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.

Complete Chloroplast Genome Sequence of Decaisnea insignis: Genome Organization, Genomic Resources and Comparative Analysis

“…Similar to the SSRs, D . insignis contained a lower number of repeat elements compared with other plants 34 , 35 . The presence of these repeats indicated that the locus was a crucial mutation hotspot in the genome because the repeat sequences led to sequence variations and genome rearrangements due to the slipped-strand mispairing and improper recombination 36 .…”

The complete chloroplast genome sequence of strawberry (Fragaria × ananassaDuch.) and comparison with related species of Rosaceae

“…roxburghii ( KX768420 ) and most divergent from that of P. persica ‘Nemared’. Overall, the results revealed SC regions to be more divergent than IR regions, with higher divergence being observed in non-coding regions than in coding regions, which is a common phenomenon in the chloroplast genomes of angiosperms ( Yao et al, 2015 ; Ni et al, 2016 ; Asaf et al, 2016 ). The coding regions with marked differences include the ycf1 , matK and psaI genes.…”

The Complete Chloroplast Genome Sequences of the Medicinal Plant Forsythia suspensa (Oleaceae)

“…Out of the 49 repeats, 34 repeats (69.4%) were 30–39 bp long, 11 repeats (22.4%) were 40–49 bp long, four repeats (8.2%) were 50–59 bp long, and the longest repeat was 58 bp. Generally, repeats were mostly distributed in noncoding regions [ 32 , 33 ]; however, 53.1% of the repeats in the F. suspensa cp genome were located in coding regions (CDS) ( Figure 3 A), mainly in ycf2 ; similar to that of S. dentata and S. takesimensis [ 34 ]. Meanwhile, 40.8% of repeats were located in intergenic spacers (IGS) and introns, and 6.1% of repeats were in parts of the IGS and CDS.…”