Browse
Submit Data
Databases
API
Help

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of Elsholtzia densa, a herb with volatile aroma component.

ABSTRACT: The complete chloroplast genome sequence of Elsholtzia densa was analysed. The results indicated that the size of the chloroplast genome was 149,095 bp in length with a large single-copy region (LSC) of 81,497 bp, a small single-copy region (SSC) of 17,364 bp, and a pair of inverted repeat (IR) regions of 25,117bp. The overall GC content of the cpDNA genome was 37.86%, while the corresponding values of the LSC, SSC, and IR regions were 35.96%, 31.92%, and 43.16%, respectively. A total of 132 functional genes were identified, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The maximum likelihood phylogenetic tree suggested that E. densa was closely related to the species in the family Labiatae.

SUBMITTER: Fu G

PROVIDER: S-EPMC7748739 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome sequence of Vincetoxicum mongolicum (Apocynaceae), a perennial medicinal herb.

Project description:Vincetoxicum mongolicum Maxim. (1876), is a perennial medicinal herb, widely distributed in the Loess Plateau of China. Here, we sequenced, assembled, and annotated the complete chloroplast (cp) genome of V. mongolicum, and compared the highly variable gene regions and phylogenetic positions between V. mongolicum and other related species. Results showed that the complete cp genome of V. mongolicum was 160,157 bp in length, containing a large single copy (LSC) region of 91,263 bp, a pair of inverted repeats (IR) region of 23,892 bp, and a small single copy (SSC) region of 21,110 bp. The GC content accounts for 37.8%, and we annotated 131 single genes, which include 86 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. By comparing and analyzing the variable region of the cp gene of V. mongolicum and other Vincetoxicum, we found that the variable sequences of rpoC1-rpoB, ycf4-cemA, ndhF, ndhF-rpl32, and rpl32-ccsA fragments were highly significant, which could be targeted as the DNA barcodes for evidence of V. mongolicum and its relatives in Apocynaceae. Maximum-likelihood (ML) phylogenetic tree analysis elucidated that V. mongolicum was sister to V. pycnostelma with strong support. Our results provide useful information for future phylogenetic studies and plastid super-barcodes of the family Apocynaceae.

| S-EPMC10241319 | biostudies-literature

The complete chloroplast genome of copper-tolerance plant Elsholtzia splendens.

Project description:Elsholtzia splendens is a copper-tolerance plant colonized in copper mines in southern China. In this study, we sequenced and de novo assembled the complete chloroplast genome of E. splendens. The complete chloroplast genome is 150,761 bp (37.8% of GC) in length and contains 87 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis revealed that among the 11 Lamiaceae species, Perilla citriodor is the closest relative of E. splendens. The complete chloroplast genome of E. splendens provides a valuable resource for comparative and evolutionary analysis among Lamiaceae species and may be helpful in understanding the molecular mechanism of copper tolerance in E. splendens.

| S-EPMC7706683 | biostudies-literature

The complete chloroplast genome sequence of a medicinal herb Liriope Platyphylla (Asparagaceae).

Project description:Liriope platyphylla is herbaceous perennial plant belonging to the Asparagaceae family and widely used both as ornamental plant and herbal medicine. The complete chloroplast genome of L. platyphylla was 156,754 bp in length, which was composed of four distinct parts; a large single copy (LSC) of 85,118 bp, a small single copy (SSC) of 18,680 bp, and a pair of inverted repeat regions (IRa and IRb) of 26,478 bp. A total of 130 genes including 83 protein-coding genes, 39 tRNA genes and 8 rRNA genes were identified. The phylogenetic tree showed that L. platyphylla has a close relationship with other Nolinoideae plants, especially with Maianthemum dilatatum and Nolina atopocarpa.

| S-EPMC7720963 | biostudies-literature

The complete chloroplast genome sequence of herb Nardostachys jatamans (family: Valerianaceae) in China.

Project description:Nardostachys jatamans is an endemic herb in China, distributes mainly in Southeast Gansu, South Qinghai and West Sichuan of Qinghai-Tibet Plateau. In this study, the complete chloroplast genome (a typical quadripartite structure) sequence of N. jatamans was reported. The length of the DNA molecule was 155,268 bp with a large single-copy region (LSC: 87,263 bp), small single-copy region (SSC: 17,327 bp) and inverted repeats (IRa and IRb: 25,339 bp). The overall GC content was 38.56%. It has a total of 129 genes, containing 83 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The phylogenetic analysis has shown that N. jatamans is sister to Valeriana offcinalis. The chloroplast genome provides the basis for development and utilization of N. jatamans in future.

| S-EPMC7872520 | 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 sequence of Pueraria lobata (Willd.) Ohwi (Fabaceae): a traditional Chinese medicinal herb.

