Complete chloroplast genome sequences of the medicinal plant Piper hancei.
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ABSTRACT:
SUBMITTER: Zhang L
PROVIDER: S-EPMC8405093 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Pogostemon cablin, the natural source of patchouli alcohol, is an important herb in the Lamiaceae family. Here, we present the entire chloroplast genome of P. cablin. This genome, with 38.24% GC content, is 152,460 bp in length. The genome presents a typical quadripartite structure with two inverted repeats (each 25,417 bp in length), separated by one small and one large single-copy region (17,652 and 83,974 bp in length, respectively). The chloroplast genome encodes 127 genes, of which 107 genes are single-copy, including 79 protein-coding genes, four rRNA genes, and 24 tRNA genes. The genome structure, GC content, and codon usage of this chloroplast genome are similar to those of other species in the family, except that it encodes less protein-coding genes and tRNA genes. Phylogenetic analysis reveals that P. cablin diverged from the Scutellarioideae clade about 29.45 million years ago (Mya). Furthermore, most of the simple sequence repeats (SSRs) are short polyadenine or polythymine repeats that contribute to high AT content in the chloroplast genome. Complete sequences and annotation of P. cablin chloroplast genome will facilitate phylogenic, population and genetic engineering research investigations involving this particular species.
| S-EPMC4926354 | biostudies-literature
Project description:Forsythia suspensa is an important medicinal plant and traditionally applied for the treatment of inflammation, pyrexia, gonorrhea, diabetes, and so on. However, there is limited sequence and genomic information available for F. suspensa. Here, we produced the complete chloroplast genomes of F. suspensa using Illumina sequencing technology. F. suspensa is the first sequenced member within the genus Forsythia (Oleaceae). The gene order and organization of the chloroplast genome of F. suspensa are similar to other Oleaceae chloroplast genomes. The F. suspensa chloroplast genome is 156,404 bp in length, exhibits a conserved quadripartite structure with a large single-copy (LSC; 87,159 bp) region, and a small single-copy (SSC; 17,811 bp) region interspersed between inverted repeat (IRa/b; 25,717 bp) regions. A total of 114 unique genes were annotated, including 80 protein-coding genes, 30 tRNA, and four rRNA. The low GC content (37.8%) and codon usage bias for A- or T-ending codons may largely affect gene codon usage. Sequence analysis identified a total of 26 forward repeats, 23 palindrome repeats with lengths >30 bp (identity > 90%), and 54 simple sequence repeats (SSRs) with an average rate of 0.35 SSRs/kb. We predicted 52 RNA editing sites in the chloroplast of F. suspensa, all for C-to-U transitions. IR expansion or contraction and the divergent regions were analyzed among several species including the reported F. suspensa in this study. Phylogenetic analysis based on whole-plastome revealed that F. suspensa, as a member of the Oleaceae family, diverged relatively early from Lamiales. This study will contribute to strengthening medicinal resource conservation, molecular phylogenetic, and genetic engineering research investigations of this species.
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Project description:BackgroundAconitum transsectum Diels. (Ranunculaceae) is an important medicinal plant that is widely used in traditional Chinese medicine, but its morphological traits make it difficult to recognize from other Aconitum species. No research has sequenced the chloroplast genome of A.transsectum, despite the fact that phylogenetic analysis based on chloroplast genome sequences provides essential evidence for plant classification.ResultsIn this study, the chloroplast (cp) genome of A. transsectum was sequenced, assembled, and annotated. A. transsectum cp genome is a 155,872 bp tetrameric structure including a large single copy (LSC, 87,671 bp) and a small single copy (SSC, 18,891 bp) section, as well as a pair of inverted repeat sequences (IRa and IRb, 25,894 bp each). 131 genes are encoded by the complete cp genome, comprising 86 protein-coding genes, 37 tRNAs, and 8 rRNAs. The most favored codon in the A. transsectum cp genome is AUG, and 46 repeats and 241 SSRs were also identified. The A. transsectum cp genome is similar in size, gene composition, and IR expansion and contraction to the cp genomes of seven Ranunculaceae species. Phylogenetic analysis of cp genomes of 28 plants from the Ranunculaceae family shows that A. transsectum is most closely related to A. vilmorinianum, A. episcopale, and A. forrestii of Subgen. Aconitum.ConclusionsOverall, this study provides complete cp genome resources for A. transsectum that will be beneficial for identifying potential.
