Browse
Submit Data
Databases
API
Help

Dataset Information

28 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Dendrobium nobile, an endangered medicinal orchid from north-east India and its comparison with related Dendrobium species.

ABSTRACT: The medicinal orchid genus Dendrobium belonging to the Orchidaceae family is a huge genus comprising about 800-1,500 species. To better illustrate the species status in the genus Dendrobium, a comparative analysis of 33 available chloroplast genomes retrieved from NCBI RefSeq database was compared with that of the first complete chloroplast genome of D. nobile from north-east India based on next-generation sequencing methods (Illumina HiSeq 2500-PE150). Our results provide comparative chloroplast genomic information for taxonomical identification, alignment-free phylogenomic inference and other statistical features of Dendrobium plastomes, which can also provide valuable information on their mutational events and sequence divergence.

SUBMITTER: Konhar R

PROVIDER: S-EPMC6830405 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Chloroplast Genome Sequence Annotation of Dendrobium nobile (Asparagales: Orchidaceae), an Endangered Medicinal Orchid from Northeast India.

Project description:Orchidaceae constitutes one of the largest families of angiosperms. Owing to the significance of orchids in plant biology, market needs and current sustainable technology levels, basic research on the biology of orchids and their applications in the orchid industry is increasing. Although chloroplast (cp) genomes continue to be evolutionarily informative, there is very limited information available on orchid chloroplast genomes in public repositories. Here, we report the complete cp genome sequence of Dendrobium nobile from Northeast India (Orchidaceae, Asparagales), bearing the GenBank accession number KX377961, which will provide valuable information for future research on orchid genomics and evolution, as well as the medicinal value of orchids. Phylogenetic analyses using Bayesian methods recovered a monophyletic grouping of all Dendrobium species (D. nobile, D. huoshanense, D. officinale, D. pendulum, D. strongylanthum and D. chrysotoxum). The relationships recovered among the representative orchid species from the four subfamilies, i.e., Cypripedioideae, Epidendroideae, Orchidoideae and Vanilloideae, were consistent within the family Orchidaceae.

| S-EPMC5501700 | biostudies-literature

Complete Chloroplast Genome Sequence of Dendrobium nobile from Northeastern India.

Project description:The orchid species Dendrobium nobile belonging to the family Orchidaceae and genus Dendrobium (a vast genus that encompasses nearly 1,200 species) has an herbal medicinal history of about 2000 years in east and south Asian countries. Here, we report the complete chloroplast genome sequence of D. nobile from northeastern India for the first time.

| S-EPMC5054326 | biostudies-literature

Genetic stability and phytochemical analysis of the in vitro regenerated plants of Dendrobium nobile Lindl., an endangered medicinal orchid.

Project description:An efficient genetically stable regeneration protocol with increased phytochemical production has been established for Dendrobium nobile, a highly prized orchid for its economic and medicinal importance. Protocorm like bodies (PLBs) were induced from the pseudostem segments using thidiazuron (TDZ; 1.5 mg/l), by-passing the conventional auxin-cytokinin complement approach for plant regeneration. Although, PLB induction was observed at higher concentrations of TDZ, plantlet regeneration from those PLBs was affected adversely. The best rooting (5.41 roots/shoot) was achieved in MS medium with 1.5 mg/l TDZ and 0.25% activated charcoal. Plantlets were successfully transferred to a greenhouse with a survival rate of 84.3%, exhibiting normal development. Genetic stability of the regenerated plants was investigated using randomly amplified polymorphic DNA (RAPD) and start codon targeted (SCoT) polymorphism markers which detected 97% of genetic fidelity among the regenerants. The PIC values of RAPD and SCoT primers were recorded to be 0.92 and 0.76 and their Rp values ranged between 3.66 and 10, and 4 and 12 respectively. The amplification products of the regenerated plants showed similar banding patterns to that of the mother plant thus demonstrating the homogeneity of the micropropagated plants. A comparative phytochemical analysis among the mother and the micropropagated plants showed a higher yield of secondary metabolites. The regeneration protocol developed in this study provides a basis for ex-situ germplasm conservation and also harnesses the various secondary metabolite compounds of medicinal importance present in D. nobile.

| S-EPMC4287867 | biostudies-other

The complete chloroplast genome sequence of an Endangered orchid species Dendrobium bellatulum (Orchidaceae).

Project description:Dendrobium bellatulum Rolfe is an Endangered orchid species that is distributed in the subtropical regions of Yunnan Province, China. It was listed in the category of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Here, we reported the complete chloroplast (cp) genome sequence and the cp genomic features of D. bellatulum. The genome was 152,107?bp long with 129 genes comprising 83 protein-coding genes, 40 tRNA genes, and 6 rRNA genes. Phylogenetic analysis of a data set of cp genomes indicated that D. bellatulum is clustered with other species in Dendrobium.

| S-EPMC7800090 | biostudies-literature

The complete chloroplast genome of an endangered orchid Paphiopedilum spicerianum.

