Browse
Submit Data
Databases
API
Help

Dataset Information

28 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete plastid genome sequence of Dracaena fragrans (L.) Ker Gawl. (Asparagaceae).

ABSTRACT: Dracaena fragrans is a shrub native to tropical Africa classified in the family Asparagaceae. It is a common horticultural plant grown as a hedge as well as an ornamental house plant for its green leaves, attractive shape and fragrant flowers. The species has been used for many medicinal purposes including inducing labor, treating malnutrition and fighting illness. Here, we investigated the complete plastid genome of D. fragrans using Illumina 150 bp next-generation sequencing technologies. De novo assembly and annotation showed that the chloroplast genome is a typical quadripartite structure with 37.5% GC content. A pair of inverted repeats (IRs, 26,507 bp each) were separated by one large single-copy region (LSC, 83,703 bp) and one small single-copy region (SSC, 18,466 bp). The chloroplast genome is 155,183 bp in length and contained 131 genes of which 12 are intron-containing genes, comprising 85 protein-coding, 38 tRNA, and 8 rRNA genes. Phylogenetic analysis of D. fragrans and 11 plastomes obtained from GenBank shows that it is closely related to D. elliptica.

SUBMITTER: Jiang H

PROVIDER: S-EPMC7928031 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome sequence of the Canna edulis Ker Gawl. (Cannaceae).

Project description:Canna edulis Ker Gawl. is an essential traditional tuber crop used for fresh consumption and to isolate starch in some tropical and semitropical regions. The complete chloroplast genome sequence of C. edulis has been determined in this study. The total genome size is 164,650 bp in length and contains a pair of inverted repeats (IRs) of 27,278 bp, which were separated by large single-copy (LSC) and small single-copy (SSC) of 91,421 bp and 18,673 bp, respectively. A total of 131 genes were predicted including 86 protein-coding genes, 8 rRNA genes and 37 tRNA genes. Further, maximum-likelihood phylogenetic analysis revealed that C. edulis belongs to Cannaceae in Zingiberales. The chloroplast genome of C. edulis is first complete genome sequence in Cannaceae and would play a significant role in the development of molecular markers in plant phylogenetic and population genetic studies.

| S-EPMC7782134 | 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

The complete chloroplast genome of a rare species in Korea, Lilium Dauricum Ker Gawl.

Project description:Lilium dauricum Ker Gawler is a wild lily species that belongs to section Sinomartagon and is one of the ancestors of the Asiatic hybrid lilies. Unique traits such as disease resistance and early flowering make L. dauricum a desirable resource for interspecific hybridization. However, in Korea, the natural resources of L. dauricum are being exhausted by excessive exploitation and require urgent conservation. In this study, the complete chloroplast genome of L. dauricum was generated using Illumina paired-end sequencing technology, and its structure was compared with that of other Lilium species. The chloroplast genome was 152,063 bp long, with a typical quadripartite structure including a pair of inverted repeat regions (26,492 bp) separated by a large (81,485 bp) and small (17,584 bp) single-copy (SC) region. The genome encodes 131 different genes, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. A phylogenetic analysis strongly supported the relationship of L. dauricum with other members of Sinomartagon and Martagon lilies.

| S-EPMC7707306 | biostudies-literature

Complete plastome sequence of Dracaena cambodiana (Asparagaceae): a species considered "Vulnerable" in Southeast Asia.

Project description:Dracaena cambodiana (Asparagaceae) is a treelike plant ranging from 3 to 10 m tall. It grows in low-elevation forests (0-300 m) having dry and sandy soils. It is distributed in Southern Hainan Island in China and other Southeast Asian countries (e.g. Cambodia, Laos, Thailand and Vietnam). The dried resin can be used medicinally as a substitute for that of Dracaena cochinchinensis. It has been ranked as a Vulnerable (VU) species in China. Here we report and characterize the complete plastid genome sequence of D. cambodiana. The complete plastome is 156,697?bp in length. It contains the typical structure and gene content of angiosperm plastomes, including two Inverted Repeat (IR) regions of 26,526?bp, a Large Single-Copy (LSC) region of 84,988?bp and a Small Single-Copy (SSC) region of 18,657?bp. The plastome contains 113 genes, consisting of 76 unique protein-coding genes, 30 unique tRNA genes, four unique rRNA genes and three pseudogenes (i.e. matK, infA, ndhF). The overall A/T content in the plastome of D. cambodiana is 62.4%. We performed phylogenetic analyses using the entire plastome, including spacers, introns, etc., and we determined that D. cambodiana and Maianthemum bicolor were closely related. The complete plastome sequence of D. cambodiana will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Asparagales.

