Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete chloroplast genome of Paphiopedilum micranthum, an Endangered orchid in China.

ABSTRACT: Paphiopedilum micranthum is a rare species of terrestrial herb in the Orchidaceae. It is naturally distributed in southwestern China and north of Vietnam. Here, we reported the first complete chloroplast genome (cpDNA) of P. micranthum. The length is 163,243 bp, with 129 genes, including 77 protein coding genes, 38 tRNA genes, and 8 rRNA genes. It includes two inverted repeat regions (IRs) of 36,128 bp each, which were separated by a large single copy region (LSC) of 89,245 bp and a small single copy region (SSC) of 1742 bp. The overall GC-content of the whole chloroplast is 35.8%, while the corresponding values of the LSC, SSC, and IR regions are 33.2, 20, and 39.3, respectively. The complete chloroplast genome sequence of P. micranthum (GenBank accession number: MN535014) can be used as a useful resource for the evolutionary biology study of phylogenetic studies in Orchidaceae.

SUBMITTER: Chen XD

PROVIDER: S-EPMC7721024 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Characterization of the complete chloroplast genome of Paphiopedilum micranthum, an Endangered orchid in China.

Chen Xian-De XD Peng Dong-Hui DH Lan Si-Ren SR Chen Jun J Fu Wen-Qun WQ

Mitochondrial DNA. Part B, Resources 20191212 1

Paphiopedilum micranthum is a rare species of terrestrial herb in the Orchidaceae. It is naturally distributed in southwestern China and north of Vietnam. Here, we reported the first complete chloroplast genome (cpDNA) of P. micranthum. The length is 163,243 bp, with 129 genes, including 77 protein coding genes, 38 tRNA genes, and 8 rRNA genes. It includes two inverted repeat regions (IRs) of 36,128 bp each, which were separated by a large single copy region (LSC) of 89,245 bp and ...[more]

PMID: 33366446

Similar Datasets

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

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

Project description:Paphiopedilum wenshanense, a species of the family Orchidaceae, is endangered in the world with highly ornamental and biological value, the morphology of P. wenshanense is very similar to its relative species, P. bellatulum and P. concolor. However, there are few studies on the molecular biology and phylogeny of this species currently. Therefore, we report its complete chloroplast (cp) genome sequence at the first time, hoping to provide a foundation for its future phylogenetic analysis. The complete chloroplast genome of P. wenshanense was 161,750 bp in size, which contained a large single-copy (LSC) region of 90,656 bp, a small single-copy (SSC) region of 1886 bp, and two inverted repeat (IR) regions of 34,604 bp each. The total GC content was 35.66%. The genome encodes 38 transfer RNA genes, eight ribosomal RNA genes, and 80 protein-coding genes. The phylogenetic analysis indicated that the genetic relationship between P. wenshanense and P. concolor was very close.

| S-EPMC9673805 | 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

Characterization of the complete chloroplast genome of orchid family species Paphiopedilum bellatulum.

Project description:The genus Paphiopedilum is well known as the lady's slipper orchid in Orchidaceae family. Paphiopedilum bellatulum (Rchb.f.) Stein 1892, has important medicinal and ornamental value, which occurs in the tropical Asia. However, in recent decades, it was threatened with extinction by significantly reduced small population size. In this study, we sequenced and characterized the complete chloroplast genome of P. bellatulum based on the Illumina Hiseq platform. The size of P. bellatulum chloroplast genome was 156,567 bp, including a large single-copy (LSC) region of 88,243 bp, a small single-copy (SSC) region of 3652 bp, and two inverted repeat regions (IRs) of 32,336 bp. The overall GC contents of the chloroplast genome were 35.71%. A total of 122 genes were annotated, including 76 protein-coding genes, 38 transfer RNAs (tRNAs), and eight ribosomal RNAs (rRNAs). The phylogenetic analysis indicated that P. bellatulum formed a close relationship with another Paphiopedilum species P. wenshanense. The results will provide helpful genetic resource for further phylogenetic studies of the genus Paphiopedilum.

| S-EPMC9297714 | biostudies-literature

The complete chloroplast genome of the endangered plant Paphiopedilum wardii (Orchidaceae).

