Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of Melampyrum koreanum (Orobanchaceae), an endemic and hemi-parasitic herb in Korea.

ABSTRACT: Melampyrum koreanum K.-J. Kim and S.-M. Yun 2012 (Orobanchaceae) is a hemi-parasitic herb, endemic to Korea. Here, the chloroplast genome of this species is reported. It was found to be 143,865 bp long, with a large single-copy region of 83,133 bp, a small single-copy region of 10,308 bp, and a pair of inverted repeat regions of 25,212 bp each. The chloroplast genome harbors 124 genes, including 79 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. Among the identified genes, rpoA and several ndh genes were determined to be pseudogenized due to the stop codon in the middle of the gene. The phylogenetic tree of the family was reconstructed based on 20 protein-coding genes, conserved across studied taxa. As a result, Melampyrum L. 1753 species were found to form a monophyletic group in the family.

SUBMITTER: Jin DP

PROVIDER: S-EPMC8510606 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome of hemi-parasitic Pedicularis hallaisanensis (Orobanchaceae).

Project description:We determined the complete chloroplast genome of Pedicularis hallaisanensis (Orobanchaceae), a hemi-parasitic perennial herb. This genome is 143,469?bp long and features a large single-copy region (81,664?bp) and a small single-copy region (12,203?bp), separated by two inverted-repeat regions (24,801?bp each). It contains 115 genes - 70 for coding, eight for rRNA, and 37 for tRNA. However, 11 ndh genes have been pseudogenized, truncated, or deleted. Our phylogenetic tree showed that these hemi-parasitic plants are sister to holo-parasitic genera within Orobanchaceae.

| S-EPMC7800071 | biostudies-literature

The complete chloroplast genome of Artemisia hallaisanensis Nakai (Asteraceae), an endemic medicinal herb in Korea.

Project description:We determined the complete chloroplast DNA sequence of Artemisia hallaisanensis Nakai, an endemic herbal species distributed on Jeju Island, Korea. The chloroplast DNA is 151,015?bp in length and encodes 4 rRNA, 30 tRNA, and 80 protein-coding genes. Phylogenetic analysis and sequence comparison of protein-coding genes with other Artemisa chloroplast DNAs revealed that the chloroplast genome of A. hallaisanensis is closely related to that of A. capillaris. Additionally, a unique 9?bp deletion in ycf1 gene is specific to A. hallaisanensis.

| S-EPMC7800851 | biostudies-literature

The complete chloroplast genome sequence of Ostericum koreanum (Apiaceae).

Project description:Ostericum koreanum Kitagawa is an important herbal medicine, whose taxonomic status has been changed to Angelica reflexa as a new species. This study generated the complete chloroplast genome sequence of O. koreanum, and reconsidered its molecular taxonomic status in Angelica by comparing it with related species. The length of the complete chloroplast genome was 147,282?bp, and there were four structures that included the large single copy region (93,185?bp), the small single copy region (17,663?bp) and the duplicated inverted regions (18,217?bp of each). Based on its phylogenetic trees, O. koreanum was grouped by high bootstrap value with the Angelica species. This result proved that O. koreanum is included in Angelica. Therefore, this chloroplast genome data generated for the first time a valuable genetic resource for the discrimination of herbal materials, phylogeny, and evolution.

| S-EPMC7800663 | biostudies-literature

The complete chloroplast genome sequence of Taxillus yadoriki (Loranthaceae): a hemi-parasitic evergreen shrub in East Asia.

Project description:Taxillus yadoriki (Loranthaceae) is a hemiparasitic evergreen shrub distributed in Korea and Japan. We report the complete chloroplast genome of T. yadoriki to provide insight into the phylogenetic relationship of Loranthaceae. This genome is 122,192 bp long, with two IR regions (22,756 bp each) that separate a large single-copy (LSC) region (70,628 bp) and a small single-copy (SSC) region (6052 bp). It contains 109 genes that encode 68 proteins, 8 rRNAs, and 33 tRNAs. All of ndh genes have been lost and the SSC region consists of only four genes similar to other Taxillus species. In ML phylogenetic, monophyly of Taxillus was strongly supported with high bootstrap value and formed a sister group with Scurrula.

| S-EPMC7781972 | 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 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

Complete chloroplast genome sequence of Stauntonia hexaphylla (Ranunculales: Lardizabalaceae), a species endemic to Korea.

Project description:The complete chloroplast (cp) genome of Stauntonia hexaphylla, a monotypic genus native to Korea, was determined. The whole cp genome is 158,390 bp in size, containing a large single-copy (LSC) region of 87,115 bp and a small single-copy region (SSC) of 18,928 bp, separated by a pair of inverted repeats (IRs) of 26,174 bp. The cp genome encodes 117 genes, including 79 protein-coding, 38 tRNA-coding, and 8 rRNA-coding genes. The overall GC content is 37.8%. A phylogenetic analysis demonstrated a close relationship between S. hexaphylla and S. obovatifoliola subsp. urophylla. The cp genome will provide new insight into the evolution of Lardizabalaceae.

| S-EPMC7971286 | biostudies-literature

The complete nucleotide sequence of chloroplast genome of Gentiana apiata (Gentianaceae), an endemic medicinal herb in China.

Project description:Gentiana apiata N. E. Brown (Gentianaceae) is a perennial herb plant and only grows in Qinba Mountains in China. Here, we first characterized the complete nucleotide sequence of chloroplast (cp) genome of G. apiata via Illumina next generation sequencing platform. The complete chloroplast genome of G. apiata was 144,274 bp in length, comprising of a large single copy (LSC) region of 77,353 bp, a small single copy (SSC) region of 17,009 bp, and two inverted repeat regions (IRs) of 24,956 bp. The cp genome contains 127 genes, including 82 protein-coding genes, 35 tRNA, eight rRNA genes, and two pseudogenes. Phylogenetic analysis based on 18 cp genome sequences showed that G. apiata closely related to congeneric species.

| S-EPMC7706864 | biostudies-literature

The complete chloroplast genome of Polygonatum odoratum (Liliaceae), an endemic medicinal herb.

Project description:In this study, we sequenced the complete chloroplast genome of Polygonatum odoratum with Illumina sequencing technology. The complete chloroplast genome length is 156,082 bp shows a typical tetrad structure, which manifests as one large and one small single copy (LSC and SSC) regions of 85,009 and 18,513 bp, isolated by two inverted repeat regions (IRs) of 26,280 bp. This study annotated altogether 131 unique genes, consisting of 86 protein-encoding genes, 8 rRNA, and 38 tRNA. According to the maximum likelihood phylogenetic tree based on eight complete chloroplast genomes, P. odoratum shows a close association with additional Maianthemum genus. The chloroplast genome-wide for P. odoratum would help to conserve the precious natural populations.

| S-EPMC7671610 | biostudies-literature

The complete chloroplast genome of Polygonatum odoratum (Liliaceae), an endemic medicinal herb.

Project description:In this study, we sequenced the complete chloroplast genome of Polygonatum odoratum with Illumina sequencing technology. The complete chloroplast genome length is 156,082bp, shows a typical tetrad structure, which manifests as one large and one small single copy (LSC and SSC) regions of 85,009 and 18,513bp, isolated by two inverted repeat regions (IRs) of 26,280bp. This study annotated altogether 131 unique genes, consisting of 86 protein-encoding genes, 8 rRNA and 38tRNA. According to the maximum likelihood phylogenetic tree based on 8 complete chloroplast genomes, P. odoratum shows close association with additional Maianthemum genus. The chloroplast genome-wide for P. odoratum would help to conserving the precious natural populations.

| S-EPMC7655049 | 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