Browse
Submit Data
Databases
API
Help

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of Rehmannia glutinosa (Gaertn.) DC. Wild. (Rehmannia).

ABSTRACT: In this study, we constructed and annotated a complete circular chloroplast genome of wild R. glutinosa. The chloroplast genome of wild R. glutinosa is 153,678 bp in length, including two inverted repeat (IR) regions of 25,759 bp, separated by a large single copy (LSC) region of 84,544 bp and a small single copy (SSC) region of 17,616 bp. The genome contains 149 genes, including 104 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Neighbor-joining method phylogenomic analysis showed that wild R. glutinosa formed a monophyletic group, and was sister to other groups of R. glutinosa.

SUBMITTER: Yang H

PROVIDER: S-EPMC7954418 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Complete Genome Sequence of Rehmannia Mosaic Virus Infecting Rehmannia glutinosa in Japan.

Project description:The complete genome sequence of isolate Jiou of rehmannia mosaic virus (ReMV) infecting Rehmannia glutinosa in Japan was obtained via Sanger sequencing. Isolate Jiou shared high nucleotide sequence identity (>94%) with other known ReMV isolates.

| S-EPMC8407759 | biostudies-literature

Complete Genome Sequence of Rehmannia Mosaic Virus Infecting Rehmannia glutinosa in South Korea.

Project description:The complete genome sequence of a South Korean isolate of Rehmannia mosaic virus (ReMV) infecting Rehmannia glutinosa was determined through next-generation sequencing and Sanger sequencing. To our knowledge, this is the first report of a natural infection of R. glutinosa by ReMV in South Korea.

| S-EPMC4732330 | biostudies-literature

The complete chloroplast genome of Chinese medicine cultivar species of Rehmannia glutinosa (Orobanchaceae).

Project description:The cultivar of Rehmannia glutinosa (Orobanchaceae) is one of the four famous 'Huai' medicine cultivar species endemic to Henan Province in central China. In this study, we report the complete chloroplast (cp) genome of R. glutinosa cultivar Wen 85-5. The cp genome of R. glutinosa cultivar Wen 85-5 was 155,499 bp in length and contained a pair of inverted repeat regions (IR, 25,748 bp) separated by a small single copy (SSC, 17,600 bp) and a large single copy (LSC, 84,403 bp) region. Chloroplast genome sequences of two cultivar of R. glutinosa (Wen 85-5 and Jiwang 1) are identical to each other. The sequence of cp genome of R. glutinosa cultivar Wen 85-5 was 99.70% similar to the wild population of R. glutinosa. Some distinctive insert and deletion in R. glutinosa cultivar Wen 85-5 by comparison with wild population were reported. The maximum-likelihood phylogenetic analysis revealed that R. glutinosa cultivar Wen 85-5.was sister to the R. glutinosa cultivar Jiwang 1 (BS = 100%), and further clustering with R. glutinosa (BS = 100%). This result will be helpful for the conservation and breeding programs of the cultivar of R. glutinosa.

| S-EPMC7872587 | biostudies-literature

The Complete Chloroplast Genome Sequences of Six Rehmannia Species.

Project description:Rehmannia is a non-parasitic genus in Orobanchaceae including six species mainly distributed in central and north China. Its phylogenetic position and infrageneric relationships remain uncertain due to potential hybridization and polyploidization. In this study, we sequenced and compared the complete chloroplast genomes of six Rehmannia species using Illumina sequencing technology to elucidate the interspecific variations. Rehmannia plastomes exhibited typical quadripartite and circular structures with good synteny of gene order. The complete genomes ranged from 153,622 bp to 154,055 bp in length, including 133 genes encoding 88 proteins, 37 tRNAs, and 8 rRNAs. Three genes (rpoA, rpoC2, accD) have potentially experienced positive selection. Plastome size variation of Rehmannia was mainly ascribed to the expansion and contraction of the border regions between the inverted repeat (IR) region and the single-copy (SC) regions. Despite of the conserved structure in Rehmannia plastomes, sequence variations provide useful phylogenetic information. Phylogenetic trees of 23 Lamiales species reconstructed with the complete plastomes suggested that Rehmannia was monophyletic and sister to the clade of Lindenbergia and the parasitic taxa in Orobanchaceae. The interspecific relationships within Rehmannia were completely different with the previous studies. In future, population phylogenomic works based on plastomes are urgently needed to clarify the evolutionary history of Rehmannia.

| S-EPMC5368707 | biostudies-literature

The complete chloroplast genome sequence of Bupleurum chinense DC. (Apiaceae).

