The complete chloroplast genome of Bletilla ochracea Schltr., a medicinal plant with yellow flowers.
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ABSTRACT:
SUBMITTER: Zhao D
PROVIDER: S-EPMC9225769 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Bletilla striata (Thunb.) Reichb. f. is one of the commonly used traditional Chinese medicine with tuber as medicine. We report herein the complete chloroplast genome sequence of Bletilla striata (Thunb.) Reichb. f. It has a length of 159,491 bp, which contained a small single-copy (SSC) region of 18,778 bp and a large single-copy (LSC) region of 87,139 bp, separated by two copies of an inverted repeat (IR) of 26,787 bp. The chloroplast genome contains 114 unique genes, including 80 PCG, 30 tRNA, and 4 rRNA genes. In addition, 18 genes contained one or two introns, which of those including 10 PCG genes possess a single intron, and 2 PCG genes harbor two introns; and 6 tRNA genes harbor a single intron. In this study, Bletilla stariata is sister to Bletilla formosana and clustered within the group consisting of the species that belong to Orchiidaceae.
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Project description:The family Orchidaceae is renowned for its extensive diversity. Within this family, the genus Goodyera R. Br. is classified under the subtribe Goodyerinae, comprising approximately 99 species. In this study, a species Goodyera yunnanensis Schltr., its plastid genome was characterized. The plastid genome of G. yunnanensis is 146,197 bp in size and exhibits a typical quadripartite structure with a pair of inverted repeat regions (IRs) of 25,611 bp, a large single-copy region (LSC) of 81,300 bp and a small single-copy region (SSC) of 13,675 bp. A total of 126 genes were identified, containing 80 protein-coding genes, 38 tRNA genes and 8 rRNA genes. The overall GC content is 37.2%, with corresponding values of 43.3%, 34.7% and 29.1% in IR, LSC and SSC regions, respectively. Forty-seven simple sequence repeats (SSRs) are found in G. yunnanensis plastome, and the frequency of mononucleotide repeats is significantly higher than other repeat types. Phylogenetic analysis indicates that Goodyera is resolved into four clades. G. yunnanensis belongs to the monophyletic clade A, and its phylogenetic position can be reasonably supported by morphological and molecular data.
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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.
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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.
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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.
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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.
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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:The complete chloroplast genome sequence of Artemisia gmelinii was characterized from Illumina pair-end sequencing. The chloroplast genome of A. gmelinii was 151,050 bp in length, containing a large single-copy region (LSC) of 80,976 bp, a small single-copy region (SSC) of 16,006 bp, and two inverted repeat (IR) regions of 27,034 bp, each. The overall GC content is 30.70%, while the correponding values of the LSC, SSC, and IR regions are 64.6, 69.2, and 60.1%, respectively. The genome contains 131 complete genes, including 86 protein-coding genes (62 protein-coding gene species), 37 tRNA genes (29 tRNA species) and 8 rRNA genes (4 rRNA species). The Neighbour-joining phylogenetic analysis showed that A. gmelinii and Artemisia scoparia clustered together as sisters to other Artemisia species.
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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.
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