Browse
Submit Data
Databases
API
Help

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete plastome sequence of Pseuderanthemum haikangense C.Y. Wu & H.S. Lo (Acanthaceae): a medicinal plant in South China.

ABSTRACT: Pseuderanthemum haikangense (Acanthaceae) is a shrubs native to Guangdong, Hainan, Yunnan province of China. In this study, we report and characterize the complete plastome sequence of P. haikangense in order to provide genomic resources helpful for promoting its conservation and medicinal utilization. The complete plastome is 152,849 bp in length and contains the typical quadripartite structure of angiosperm, including two Inverted Repeat (IRs) regions of 25,849 bp, a Large Single-Copy (LSC) region of 83,878 bp and a Small Single-Copy (SSC) region of 17,273 bp. The plastome contains 113 genes, consisting of 79 unique protein-coding genes, 30 unique tRNA gene and 4 unique rRNA genes. The overall A/T content in the plastome of P. haikangense is 61.60%. The complete plastome sequence of P. haikangense will provide a useful resource for the conservation and garden utilization of this species as well as for the phylogenetic studies of Acanthaceae.

SUBMITTER: Gao X

PROVIDER: S-EPMC7782011 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Complete plastome sequence of Piper laetispicum (Piperaceae): An endemic plant species in South China.

Project description:Piper laetispicum is dioecious climbers woody with 10 m tall, which is an endemic species in China. It grows on trees or rocks in forests (100-600 m) in Guangdong and Hainan Province of China. Here, we report and characterize the complete plastid genome sequence of P. laetispicum in an effort to provide genomic resources useful for promoting its conservation. The complete plastome is 161,721?bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 27,125?bp, a large single copy (LSC) region of 89,224?bp and a small single copy (SSC) region of 18,247?bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA gene, and four unique rRNA genes. The overall A/T content in the plastome of P. laetispicum is 61.70%. The complete plastome sequence of P. laetispicum will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for Piper.

| S-EPMC7800576 | biostudies-literature

The complete plastome sequence of Rumex japonicus Houtt.: a medicinal plant.

Project description:Rumex japonicus is a medicinal plant distributed in East Asia. Here, we report and characterize the complete plastid genome sequence of R. japonicus and size is 159,292 bp in length and contains the typical structure and gene content of other angiosperm plastomes, including two inverted repeat regions of 30,629 bp, a large single-copy region of 85,028 bp and a small single-copy region of 13,006 bp. There are 112 unique genes, including 78 protein-coding, 30 tRNAs and 4 rRNAs. We constructed a phylogenetic tree with 14 species and the phylogenetic topologies showed that R. japonicus was closely related to Rheum wittrockii.

| S-EPMC7748881 | biostudies-literature

Complete plastome sequence of Callicarpa nudiflora Vahl (Verbenaceae): a medicinal plant.

Project description:Callicarpa nudiflora Vahl is a medicinal plant occurring in Guangdong, Guangxi, Hainan provinces of China. Here, we report and characterize the complete plastid genome sequence of C. nudiflora in an effort to provide genomic resources useful for promoting its conservation. The complete plastome is 154,080 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 25,657 bp, a large single-copy (LSC) region of 84,949 bp, and a small single-copy (SSC) region of 17,817 bp. There are 113 genes annotated, including 79 unique protein-coding genes, 4 unique ribosomal RNA genes, and 30 transfer RNA genes. To investigate the evolution status of C. nudiflora, as well as Verbenaceae, we constructed a phylogenetic tree with C. nudiflora and other 11 species based on their complete chloroplast genomes. According to the phylogenetic topologies, C. nudiflora was closely related to Lancea hirstua.

| S-EPMC7687407 | biostudies-literature

The complete chloroplast genome sequence of the medicinal plant Stephania epigaea H. S. Lo, 1978 (Menispermaceae) from Yunnan, China.

Project description:Stephania epigaea H. S. Lo, 1978 is a medicinal plant commonly used in southwest China. This study characterized the first complete chloroplast (cp) genome sequence of this species. The complete cp was 157,738 bp in length, containing a large single-copy region (LSC) of 88,460 bp, a small single-copy region (SSC) of 19,778 bp, and a pair of inverted repeat regions (IRs) of 24,750 bp. It encoded 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The GC content of the complete genome was 36.7%. Phylogenetic analysis of complete cp sequences revealed that S. epigaea was clustered with S. japonica from the Menispermaceae family.

| S-EPMC9341361 | biostudies-literature

Complete plastome sequence of Tetrataenium Candicans (tribe Tordylieae, Apiaceae): a medicinal plant.

Project description:Tetrataenium candicans is a Himalayan native medicinal plant species. In this study, we report and characterize the complete plastid genome sequence of T. candicans in order to provide genomic resources helpful for promoting its systematics research and conservation. The complete chloroplast (cp) genome is a circular structure and 147,335 bp in length, composing of one large single-copy (LSC) region of 92,996 bp, one small single-copy (SSC) region of 17,473 bp, and separated by a pair of inverted repeat (IR) regions of 18,433 bp each. It encodes 129 genes, including 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The GC content is 37.5%. Phylogenetic analysis of 31 representative plastomes indicated that the T. candicans was close to Semenovia gyirongensis.

| S-EPMC7707242 | biostudies-literature

Complete plastome sequence of Mallotus peltatus (Geiseler) Mull. Arg. (Euphorbiaceae): A beverage and medicinal plant in Hainan, China.