Project description:Chloroplast (cp) genome sequences provide a valuable source for phylogenetic analysis, which becomes a popular tool for population and phylogeny in a recent report. Here, the complete chloroplast genome of the Paphiopedilum wardii has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 169,820 bp in size and comprises a pair of inverted repeat (IR) regions of 33,641 bp each, a large single-copy (LSC) region of 98,872 bp and a small single-copy (SSC) region of 3666 bp. The total GC content is 33.8%, while the corresponding values of the IR regions, LSC, and SSC and are 38.7%, 31.7% and 26.7%, respectively. The chloroplast genome contains 151 genes, including 91 protein-coding genes, eight ribosomal RNA genes and 52 transfer RNA genes. Two genes (ndhA and ndhB) are pseudogenized or lost in its cpDNA. The maximum-likelihood phylogenetic analysis showed a close relationship with P. armeniacum in Orchidaceae. Our findings provide useful information for phylogenetic and evolutionary research of Paphiopedilum species.

| S-EPMC7800172 | biostudies-literature

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

Complete chloroplast genome of Paphiopedilum emersonii (Orchidaceae).

Project description:Paphiopedilum emersonii is an endemic terrestrial orchid in China. In this study, the chloroplast genome of P. emersonii was determined from BGISEQ-500 sequencing data. The total chloroplast genome was 162,590 bp in length, consisting of a large single-copy region (LSC, 87,852 bp), a small single-copy region (SSC, 870 bp), and two inverted repeat regions (IRA and IRB, 36,934 bp, each). The complete chloroplast genome contains 131 genes, including 81 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. In addition, the phylogenetic analysis indicates that P. emersonii was sister to Paphiopedilum micranthum. The chloroplast genome will contribute to the research and conservation of P. emersonii.

| S-EPMC7783058 | biostudies-literature

The complete chloroplast genome of Paphiopedilum tranlimianum (Orchidaceae).

Project description:Chloroplast (cp) genome sequences have become a useful tool for phylogeneitc and evolutionary study in recent reports. Here the complete chloroplast genome of the Paphiopedilum tranlimianum has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 162,127 bp in size, and comprises of a pair of inverted repeat (IR) regions of 31,457 bp each, a large single-copy (LSC) region of 91,711 bp, and a small single-copy (SSC) region of 7,502 bp. The total GC content is 35.4%, while the corresponding values of the LSC, SSC, and IR regions are 32.7%, 26.9%, and 40.9%, respectively. The chloroplast genome contains 133 genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 38 transfer RNA genes. Three genes (ndhA, ndhE, and ndhI) are pseudogenized or lost in its cpDNA. The Maximum-Likelihood phylogenetic analysis showed a close relationship with P. niveum in Orchidaceae. Our findings provide useful information for phylogenetic and evolutionary research of Paphiopedilum species.

| S-EPMC7799620 | biostudies-literature

The complete chloroplast genome of Paphiopedilum malipoense (Orchidaceae).

Project description:Paphiopedilum malipoense S.C.Chen & Z.H.Tsi is a new orchid species found in Malipo county, Yunnan. Here we report the complete chloroplast (cp) genome sequence and the features of P. malipoense. Its cp genome sequence of P. malipoense is 158,708 bp, including one large single-copy region (LSC, 89,452 bp), one small single-copy region (SSC, 17,692 bp), and two inverted repeat regions (IRs, 25,782 bp). The cp genome encoded 132 genes, of which 112 were unique genes (79 protein-coding genes, 29 tRNAs, and 4 rRNAs). The phylogenetic relationships show that P. malipoense is sister with P. armeniacum-P. wardii.

| S-EPMC7706870 | biostudies-literature