| S-EPMC9976445 | biostudies-literature
Project description:Salvia miltiorrhiza is an important medicinal plant with great economic and medicinal value. The complete chloroplast (cp) genome sequence of Salvia miltiorrhiza, the first sequenced member of the Lamiaceae family, is reported here. The genome is 151,328 bp in length and exhibits a typical quadripartite structure of the large (LSC, 82,695 bp) and small (SSC, 17,555 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,539 bp). It contains 114 unique genes, including 80 protein-coding genes, 30 tRNAs and four rRNAs. The genome structure, gene order, GC content and codon usage are similar to the typical angiosperm cp genomes. Four forward, three inverted and seven tandem repeats were detected in the Salvia miltiorrhiza cp genome. Simple sequence repeat (SSR) analysis among the 30 asterid cp genomes revealed that most SSRs are AT-rich, which contribute to the overall AT richness of these cp genomes. Additionally, fewer SSRs are distributed in the protein-coding sequences compared to the non-coding regions, indicating an uneven distribution of SSRs within the cp genomes. Entire cp genome comparison of Salvia miltiorrhiza and three other Lamiales cp genomes showed a high degree of sequence similarity and a relatively high divergence of intergenic spacers. Sequence divergence analysis discovered the ten most divergent and ten most conserved genes as well as their length variation, which will be helpful for phylogenetic studies in asterids. Our analysis also supports that both regional and functional constraints affect gene sequence evolution. Further, phylogenetic analysis demonstrated a sister relationship between Salvia miltiorrhiza and Sesamum indicum. The complete cp genome sequence of Salvia miltiorrhiza reported in this paper will facilitate population, phylogenetic and cp genetic engineering studies of this medicinal plant.
| S-EPMC3584094 | biostudies-literature
Project description:Sophora tonkinensis belongs to genus Sophora of the Fabaceae family. It is mainly distributed in the ridge and peak regions of limestone areas in western China and has high medicinal value and important ecological functions. Wild populations of S. tonkinensis are in danger and need urgent conservation. Furthermore, wild S. tonkinensis resources are very limited relative to the needs of the market, and many adulterants are present on the market. Therefore, a method for authenticating S. tonkinensis and its adulterants at the molecular level is needed. Chloroplast genomes are valuable sources of genetic markers for phylogenetic analyses, genetic diversity evaluation, and plant molecular identification. In this study, we report the complete chloroplast genome of S. tonkinensis. The circular complete chloroplast genome was 154,644 bp in length, containing an 85,810 bp long single-copy (LSC) region, an 18,321 bp short single-copy (SSC) region and two inverted repeat (IR) regions of 50,513 bp. The S. tonkinensis chloroplast genome comprised 129 genes, including 83 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The structure, gene order and guanine and cytosine (GC) content of the S. tonkinensis chloroplast genome were similar to those of the Sophora alopecuroides and Sophora flavescens chloroplast genomes. A total of 1,760 simple sequence repeats (SSRs) were identified in the chloroplast genome of S. tonkinensis, and most of them (93.1%) were mononucleotides. Moreover, the identified SSRs were mainly distributed in the LSC region, accounting for 60% of the total number of SSRs, while 316 (18%) and 383 (22%) were located in the SSC and IR regions, respectively. Only one complete copy of the rpl2 gene was present at the LSC/IRB boundary, while another copy was absent from the IRA region because of the incomplete structure caused by IR region expansion and contraction. The phylogenetic analysis placed S. tonkinensis in Papilionoideae, sister to S. flavescens, and the genera Sophora and Ammopiptanthus were closely related. The complete genome sequencing and chloroplast genome comparative analysis of S. tonkinensis and its closely related species presented in this paper will help formulate effective conservation and management strategies as well as molecular identification approaches for this important medicinal plant.
