Browse
Submit Data
Databases
API
Help

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete chloroplast genome of Sphagnum subsecundum Nees from Korea.

ABSTRACT: We determined the complete chloroplast genome sequence of the peatmoss Sphagnum subsecundum Nees from Mt. Halla in Korea. The total size of the chloroplast genome was 140,136 bp, and it consisted of a large single-copy region (LSC) of 98,064 bp, a small single-copy region (SSC) of 21,388 bp, and two copies of inverted repeat (IRa and IRb) regions of 10,342 bp each. The genome encoded a set of 130 genes, comprising 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. This species formed a monophyletic clade with S. orientale and S. lenese as the result of ML phylogenetic analysis based on whole gemone sequence of 15 species including one outgroup species.

SUBMITTER: Kim W

PROVIDER: S-EPMC8635543 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome sequence of Goodyera schlechtendaliana in Korea (Orchidaceae).

Project description:Goodyera schlechtendaliana is a common orchid species in East Asia, providing a case to study phylogeographic structure of understory plants in warm temperate forests. Here, we present the complete chloroplast genome of the Korean G. schlechtendaliana. Its length is 153,801?bp and it has four subregions; 82,683?bp of large-single-copy and 18,048?bp of small-single-copy regions are separated by 26,535?bp of inverted repeat regions, including 133 genes (86 protein-coding genes, eight rRNAs, and 39 tRNAs). Phylogenetic analyses suggest that the chloroplast genomic data should be useful in future phylogeographic and phylogenetic studies of Goodyera.

| S-EPMC7706595 | biostudies-literature

The complete chloroplast genome sequence of Phedimus Kamtschaticus (Crassulaceae) in Korea.

Project description:The complete chloroplast genome sequence of Phedimus kamtschaticus, which commonly occurs in northeastern Asia was determined. The genome size was 151,652?bp, composed of one pair of inverted repeats (IRs) of 25,977?bp, which were separated by one large single-copy (LSC; 83,010?bp) and one small single-copy (SSC; 16,688?bp) region. The chloroplast genome contained 132 genes, including 88 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The overall GC content was 37.8%. Phylogenetic analysis of the complete chloroplast genome suggested that P. kamtschaticus was most closely related to Ulleung Island insular endemic P. takesimensis.

| S-EPMC7800960 | biostudies-literature

The complete chloroplast genome of Utricularia tenuicaulis Miki (Lentibulariaceae) isolated in Korea.

Project description:Utricularia tenuicaulis Miki 1935 is an aquatic carnivorous plant species found in East Asia including Korea and Japan. In this study, the chloroplast genome of U. tenuicaulis was successfully sequenced. The assembled genome (153,976 bp; GC ratio, 37.0%) contains four subregions, with the large single copy (LSC; 84,596 bp; 34.9%) and small single copy (SSC; 17,946 bp; 30.5%) regions separated by 25,718 bp of inverted repeat regions (42.7%), and includes 126 genes (81 protein-coding genes, 8 rRNAs, and 37 tRNAs). Phylogenetic analyses based on the whole-chloroplast genomes of 18 species, including 17 Lentibulariaceae species and one outgroup species, suggest a close relationship between U. tenuicaulis and Utricularia macrorhiza Leconte 1824. A comparison of genomic variation between U. tenuicaulis and U. macrorhiza confirmed the validity of the specific discrimination of U. tenuicaulis.

| S-EPMC9225771 | biostudies-literature

The complete chloroplast genome sequence of Liparis yongnoana, an endemic orchid of Korea.

Project description:The complete chloroplast genome sequence of Liparis yongnoana was determined and analyzed in this study. The chloroplast genome size is 153,165?bp in length with 36.9% GC content. It comprises a large single-copy region (LSC) of 83,690?bp, a small single copy region (SSC) of 17,661?bp, and a pair of inverted repeat regions (IRa and IRb) of 25,907?bp separated by the SSC. The genome contains 132 genes, including 86 protein-coding, eight ribosomal RNA, and 38 transfer RNA genes. Phylogenetic analysis inferred from 16 Orchidaceae chloroplast genomes suggested that L. yongnoana was closely related to L. loeselii.

| S-EPMC7706914 | biostudies-literature

The complete chloroplast genome of Euscaphis japonica (Thunb.) Kanitz (Staphyleaceae) isolated in Korea.

