561139); Cynanchum auriculatum (KU900231); Gelsemium elegans (MH327990); Hemsleya lijiangensis (NC_039653).

In summary, the complete cp genome from this study provides significant insight for elucidating the phylogenetic relationship of taxa genus Buddleja.

Disclosure statement

No potential conflict of interest was reported by the authors.