Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete chloroplast genome of a medicinal species Euodia ruticarpa in China (Rutaceae).

ABSTRACT: Euodia ruticarpa is a medicinal plant recorded in in Chinese Pharmacopeia. Here we report on the complete chloroplast genome sequence of Euodia ruticarpa. The chloroplast genome is 158,762 bp in size and includes two inverted repeat regions of 54,230 bp, which is separated by a large single-copy region of 86,267 bp and a small single copy region of 18,265 bp. A total of 131 genes were predicted, including 37 tRNA, 8 rRNA, and 86 protein-coding genes. Phylogenetic analysis placed Euodia ruticarpa under the family Rutaceae.

SUBMITTER: Liu H

PROVIDER: S-EPMC7781893 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome of Phellodendron chinense (Rutaceae), an Endangered medicinal plant in southern China.

Project description:Phellodendron chinense is an Endangered medicinal plant in southern China. In this study, the complete chloroplast genome sequence of P.chinense was characterized by de novo assembly. The length of the whole chloroplast genome was 158,537 bp, containing a large single copy region (LSC) of 86,250 bp and a small single copy region (SSC) of 18,287 bp, which were separated by a pair of 27,000 bp inverted repeat regions (IRs). The sequence contains 114 unique genes, including 30 tRNA, 4 rRNA, and 80 protein-coding genes. The overall GC content of the chloroplast genome is 38.4% and those in the LSC, SSC, and IR regions are 36.6, 33.2, and 42.9%, respectively. The phylogenetic analysis based on reported chloroplast sequences of Rutaceae showed that P. chinense is sister to P. amurense, consisting a monophyletic group, and that Phellodendron is closely related to Zanthoxylum.

| S-EPMC7703704 | biostudies-literature

The complete chloroplast genome of Melicope pteleifolia (Rutaceae), a traditional medicinal plant in Southeast China.

Project description:Meclicope pteleifolia is a traditional medicinal herb and edible plant in Southeast China. Here, we report the complete chloroplast genome of M. pteleifolia. The chloroplast genome is 159,012 bp in length with 38.33% GC content, containing a small single-copy (SSC) region (18,609 bp), a large single-copy (LSC) region (851 bp), and a pair of inverted repeats (IRs: 27,640 bp each). A total of 131 genes were predicted, including 84 protein-coding genes, 8 ribosomal RNA genes, 37 tRNA genes, and 2 pseudogenes. Phylogenetic analysis based on chloroplast genomes of 17 plant species shows that M. pteleifolia is closest to Zanthoxylum and Casimiroa. These complete chloroplast genomes can be subsequently used for researches of Rutaceae.

| S-EPMC7819110 | biostudies-literature

Complete chloroplast genome sequence of Zanthoxylum nitidum (Rutaceae), an important medicinal shrub.

Project description:Zanthoxylum nitidum (Rutaceae) is a scandent prickly shrub and widely distributed in South China. It's well known for its valuable medicinal values due to contains some important secondary metabolites. Here, we first report and characterize its complete chloroplast genome based on Illumina paired-end sequencing data. The complete plastid genome was 157,253 bp, which contained inverted repeats (IR) of 27,618 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 84,382 bp and 17,635 bp, respectively. The cpDNA contains 132 genes, comprising 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes. The overall GC content of the plastome is 38.5%. The phylogenetic analysis of 20 selected chloroplast genomes demonstrated that Z. nitidum is closely related to the congeneric Z. bungeanum.

| S-EPMC7707648 | biostudies-literature

Characterization of the complete chloroplast genome of the medicinal plant Orixa japonica (Rutaceae) in Zhejiang Province and its phylogenetic analysis within family Rutaceae.

Project description:Orixa japonica Thunb. is an important medicinal plant belonging to the family Rutaceae. In this study, we determined the the complete chloroplast (cp) genome of O. japonica, which was 158,525 bp in length containing one large single copy region (85,965 bp), one small single copy region (18,552 bp), and a pair of inverted repeat regions (27,004 bp each). A total of 134 genes were annotated in the cp genome, including 88 protein coding genes, 37 tRNA genes, eight rRNA genes, and one pseudo gene ycf1. According to the phylogenetic analysis, O. japonica clustered together with Casimiroa edulis with high bootstrap value, indicating a close genetic relationship with subfamily Amyridoideae.

| S-EPMC8158279 | biostudies-literature

The complete chloroplast genome of Zanthoxylum stenophyllum Hemsl. (Rutaceae), a traditional Chinese medicinal plant.

