The complete chloroplast genome sequence of medicinal plant: Lepidium apetalum (Brassicaceae).
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ABSTRACT:
SUBMITTER: Liu Y
PROVIDER: S-EPMC7782362 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Lepidium meyenii Walp. is a frequently used medicinal plant (namely, 'maca') in Yunnan Province of China. In this study, we sequenced the complete chloroplast (cp) genome sequence of L. meyenii to investigate its phylogenetic relationship in the family Cruciferae. The chloroplast genome of L. meyenii was 154,839 bp in length with 36.39% overall GC content, including a large single copy (LSC) region of 83,943 bp, a small single copy (SSC) region of 17,978 bp and a pair of inverted repeats (IRs) of 52,918 bp. The cp genome contained 103 genes, including 78 protein-coding genes, 21 tRNA genes, and four rRNA genes. The phylogenetic analysis indicated L. meyenii was closely related to the genus Capsella.
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Project description:Chloroplast (cp) genome sequences provide a valuable source for phylogenetic analysis. It becomes a popular useful tool for population and phylogeny in recently report. Here, the complete chloroplast genome of the Isatis indigotica has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 156,670 bp in size and comprises a pair of inverted repeat (IR) regions of 26,995 bp each, a large single-copy (LSC) region of 84,907 bp and a small single-copy (SSC) region of 17,773 bp. The total GC content is 36.5%, while the corresponding values of the LSC, SSC and IR region are 34.2%, 29.7% and 42.3%, respectively. The chloroplast genome contains 140 genes, including 94 protein-coding genes. The phylogenetic analysis showed a strong sister relationship with Raphanus sativus in Brassicaceae. These findings provide a foundation for further investigation of cp genome evolution in I. indigotica and other higher plants.
| S-EPMC7799964 | 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.
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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:Garden cress, Lepidium sativum L., is not only an important vegetable which is cultivated in the entire world, but also a widely used folk medicine for the treatment of hyperactive airways disorders. However, as a member of Brassicaceae, few studies have been carried out on its phylogenetic relationship with other Brassicaceae members. Herein, the complete chloroplast (cp) genome of garden cress wa deciphered by the combination of Illumina Hiseq and PacBio Hiseq Platform after extracting of its cp DNA. The cp genome showed a typically quadripartite cycle with 154997 bp, including a pair of inverted repeats (IRa and IRb) of 26491 bp intersected by a large single copy (LSC) region of 84007 bp and a small single copy (SSC) region of 18008 bp. Totally, 128 unique genes were assembled in this cp genome, including 83 protein genes, 37 tRNAs and 8 rRNAs. A total of 73 simple sequence repeats (SSRs) with a length of at least 10 bp were detected. Phylogenetic analysis based on 30 cp genome of Brassicaceae family showed that the L. sativum was closely related to L. virginicum. This study provides important information for future evolution, genetic and molecular biology studies of L. sativum.
| S-EPMC7710307 | 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: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.
| S-EPMC7782189 | 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.
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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.
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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