Project description:Pueraria lobata is a traditional Chinese herb which has been used medically since ancient times. In this study, we sequenced the complete chloroplast genome of P. lobata based on next-generation sequencing and used the data to assess genomic resources. The chloroplast genome of P. lobata is 153,411 bp in length consisting of large and small single-copy regions of length 84,142 and 17,989 bp, separated by two IR regions of 25,640 bp. The overall GC content was 35.4%. De novo assembly and annotation showed the presence of 112 unique genes with 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. A maximum-likelihood phylogenomic analysis showed that Pueraria was sister to Pediomelum + Glycine.

| S-EPMC7720969 | biostudies-literature

The complete chloroplast genome of Lycoris aurea (L'Her.) Herb.

Project description:Lycoris aurea (L'Hér.) Herb is a herb widely growing in Chinese southen region, such as Guangxi, Guangdong, Fujian , Yunnan and Sichuan provinces. It not only has medicinal value, but also can be used as ornamental garden plant. The circular chloroplast genome of L. aurea was 158,690 bp in size, consisting of a pair of inverted repeat (IR) regions (26,782 bp) separated by a large single-copy (LSC) region (85,467 bp) and a small single-copy (SSC) region (18,541 bp) regions. And, it contained 127 genes, including 38 tRNA genes, 8 rRNA genes and 81 mRNA genes. The overall GC content of L. aurea is 37.73%. Phylogenetic analysis strongly supported that L. aurea and its congeneric species, L. radiata and L. squamigera, as sister group with 100% bootstrap value.

| S-EPMC7748574 | biostudies-literature

The complete chloroplast genome of Elsholtzia byeonsanensis M. Kim, an endemic species in Korea.

Project description:Elsholtzia byeonsanensis M. Kim. is an endemic species in Korea, and its leaves are distinguished from other taxa of Elsholtzia by the leathery texture. In this study, we first presented the complete chloroplast genome of E. byeonsanensis. The complete chloroplast genome was 150,628 bp, including a large-single copy region (LSC) of 82,738 bp, a small-single copy region (SSC) of 17,492 bp, and a pair of inverted repeat regions (IRs) of 25,199 bp. It contained 112 genes including 78 protein-coding genes, four rRNA, and 30 tRNA genes. The phylogenetic analysis indicated that E. byeonsanensis and E. splendens formed a monophyletic clade and showed a close relationship. The complete chloroplast genome of E. byeonsanensis will provide useful information for phylogenetic and evolutionary studies.

| S-EPMC9754010 | biostudies-literature

The complete nucleotide sequence of chloroplast genome of Euphorbia kansui (Euphorbiaceae), an endemic herb in China.

Project description:Euphorbia kansui T.N. Liou ex S.B. Ho (Euphorbiaceae) is a perennial herb plant endemic to China. This species has important economic and medicinal values. In this study, we first characterized the complete nucleotide sequence of chloroplast (cp) genome of E. kansui using the Illumina Hiseq platform. The cp genome was 161,061?bp in length, comprising of a large single copy (LSC) region of 91,288?bp, a small single copy (SSC) region of 17,086?bp, and two inverted repeat regions of 26,343?bp each. The cp genome contains 130 genes, including 86 protein-coding genes, 8 ribosomal RNAs (rRNAs), and 36 transfer RNAs (tRNAs). The phylogenetic analysis indicated that E. kansui was placed as a sister to the congeneric Euphorbia esula.

| S-EPMC7800493 | biostudies-literature

The complete chloroplast genome of Hippeastrum rutilum (Ker-Gawl.) Herb.

Project description:Hippeastrum rutilum (Ker-Gawl.) Herb. is a high-end ornamental flower in the family Amaryllidaceae. In this study, the complete chloroplast genome sequence of H. rutilum (Ker-Gawl.) Herb. was determined from Illumina pair-end sequencing data. The sequencing results indicated the complete chloroplast genome sequence of H. rutilum (Ker-Gawl.) Herb. 162,696 base pairs (bp) in length, including one large single-copy region (LSC, 86,933 bp), one small single-copy region (SSC, 5418 bp), and a pair of inverted repeat regions (IRs) of 34,932 bp. Besides, the complete chloroplast genome contained 128 genes, including 82 protein-coding genes, 38 tRNA, and 8 rRNA. The phylogenetic analysis suggested that H. rutilum (Ker-Gawl.) Herb. is closely related to H. rutilum. The complete chloroplast genome sequencing results will provide a reference for the further investigation and research of H. rutilum (Ker-Gawl.) Herb.

| S-EPMC7995863 | 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