Project description:Zanthoxylum stenophyllum Hemsl., a type species for the genus Zanthoxylum (Rutaceae), is a traditional medicinal plant. We studied the complete chloroplast genome of this species using BGISEQ-500 platform. The chloroplast genome was 158,314 bp in size with a GC content of 38.45%. The genome contained two short inverted repeat (IRa and IRb) regions of 27,052 bp, a large single-copy region (LSC, 86,029 bp) and a small single-copy region (SSC, 18,181 bp). The annotated complete chloroplast genome contains 133 distinct genes, including 88 protein-coding genes, 37 transfer RNAs (tRNAs), and 8 ribosomal RNAs (rRNAs). Phylogenetic analysis indicated that Z. stenophyllum is clustered with Z. schiniflium and Z. pinnatum in the same branch with 100% bootstrap support. This complete chloroplast genome provides valuable genomic information for the molecular phylogeny and sustainable utilization of Zanthoxylum.

| S-EPMC9487917 | biostudies-literature

Complete chloroplast genome sequence of Murraya paniculata (Rutaceae): a widely used folk medicinal herb.

Project description:Murraya paniculate, is traditionally used for management of gut, air way and cardiovascular disorders. In this study, we sequenced the complete chloroplast genome of M. paniculata based on next-generation sequencing and used the data to assess genomic resources. The chloroplast genome of M. paniculata is 160,280 bp in length consisting of large and small single-copy regions of length 87,605 and 18,609 bp, separated by two IR regions of 27,033 bp. The overall GC content was 38.61%. De novo assembly and annotation showed the presence of unique genes with 85 protein-coding genes, 29 tRNA genes, and eight rRNA genes. A maximum-likelihood phylogenomic analysis showed that M. paniculata was closely related to M. caloxylon.

| S-EPMC7671698 | biostudies-literature

Complete chloroplast genome of a medicinal species Polygonatum kingianum in China (Asparagaceae, Asparagales).

Project description:Polygonatum kingianum is a medicinal and food plant distributed in most of countries throughout the temperate Northern Hemisphere. Here we report on the complete chloroplast (cp) genome sequence of P. kingianum. The cp genome is 155,399 bp in size and includes two inverted repeat regions of 52,7411 bp, which is separated by a large single-copy region of 84,234 bp and a small single copy region of 18,424 bp. A total of 130 genes were predicted, including 38 tRNA, 8 rRNA, and 84 protein-coding genes. Phylogenetic analysis placed P. kingianum under the subfamily Nolinoideae of the family Asparagaceae.

| S-EPMC7748866 | biostudies-literature

Characterization of the complete chloroplast genome of Zanthoxylum esquirolii Levl. (Rutaceae).

Project description:Zanthoxylum esquirolii Léveillé 1914 is mainly distributed in southwest China, and its wild germplasm resources are scarce and in urgent need of conservation. In this study, we report the first complete chloroplast genome sequence of Z. esquirolii using next-generation sequencing. The circular genome is 158,390 bp in length, containing two inverted repeat (IR) regions of 27,622 bp separated by a large single copy (LSC) region of 85,580 bp and a small single copy (SSC) region of 17,566 bp. The chloroplast genome contains a total of 132 genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the chloroplast genome was 38.46%, with corresponding values in the LSC, SSC, and IR regions of 36.84%, 33.55%, and 42.51%, respectively. The phylogenetic tree revealed that Z. esquirolii Levl. formed a clade with Z. piperitum DC., Z. bungeanum Maxim., Z. simulans Hance and Z. sp. NH-2018, and had a strongly supported sister relationship with Z. bungeanum.

| S-EPMC9518235 | biostudies-literature

The third complete chloroplast genome of Melicope pteleifolia (Rutaceae): a widely used folk medicinal herb.

Project description:Melicope pteleifolia commonly known as thin evodia, is an herb used to therapy eczema, dermatitis, and other ailments in traditional Chinese medicine. Here, we reported the third complete chloroplast genome of M. pteleifolia based on next-generation sequencing. The third chloroplast genome of M. pteleifolia is 158,933 bp in length consisting of large and small single-copy regions of length 85,020 and 18,607 bp, separated by two IR regions of 27,683 bp. The overall GC content was 38.30%. De novo assembly and annotation showed the chloroplast genome of M. pteleifolia encodes 134 genes, including 89 protein-coding genes, 37 tRNA genes, and eight rRNA genes. A huge intraspecies variation was found with 248 SNPs and 97 INDELs among three assemblies of M. pteleifolia. Phylogenetic tree indicated that three assemblies of M. pteleifolia form a clade, sister to the genus Phellodendron and Casimiroa.

| S-EPMC7995855 | biostudies-literature

Complete chloroplast genome sequence of Swertia mileensis (Gentianaceae): a medicinal species endemic to China.

Project description:Swertia mileensis is an important medicinal plant endemic to South-east Yunnan, China, which has been widely used to treat icteric hepatitis. The complete chloroplast genome sequence of S. mileensis is presented in this study, the total size is 153,015 bp in length with a typical quadripartite structure including a pair of inverted repeat (IRs, 25,786 bp) regions separated by a large single copy (LSC, 83,048 bp) region and a small single copy (SSC, 18,395 bp) region. The overall GC content of it is 38.2%. The cp genome has 134 annotated genes, including 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Among these genes, nine genes have one intron and two genes contain two introns. The phylogenetic tree based on 16 complete plastomes of support close relationships among two species of Swertia with 100% bootstrap value.

| S-EPMC7707743 | 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