| S-EPMC7385175 | biostudies-literature
Project description:We report the complete chloroplast genome sequence of Gynostemma pentaphyllum, a well-known traditional Chinese medicine, which produces triterpenoid saponins similar to Panax ginseng. The assembled chloroplast genome (cpDNA) was 157,654?bp in length and structurally divided into four distinct regions, namely, large single copy region (86,794?bp), small single copy region (18,654?bp) and a pair of inverted repeat regions (26,103?bp). A total of 143 genes were annotated, including 87 protein-coding genes, 10 tRNA genes and 46 rRNA genes. Phylogenetic analysis revealed that the chloroplast genome sequence of G. pentaphyllum is most closely related to Cucumis melo.
| S-EPMC7800860 | biostudies-literature
Project description:Selaginella involvens distributed in East Asia region including China used as traditional medicine, which is an important medicinal plant for preventing and treating asthma. The complete chloroplast genome sequence of S. involvens was characterized from Illumina pair-end sequencing. The chloroplast genome of S. involvens was 126,340 bp in length, containing a large single-copy region (LSC) of 53,214 bp, a small single-copy region (SSC) of 47,561 bp, and two inverted repeat (IR) regions of 12,796 bp. The overall GC content is 38.70%, whereas the corresponding values of the LSC, SSC, and IR regions are 36.2%, 31.9%, and 43.2%, respectively. The genome contains 80 complete genes, including 61 protein-coding genes (45 protein-coding gene species), nine tRNA genes (six tRNA species), and eight rRNA genes (four rRNA species). The Neighbour-joining phylogenetic analysis showed that S. involvens and Selaginella tamariscina clustered together as sisters to other Salvia species.
| S-EPMC7782301 | biostudies-literature
Project description:Piptanthus nepalensis (Hooker) Sweet is a semi deciduous or deciduous shrub belonging to the genus Piptanthus, Leguminosae. P. nepalensis has been used as a folk medicinal herb in Nepal and was cultivated all over the world as an ornamental plant. In the present study, we sequenced the entire genome of the chloroplast of P. nepalensis. The total length of the chloroplast genome in P. nepalensis is 152,195 bp, including a large single-copy region of 82,048 bp, a small single-copy region of 17,675 bp, and a pair of inverted repeats regions of 26,236 bp. The overall guanine-cytosine (GC) content of the genome was 36.7%. There are 131 genes in the chloroplast genome of P. nepalensis, including 85 protein-coding genes, 8 rRNA genes and 38 tRNA genes. Phylogenetic analysis showed that P. nepalensis is closely related to Maackia floribunda.
| S-EPMC9090406 | biostudies-literature
Project description:Abstract Dracocephalum rupestre (tribe Mentheae; Lamiaceae) is a perennial herb from Korea and China with high ornamental and medicinal value. Here, we report its complete chloroplast genome to provide insight into the phylogenetic relationships of Dracocephalum. The genome is 151,230 bp long, with two inverted repeat regions (25,643 bp each) that separate a large single-copy region (82,536 bp) and a small single-copy region (17,408 bp). It contains 133 genes that encode 88 proteins, eight rRNAs, and 37 tRNAs. The maximum-likelihood phylogenetic analysis strongly supported Dracocephalum monophyly, showing that the genus forms a sister group with the subtribe Menthinae in the tribe Mentheae.
| S-EPMC9902028 | biostudies-literature
Project description:Artemisia argyi, called wormwood, is widely distributed in northeastern Asia. The complete chloroplast genome sequence of A. argyi was generated by de novo assembly using whole genome next generation sequences. The complete chloroplast genome sequence of A. argyi is 151 192 bp in size. It is composed of a large single-copy (LSC), a small single-copy (SSC) and two inverted repeat (IR) regions of 82 930 bp, 18 344 bp and 24 959 bp, respectively. Overall GC contents of the genome were 37.46%. The A. argyi chloroplast genome has a total of 114 genes including 80 protein-coding genes, 30 tRNA genes and four rRNA genes. Phylogenetic analysis based on the chloroplast genome demonstrated that A. argyi is most closely related to Artemisia montana.
| S-EPMC7799501 | biostudies-literature