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Background: Subtribe Swertiinae, a medicinally significant and highly speciose Subtribe of family Gentianaceae. Despite previous extensive studies based on both morphology and molecular data, intergeneric and infrageneric relationships within subtribe Swertiinae remain controversial. Methods: Here, we employed four newly generated Swertia chloroplast genomes with thirty other published genomes to elucidate their genomic characteristics. Results: The 34 chloroplast genomes were small and ranged in size from 149,036 to 154,365 bp, each comprising two inverted repeat regions (size range 25,069–26,126 bp) that separated large single-copy (80,432–84,153 bp) and small single-copy (17,887–18,47 bp) regions, and all the chloroplast genomes showed similar gene orders, contents, and structures. These chloroplast genomes contained 129–134 genes each, including 84–89 protein-coding genes, 37 tRNAs, and 8 rRNAs. The chloroplast genomes of subtribe Swertiinae appeared to have lost some genes, such as rpl33, rpl2 and ycf15 genes. Comparative analyses revealed that two mutation hotspot regions (accD-psaI and ycf1) could serve as effective molecular markers for further phylogenetic analyses and species identification in subtribe Swertiinae. Positive selection analyses showed that two genes (ccsA and psbB) had high Ka/Ks ratios, indicating that chloroplast genes may have undergone positive selection in their evolutionary history. Phylogenetic analysis showed that the 34 subtribe Swertiinae species formed a monophyletic clade, with Veratrilla, Gentianopsis and Pterygocalyx located at the base of the phylogenetic tree. Some genera of this subtribe, however, were not monophyletic, including Swertia, Gentianopsis, Lomatogonium, Halenia, Veratrilla and Gentianopsis. In addition, our molecular phylogeny was consistent with taxonomic classification of subtribe Swertiinae in the Roate group and Tubular group. The results of molecular dating showed that the divergence between subtrib Gentianinae and subtrib Swertiinae was estimated to occur in 33.68 Ma. Roate group and Tubular group in subtribe Swertiinae approximately diverged in 25.17 Ma. Conclusion: Overall, our study highlighted the taxonomic utility of chloroplast genomes in subtribe Swertiinae, and the genetic markers identified here will facilitate future studies on the evolution, conservation, population genetics, and phylogeography of subtribe Swertiinae species. [ABSTRACT FROM AUTHOR]

Bupleurum species are well-known for their antipyretic, analgesic, gallbladder and other functions so that they are very popular in traditional Chinese medicine. However, to our knowledge, there is no completed chloroplast genome of Bupleurum genus in China. In the present study, we determined the complete chloroplast genome sequences for Bupleurum longicaule var. strictum using IIumina sequencing. Bupleurum longicaule var. strictum is 155,578 bp which is composed of two inverted repeats (IR: 26,257bp), a large single copy region (LSC: 86,977 bp), and a small single-copy region (SSC: 16,087 bp). The overall AT content is 65.32%. The chloroplast genome includes a total of 51 functional genes including 15 protein-coding genes and 36 tRNA. A total of 10 genes were duplicated in the IR regions including seven tRNA and three protein-coding genes. Phylogenetic analysis suggested that B. longicaule var. strictum formed a monophyletic clade. [ABSTRACT FROM AUTHOR]

Asone of the original plants of traditional Tibetan folk medicinal 'Zangyinchen', Swertia franchetiana (S. franchetiana) was used to treat a variety of ailments. Large amount of fruiting harvesting has led to a sharp decrease and gradual depletion of its resources. As a result, the wild resource is on the verge of extinction, it needs urgent conservation. Here, we report the complete sequence of the chloroplast genome of S. franchetiana. The genome was 153,087 bp in length with 130 genes comprising 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of G. paludosa chloroplast genome was is 38.17%. Phylogenomic analysis suggested that S. franchetiana formed a clade with Swertia mussotii with high bootstrap values, indicating that the S. franchetiana was closely related to S. mussotii [ABSTRACT FROM AUTHOR]

Abstract: A thorough understanding of the levels and partitioning of genetic variation across populations and geographical regions of endangered species is a prerequisite to ensure effective conservation and/or restoration activities. Here, we examined chloroplast DNA (cpDNA) trnH-psbA intergenic spacer sequences variation within Notopterygium forbesii, an endangered and endemic perennial herb in China. Sequence data obtained from 141 individuals in 14 populations revealed twenty-two haplotypes. A high level of haplotype diversity (Hd = 0.81) and low level of nucleotide diversity (Pi = 0.0047) were detected. Low genetic differentiation among populations and also among regions was consistently indicated by both hierarchical analyses of molecular variance (AMOVA) and the structure of a neighbor-joining tree. Low level of population differentiation between populations or between regions in cpDNA sequences may be due to effects of the abundance of ancestral haplotype sharing and the high number of private haplotypes fixed for each population. Based on our results, we proposed some conservation strategies. [ABSTRACT FROM AUTHOR]

Gentianopsis paludosa (Mum.) Ma is an important species in Tibetan folk medicine, but its wild populations are shrinking roughly due to the increasing demand for it. Gentianopsis paludosa is presently at risk of over-exploitation, so it needs urgent conservation. Here, we report the complete sequence of the chloroplast genome of G. paludosa. The genome was 51,121 bp in length with 129 genes comprising 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of G. paludosa chloroplast genome was is 36.67%. The phylogenomic analysis suggested that G. paludosa forms a clade with species in Halenia and Swertia, indicating that the G. paludosa is more closely related to Halenia and Swertia than that of Gentiana. [ABSTRACT FROM AUTHOR]

Swertia tetraptera, native to the Qinghai-Tibetan Plateau, is an important traditional Chinese medicine. Although researchers have done a lot of work on it, the phylogenetic position of S. tetraptera within Swertia has still not been solved. Chloroplast genome sequences play a significant role in the development of molecular markers in plant phylogenetic and population genetic studies. In present study, we determined the complete chloroplast genome sequences for S. tetraptera using IIumina sequencing. The total length of the complete chloroplast genome of S. tetraptera is 152,840 bp, of which the GC content is 37.95%. The genome encodes 130 functional genes, including 85 protein-coding genes, 37 tRNA, and 8 rRNA. Phylogenetic analysis suggested that S. tetraptera forms monophyletic group with Halenia corniculata which shows closed relationship with the Halenia. [ABSTRACT FROM AUTHOR]