| S-EPMC7800030 | biostudies-literature

Dracaena fragrans

Project description:Dracaena fragrans overview

| PRJNA717869 | ENA

Dracaena fragrans

Project description:Dracaena fragrans Raw sequence reads

| PRJNA673642 | ENA

The complete chloroplast genome sequence of Fagraea fragrans.

Project description:The first complete chloroplast genome (cpDNA) sequence of Fagraea fragrans was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 154,416 bp in length, contains a large single copy region (LSC) of 84,405 bp and a small single copy region (SSC) of 18,285 bp, which were separated by a pair of inverted repeats (IR) regions of 25,863 bp. The genome contains 130 genes, including 85 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 38.0%, and the corresponding values of the LSC, SSC, and IR regions are 36.0%, 31.8%, and 43.4%, respectively. Further phylogenomic analysis showed that F. fragrans in a unique clade in Gentianaceae family.

| S-EPMC7748836 | biostudies-literature

The complete chloroplast genome sequence of Eriobotrya fragrans.

Project description:Eriobotrya fragrans Champion ex Bentham is a potential medicinal plant of the genus Eriobotrya Lindl in the family Rosaceae. To better determine its phylogenetic location with respect to the other Rosaceae species, the complete chloroplast genome of E. fragrans was sequenced. The whole E. fragrans chloroplast genome is 159,286 bp in length, consisting of a pair of inverted repeat (IR) regions of 26,343 bp, one large single-copy (LSC) region of 87,301 bp, and one small single-copy (SSC) region of 19,299 bp. The overall GC content of the whole chloroplast genome is 36.7%. Further, phylogenetic analysis using maximum likelihood with TVM + F+R2 model strongly supports the relationship: sisterhood of E. fragrans and E. japonica, followed by three species of Pyrus L.

| S-EPMC7707343 | biostudies-literature

The complete chloroplast genome sequence of Hosta capitata (Koidz.) Nakai (Asparagaceae).

Project description:Hosta capitata (Koidz.) Nakai is an herbaceous perennial plant belonging to the Asparagaceae family and has become a popular ornamental plant. In this study, the chloroplast genome sequence of H. capitata was completed by de novo assembly with whole genome sequence data. The chloroplast genome of H. capitata is 156,416 bp in length, which is composed of a large single-copy (LSC) of 84,788 bp, a small single-copy (SSC) of 18,206 bp, and a pair of inverted repeat regions (IRa and IRb) of 26,711 bp, as four distinct parts. In total, 114 genes were identified including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis revealed that H. capitata has a close relationship with other Hosta species, H. minor and H. ventricosa, but is farther than the distance between them.

| S-EPMC7799732 | biostudies-literature

The complete chloroplast genome sequence of Heteropolygonatum ginfushanicum (Asparagaceae) and phylogenetic analysis.

Project description:Heteropolygonatum ginfushanicum is an endemic epiphytic herb in China. The complete chloroplast (cp) genome of H. ginfushanicum is reported in this study. The total length of the cp genome is 155,508 bp with a typical quadripartite structure consisting of a large single copy region (LSC) of 84,552 bp and a small single copy region (SSC) of 18,528 bp, separated by a pair of 26,214 bp inverted repeats (IRs). It encodes a total of 113 unique genes, including 79 protein-coding, 30 tRNA, and four rRNA genes. Phylogenetic analysis indicated that H. ginfushanicum is sister to Heteropolygonatum marmoratum within subfamily Nolinoideae.

| S-EPMC8168753 | 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