Project description:The complete chloroplast genome of Euscaphis japonica (Thunb.) Kanitz isolated in Korea is 160,606 bp long and has four subregions: 89,232 bp of large single-copy and 18,734 bp of small single-copy regions are separated by 26,320 bp of inverted repeat regions including 129 genes (84 CDS, 8 rRNAs, and 37 tRNAs) and three pseudogenes. There were 424 SNPs and 809 INDELs compared with the Chinese E. japonica, useful to develop markers for phylogeographic study of the species. Phylogenetic trees show that E. japonica, representing Crossosomatales, is nested within the Malvids clade, confirming previous studies.

| S-EPMC7671708 | biostudies-literature

Complete chloroplast genome of Clematis taeguensis (Ranunculaceae), an endemic species from South Korea.

Project description:The complete chloroplast (cp) genome sequence of Clematis taeguensis Y.N.Lee (Ranunculaceae) was determined to be 159,534 bp in length, consisting of large (79,326 bp) and small (18,338 bp) single-copy regions and a pair of identical inverted repeats (30,935 bp). The genome contains 92 protein-coding genes, 32 tRNA genes, 8 rRNA genes, and 1 pseudogene (infA). Phylogenetic analysis of 19 taxa inferred from the chloroplast genome showed a relationship with C. taeguensis, which is also recognized as a species endemic to the Korean Peninsula. The complete cp genome sequence of C. taeguensis reported here provides important information for future phylogenetic and evolutionary studies in Ranunculaceae.

| S-EPMC8079032 | biostudies-literature

Keteleeria cyclolepis complete chloroplast genome

Project description:Keteleeria cyclolepis complete chloroplast genome Raw sequence reads

| PRJNA723268 | ENA

The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana.

Project description:Arabidopsis thaliana (L.) Heynh. is a model organism of plant molecular biology. More than 1,700 whole genome sequences have been sequenced, but no Korean isolate genomes have been sequenced thus far despite the fact that many A. thaliana isolated in Japan and China have been sequenced. To understand the genetic background of Korean natural A. thaliana (named as 180404IB4), we presented its complete chloroplast genome, which is 154,464?bp long and has four subregions: 85,164?bp of large single copy (LSC) and 17,781?bp of small single copy (SSC) regions are separated by 26,257?bp of inverted repeat (IRs) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). Fifty single nucleotide polymorphisms (SNPs) and 14 insertion and deletions (INDELs) are identified between 180404IB4 and Col0. In addition, 101 SSRs and 42 extendedSSRs were identified on the Korean A. thaliana chloroplast genome, indicating a similar number of SSRs on the rest five chloroplast genomes with a preference of sequence variations toward the SSR region. A nucleotide diversity analysis revealed two highly variable regions on A. thaliana chloroplast genomes. Phylogenetic trees with three more chloroplast genomes of East Asian natural isolates show that Korean and Chinese natural isolates are clustered together, whereas two Japanese isolates are not clustered, suggesting the need for additional investigations of the chloroplast genomes of East Asian isolates.

| S-EPMC7492873 | 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

The complete chloroplast genome of candidate new species from Rosa rugosa in Korea (Rosaceae).

Project description:Complete chloroplast genome of candidate new species from Rosa rugosa, named as Rosa angusta, is 156,989?bp long and has four subregions: 86,227?bp of large single copy (LSC) and 18,816?bp of small single copy (SSC) regions are separated by 25,793?bp of inverted repeat (IR) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content of this chloroplast genome is 37.2% and in the LSC, SSC, and IR regions are 35.2%, 31.1%, and 42.8%, respectively. Phylogenetic trees show that R. angusta is close to R. rugosa with enough number of sequence variations.

| S-EPMC7687460 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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