Project description:Paphiopedilum spicerianum (H. G. Reichenbach) Pfitzer is an endangered and threatened orchid species in China. The genetic and molecular data of this orchid species is deficient. With the aim to identify appropriate chloroplast markers for the use in a conservation biology study, the complete chloroplast genome of P. spicerianum was reported. We found that the chloroplast genome of P. spicerianum is 157,292 bp in length, containing a large single-copy region of 87,252 bp, a small single-copy region of 1828 bp, and a pair of inverted repeats of 34,106 bp. Genome annotation predicted 105 unique genes, including 71 protein-coding genes, 30 tRNAs, and four rRNAs. Fourteen genes contained one intron and two genes (clpP and ycf3) had two introns. The GC content of the P. spicerianum was 35.8%. Phylogenetic analysis indicated P. spicerianum was closely related to P. purpuratum.

| S-EPMC7594755 | biostudies-literature

Chloroplast genome structure and phylogeny of Spiranthes sinensis, an endangered medicinal orchid plant.

Project description:Spiranthes sinensis is an important medicinal plant of Spiranthes family and is currently in an endangered state. To better guide the systematic classification of S. sinensis, the complete genome of its chloroplast was sequenced and characterized. The complete chloroplast genome is 152,786?bp in length and contains a large single copy (LSC) region of 83,446?bp, a small single copy (SSC) region of 17,938?bp, and two inverted repeat (IRA and IRB) regions of 25,701?bp. The genome encodes 132 genes (112 unique genes), including 86 protein-coding genes (78 unique genes), 8 rRNA genes (4 unique genes), and 38 tRNA genes (30 unique genes). The total GC content of plasmid genome is 36.18%. Phylogenetic results indicated that S. sinensis is more closely related to Ludisia discolor, Goodyera schlechtendaliana, Goodyera fumata, and Goodyera procera. The study enriches the plasmid genomic information of S. sinensis and is of great significance for the genetic protection of this species.

| S-EPMC7706474 | biostudies-literature

Cloning and expression analysis of DnMSI1 gene in orchid species Dendrobium nobile Lindl.

Project description:WD40 repeat proteins, the homologs of yeast MSI1, are conserved in plants, participating in protein complexes and playing fundamental functions in plant development. Although several MSI1-like proteins have been cloned and characterized in plants, the roles of MSI1-like proteins in the biennial ornamental plant, Dendrobium nobile Lindl, are still unclear. Here, we report the cloning of the DnMSI1 gene from Dendrobium nobile Lindl with RACE technology. We found that DnMSI1 expression was induced by GA3 and TDZ but inhibited by ABA, PP333, and drought and salt stress. Furthermore, DnMSI1 over-expression in Arabidopsis resulted in decreased tolerance to NaCl stress. These results suggest that DnMSI1 plays negative regulation roles in regulating salinity-stress resistance in Dendrobium nobile Lindl.

| S-EPMC9176244 | biostudies-literature

The complete chloroplast genome sequence of a critically endangered orchid Paphiopedilum gratrixianum (Orchidaceae).

Project description:Paphiopedilum gratrixianum is a critically endangered orchid with extremely small populations and of great horticulture value. We assembled and annotated the complete chloroplast genome of P. gratrixianum in this study. The genome is 157,292 bp in length and 35.8% of the GC content. It encodes a total of 102 unique genes, including 68 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis results strongly supported that it was closely related to P. tranlienianum. The complete chloroplast genome of P. gratrixianum (GenBank accession number: MW284890) can be useful for the evolutionary study in Orchidaceae.

| S-EPMC8979525 | biostudies-literature

The complete chloroplast genome sequences of an endangered orchid species Paphiopedilum parishii (Orchidaceae).

Project description:Paphiopedilum parishii (Rchb. f.) Stein is an endangered and rare species with highly ornamental value. In this study, we report the complete chloroplast genome of P. parishii using the Illumina sequencing data. The total genome of P. parishii is 154,689 bp in length and the GC content is 35.9%, with a pair of inverted repeats (IRs) regions of 32,690 bp each, a large single-copy region (LSC) of 86,863 bp and a small single-copy region (SSC) of 2,446 bp. The chloroplast genome encoded 127 genes, including 82 protein-coding genes (CDS), 8 rRNA genes and 37 tRNA genes. The phylogenetic tree showed that P. parishii was clustered with other species in Paphiopedilum with strong support based on the complete chloroplast genome.

| S-EPMC8330699 | biostudies-literature

The complete chloroplast genome sequence of Pholidota articulata (Orchidaceae), a rarely medicinal orchid.

Project description:Pholidota Lindl. ex Hook. was placed in tribe Arethuseae Lindl. (Epidendroideae, Orchidaceae), while its generic relationship has been unclear. Since the plastid genome could play a key role in plant systematics, the complete chloroplast (cp) genome of P. articulata was reported in this paper. The cp genome was 160,114 bp in length with four typical quadripartite structures, which was consisted of a large single copy (LSC) region of 87,756 bp, a small single copy (SSC) region of 18,872 bp, and two inverted repeats (IR) of 26,734 bp. In addition, the cp genome encoded 132 genes in total, of which were 113 unique genes, including 79 protein-coding genes, 30 tRNAs, and 4 rRNAs. The phylogenetic analysis indicated that P. articulata was closely clustered with other two species of Pholidota and that they appeared to be related to Pleione in Arethuseae Lindl.

| S-EPMC7759241 | 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