Characterization of the complete chloroplast genome of Salvia hispanica (Lamiaceae)

Abstract

Salvia hispanica is an annual food and oil crop native to Mexico and Guatemala. In this study, we report the complete chloroplast genome (plastome) of S. hispanica. The plastome was 150,980 bp in length and comprises a large single-copy region (82,274 bp), a small single-copy region (17,534 bp), and a pair of inverted repeats (25,586 bp). It encodes 114 unique genes, including 80 protein-coding genes (PCGs), 30 tRNAs, and 4 rRNAs. The overall GC content of this plastome was 38.0%. Phylogenomic analysis of all PCGs revealed that S. hispanica was closely related to S. bulleyana.

Keywords:

• Salvia hispanica
• plastome
• phylogenomics

Salvia, with nearly 1000 species, belongs to Lamiaceae. It is radiated extensively in three regions of the world: Central and South America, Western Asia, and Eastern Asia (Walker and Sytsma 2007). Salvia hispanica is an annual herb native to Mexico and Guatemala (Cahill and Provance 2002). It has a long history of edible cultivation and is the third largest food crop in Mexico and other places after corn and soybeans (Muñoz et al. 2013). Its seeds are rich in unsaturated fatty acid, high-quality protein, soluble dietary fiber, vitamins, mineral elements, and a variety of antioxidant compounds. It has significant preventive and therapeutic effects on obesity, cardiovascular disease, and diabetes (Reyes-Caudillo et al. 2008; Alfredo et al. 2009; Ixtaina et al. 2011; Poudyal et al. 2012). They also have anti-inflammatory and anti-atherosclerotic effects (da Silva et al. 2019; Grancieri et al. 2019). Its serine-type protease inhibitors have shown the most positive effects with hepatocarcinoma (HCC) model (Laparra and Haros 2019). In this study, we reported the plastome of S. hispanica for resolving its phylogenetic position.

Fresh leaves of S. hispanica were collected from Kunming Botanical Garden, Chinese Academy of Sciences (N25°08′33.70″, E102°44′30.73″). Voucher specimen (SD118) has been deposited at College of Life Sciences, Shandong Normal University. Total genomic DNA was extracted by the modified CTAB method described in Wang et al. (2013). The total genomic DNA was used for library preparation and paired-end (PE) sequencing by the Illumina MiSeq instrument at Novogene (Beijing, China). The plastome was assembled using Organelle Genome Assembler (OGA, https://github.com/quxiaojian/OGA) described in Qu (2019). Plastome annotation was conducted with Plastid Genome Annotator (PGA, https://github.com/quxiaojian/PGA) (Qu et al. 2019), coupled with manual correction using Geneious v9.1.4. To determine the phylogenetic placement of S. hispanica, a maximum-likelihood (ML) tree was reconstructed using RAxML v8.2.10 (Stamatakis 2014), including tree robustness assessment using 1000 rapid bootstrap replicates with the GTRGAMMA substitution model, based on the alignment of 80 shared protein-coding genes (PCGs) using MAFFT v7.313 (Katoh and Standley 2013).

The complete plastome of S. hispanica (GenBank accession number: MT083896) was 150,980 bp in size and contained a large single-copy region (LSC: 82,274 bp), a small single-copy region (SSC: 17,534 bp), and two inverted repeats regions (IR: 25,586 bp). The overall GC content was 38.0%. In total, 114 unique genes, including 80 PCGs, 30 tRNAs, and 4 rRNAs were annotated. Among them, 14 PCGs and 6 tRNAs contained introns, in which 12 PCGs and 6 tRNAs contained one intron and 2 PCGs contained two introns. There were 11 duplicated genes in the IR. The ML phylogenetic tree showed that S. hispanica was closely related to S. bulleyana (Figure 1).

Figure 1. A maximum-likelihood (ML) tree inferred from 80 plastome genes. Spinacia oleracea and Arabidopsis thaliana from Chenopodiaceae and Brassicaceae are used as outgroup. The numbers on branches are bootstrap support values.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

The study was financially supported by Shandong Provincial Agricultural Elite Varieties Project [2019LZGC017] and Investigation on Undergrowth Herbs of Forestry Department of Shandong Province.