Project description:Mallotus peltatus is a tropical plant of the Euphorbiaceae family, which could be used as a beverage and medicine in Hainan, China. Here, we report and characterize the complete plastome of M. peltatus. The complete plastome is 163,304 bp in length and contains a typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 27,112 bp, a large single-copy (LSC) region of 89,886 bp and a small single-copy (SSC) region of 18,840 bp. The plastome contains 131 genes, consisting of 78 unique protein-coding genes, 30 unique tRNA gene, four unique rRNA genes (5S rRNA, 4.5S rRNA, 23S rRNA and 16S rRNA), and eight pseudogenes. The overall A/T content in the plastome of M. peltatus is 64.02%. The complete plastome sequence of M. peltatus will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Euphorbiaceae.

| S-EPMC7748731 | biostudies-literature

The complete plastome sequence of Lilium primulinum var. burmanicum, an ornamental and medicinal plant endemic to China.

Project description:Lilium primulinum var. burmanicum (W. W. Smith) Stearn 1948 is an ornamental and medicinal plant that has an extremely limited distribution in Yunnan, China. Here, we obtained the complete plastome of L. primulinum var. burmanicum via next-generation sequencing, and conducted phylogenomic analyses with existing species from Lilium. The total length of L. primulinum var. burmanicum was 152,206 bp with a typical quadripartite structure. The whole plastome contained a pair of inverted repeats (IRa/IRb; 26,399 bp) which divided a large single-copy (LSC; 81,854 bp) and a small single-copy (SSC; 17,563 bp). The average GC content among the whole plastome sequence and the LSC, SSC, and IR regions were 37%, 34.8%, 30.6%, and 42.5%, respectively. There were 134 genes detected from the whole plastome sequence, including 87 protein-coding genes, 39 tRNAs, and 8 rRNAs. Phylogenetic analyses using maximum likelihood showed congruent results that L. primulinum var. burmanicum together with L. primulinum var. ochraceum formed a single branch. These results demonstrate a close relationship between these variation species. The newly characterized chloroplast genome presented here will provide essential data for further phylogenomic analyses of the intraspecific relationship among Lilium species and for conservation genetics research of L. primulinum var. burmanicum.

| S-EPMC9225747 | biostudies-literature

Complete plastome sequence of Limonium aureum, a medicinal and ornamental species in China.

Project description:Limonium aureum is a perennial herb of Plumbaginaceae, and draw the attention of researchers by its medicinal and ecological value. In this study, we first report the complete chloroplast genome of L. aureum with paired-end sequencing method. The results showed that the complete chloroplast genome of L. aureum is 154,661 bp in length with a typical quadripartite structure, including a large single-copy region (LSC, 84,545 bp), a single-copy region (SSC, 12, 980 bp), and a pair of inverted repeats (IRs, 28,568 bp). There are 113 annotated genes, consisting of 79 unique protein-coding genes, 4 unique ribosomal RNA genes, and 30 transfer RNA genes. Moreover, we constructed a phylogenetic tree with L. aureum and other 34 species based on their complete chloroplast genomes. And the results of the phylogenetic topologies displayed that Plumbago auriculata was closely related to L. aureum. Our results will contribute to the better study and make use of the species.

| S-EPMC7748777 | biostudies-literature

Complete plastome sequence of Flueggea virosa (Roxburgh ex Willdenow) Voigt (Phyllanthaceae): a medicinal plant.

Project description:Flueggea virosa is a tropical plant of the Phyllanthaceae family, which has high medicinal value. Here, we report and characterize the complete plastome of F. virosa. The complete plastome is 154,961 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 27,575 bp, a large single-copy (LSC) region of 83,397 bp and a small single-copy (SSC) region of 16,414 bp. The plastome contains 130 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA gene, 4 unique rRNA genes (5S rRNA, 4.5S rRNA, 23S rRNA and 16S rRNA). The overall A/T content in the plastome of F. virosa is 63.10%. The complete plastome sequence of F. virosa will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Phyllanthaceae.

| S-EPMC7782946 | biostudies-literature

The complete plastome sequence of Platanthera japonica (Orchidaceae): an endangered medicinal and ornamental plant.

Project description:Platanthera japonica (Thunb. ex A. Marray) Lindl belongs to the genus Platanthera within family Orchidaceae, is an endangered herbal species in the East Asia area. In this study, the complete plastome sequence (cpDNA) of P. japonica was determined by next-generation Illumina sequencing. The cpDNA of this herbal plant is 155,409 bp in size, with a pair of inverted repeat (IR) regions of 26,933 bp that separate a large single-copy (LSC) region of 84,049 bp and a small single-copy (SSC) region of 17,494 bp. The GC content in plastome is 36.9%, and the IR region (43.2%) is higher than that of the LSC and SSC region (34.4% and 29.7%, respectively), which is similar with other Orchidaceae plastomes. The assembled plastome encoded 133 genes, which included 38 tRNA genes, 8 rRNA genes, and 87 protein-coding genes. A total of 24 species were used to construct the phylogenetic relationships among P. japonica and other related species within Orchidaceae. The results showed that P. japonica is closely related to Platanthera chlorantha.

| S-EPMC7748498 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data