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.
Highlights
Ye-Xing-Ba (Tibetan name), a common Tibetan herb, is traditionally used for the treatment of exanthema and fever in Traditional Tibetan Medicine (TTM)
The junction regions between inverted repeat (IR) and small single copy (SSC)/large single copy (LSC) and nine additional regions were confirmed by PCR amplification and Sanger sequencing
We compared these sequences to the assembled genome and no mismatch or indel was observed, which validated the accuracy of genome sequencing and assembly
Summary
Ye-Xing-Ba (Tibetan name), a common Tibetan herb, is traditionally used for the treatment of exanthema and fever in Traditional Tibetan Medicine (TTM). As a medicinal alpine species [1], Scrophularia dentata Royle ex Benth. (Scrophulariaceae) is one of the original plants of the Tibetan herb [2]. Our research team has been concentrating on the ethnobotanical survey of Tibetan herbs since 1992 [3, 4]. Based on our specimen collection and taxonomic identification, some chemical and pharmacological studies on S. dentata have been conducted by our team [5, 6, 7]. Because of the harsh living environment and increasing demand for medicinal use of the alpine plant, it is of utmost urgency to develop a conservation strategy for PLOS ONE | DOI:10.1371/journal.pone.0158488. Because of the harsh living environment and increasing demand for medicinal use of the alpine plant, it is of utmost urgency to develop a conservation strategy for PLOS ONE | DOI:10.1371/journal.pone.0158488 July 8, 2016
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