Project description:Bupleurum chinense DC. is a traditional medicinal herb species widely distributed in most provinces of China. In this study, we constructed and annotated a complete circular chloroplast (cp) genome of B. chinense. The cp genome of B. chinense is 155,545?bp in length, including two inverted repeat (IR) regions of 26,305?bp, separated by a large single-copy (LSC) region of 85,430?bp and a small single-copy (SSC) region of 17,505?bp. The GC content of whole cp genome is 37.68%. The genome contains 113 different genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. A maximum-likelihood phylogenomic analysis showed that Bupleurum formed a monophyletic group, and was sister to other groups of Apiaceae.

| S-EPMC7707502 | biostudies-literature

Complete sequence of wild Physalis philadelphica chloroplast genome.

Project description:Physalis philadelphica Lam. has horticultural importance because of its edible fruits. Cultivated and wild populations grow in Mexico. In this study, the complete plastome nucleotide sequence of wild plants was generated using the IonTorrent PGM sequencing technology. The plastome size was 156,804 bp and displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat regions (25,595 bp) separated by a large single copy region (87,131 bp) and a small single copy region (18,483 bp). The chloroplast genome included 80 protein-coding genes, four rRNAs, and 31 tRNAs. The phylogenetic analysis based on 19 Solanaceae chloroplast genomes recovered a clade with all Physalis species. This work revealed the importance of the plastome sequence to solve infrageneric phylogenetic relationships.

| S-EPMC7707378 | biostudies-literature

The complete chloroplast genome sequence of Tartary Buckwheat Cultivar Miqiao 1(Fagopyrum tataricum Gaertn.).

Project description:Chloroplasts (cp) are indispensable organelles in plant cells that perform photosynthesis amongst other functions, including producing pigments, synthesizing sugars and certain amino acids. The complete chloroplast genome of Tartary Buckwheat Cultivar Miqiao 1 is sequenced in this study. Miqiao 1 is currently the only Tartary Buckwheat variety that can produce the whole nutritive Tartary Buckwheat Rice by hulling. The Miqiao 1 cp genome size is 159,272?bp in length, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. A pair of inverted repeats (IRs) of 30,817?bp were disconnected by a large single copy (LSC) of 84,397?bp and a small single copy (SSC) of 13,241?bp. The cp genome with 37.9% GC content contained 113 annotated genes.

| S-EPMC7800101 | biostudies-literature

The complete chloroplast genome sequence of Kerria japonica (L.) DC. 'pleniflora' (Rosaceae).

Project description:Kerria japonica (L.) DC., a monotypic species endemic to China and Japan, is an important ornamental shrub. In this study, we reported the complete chloroplast genome sequence of K. japonica (L.) DC. 'pleniflora' (GenBank accession number: MN418902) to provide genomic resources for its conservation. The total chloroplast (cp) genome is 160,007?bp in length, including a large single-copy region (LSC) of 87,672?bp and a small single-copy region (SSC) of 19,461?bp, which are separated by two inverted repeat (IR) regions of 26,437?bp. The overall guanine-cytosine (GC) content of the genome sequence is 34.0%. The cp genome encodes 132 unique genes, including 84 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. Phylogenetic analysis of 25 cp genomes showed that K. japonica 'pleniflora' was most closely related to K. japonica and then had a close genetic relationship with Neviusia cliftonii in Rosaceae.

| S-EPMC7707439 | biostudies-literature

The complete chloroplast genome of Dipterocarpus turbinatus Gaertn. F.

Project description:Dipterocarpus turbinatus Gaertn. F., naturally distributes in Southern China, which is an elite natural tree with high economic and medicinal value. In study, all chloroplast (cp) genome of Dipterocarpus turbinatus Gaertn. F. was assembled and characterized based on Illumina pair-end sequencing data. The complete chloroplast genome length was 152,279 bp. It contained a large (LSC, 83,862 bp) and a small (SSC, 20,215 bp) single copy region, separated by a pair of inverted repeats of 24,101 bp (IRs). The overall GC content of genome was 37.3%, the corresponding values of LSC, SSC, and IR regions were 35.3, 31.6, and 43.2%, respectively. There were 128 genes in the genome including 84 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Among all genes, 14 genes contain a single intron and 1 gene has two introns. The result showed that Dipterocarpus turbinatus Gaertn. F. was closely related to Vatica mangachapoi.

| S-EPMC7707500 | biostudies-literature

The complete chloroplast genome sequence of Magnolia mexicana DC. (Magnoliaceae) from Central America.

Project description:The chloroplast genome of the Magnolia species from Central America has never been reported. With its local use for food flavoring, medicine, and wood, M. mexicana has been of good economic importance. In the present study, the complete chloroplast genome of M. mexicana was assembled via the genome skimming data. As a typical quadripartite structure, the plastome of M. mexicana with 159,906 bp in length includes two inverted repeats (26,554 bp) separated by a small single copy region (18,761 bp) as well as a large single copy region (88,037 bp). This chloroplast genome consists of 131 different genes, including 86 protein coding genes (CDS), eight rRNA genes, and 37 tRNA genes. The maximum likelihood phylogenetic analysis showed that M. mexicana from Central America was closely related to an evergreen species, M. odoratissima from East Asia.

| S-EPMC7748584 | 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