The Complete Chloroplast Genome of Ye-Xing-Ba (Scrophularia dentata; Scrophulariaceae), an Alpine Tibetan Herb

Abstract

Scrophularia dentata is an important Tibetan medicinal plant and traditionally used for the treatment of exanthema and fever in Traditional Tibetan Medicine (TTM). However, there is little sequence and genomic information available for S. dentata. In this paper, we report the complete chloroplast genome sequence of S. dentata and it is the first sequenced member of the Sect. Tomiophyllum within Scrophularia (Scrophulariaceae). The gene order and organization of the chloroplast genome of S. dentata are similar to other Lamiales chloroplast genomes. The plastome is 152,553 bp in length and includes a pair of inverted repeats (IRs) of 25,523 bp that separate a large single copy (LSC) region of 84,058 bp and a small single copy (SSC) region of 17,449 bp. It has 38.0% GC content and includes 114 unique genes, of which 80 are protein-coding, 30 are transfer RNA, and 4 are ribosomal RNA. Also, it contains 21 forward repeats, 19 palindrome repeats and 41 simple sequence repeats (SSRs). The repeats and SSRs within S. dentata were compared with those of S. takesimensis and present certain discrepancies. The chloroplast genome of S. dentata was compared with other five publicly available Lamiales genomes from different families. All the coding regions and non-coding regions (introns and intergenic spacers) within the six chloroplast genomes have been extracted and analysed. Furthermore, the genome divergent hotspot regions were identified. Our studies could provide basic data for the alpine medicinal species conservation and molecular phylogenetic researches of Scrophulariaceae and Lamiales.

Fig 1. Chloroplast genome map of Scrophularia dentata.

Genes drawn inside the circle are transcribed clockwise, and those outside are counterclockwise. Genes belonging to different functional groups are shown in different colors. The asterisks indicate genes which contain intron(s).

Fig 2. Sequence alignment of six chloroplast genomes in the Lamiales order using mVISTA program with S. dentata as reference.

The top line shows genes in order (transcriptional direction indicated with arrow). A cut-off of 70% identity was used for the plots, and the Y-scale represents the percent identity between 50–100%. Genome regions are color-coded as exon, intron, and conserved non-coding sequences (CNS).

Fig 3. Percentages of variable sites in homologous regions across the six Lamiales chloroplast genomes.

(A) coding regions; (B) introns and intergenic spacers (non-coding regions).

Fig 4. Comparison of the borders of LSC, SSC and IR regions in six Lamiales chloroplast genomes.

Ψ indicates a pseudogene. This figure is not to scale.

Fig 5. Repeat sequences and simple sequence repeats (SSRs) within Scrophularia dentata and Scrophularia takesimensis chloroplast genomes.

(A) number of different types of repeats. F = forward repeats; P = palindrome repeats; C = complement repeats; R = reverse repeats. (B) distribution of repeats. (C) number of different types of SSRs. (D) distribution of SSRs. CDS = coding sequence; IGS = intergenic spacer; CDS-IGS = part in CDS and part in IGS.