Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete chloroplast genome of the endangered Chinese species Cymbidium lowianum (Rchb.f.) Rchb.f.

ABSTRACT: Cymbidium lowianum (Rchb.f.) Rchb.f. is a Class I endangered species in China with important ornamental, economic, and breeding value, especially wild C. lowianum. This study used Illumina high-throughput sequencing technologies to sequence and analyze the complete chloroplast genome of C. lowianum. The genome features of C. lowianum and the phylogenetic relationships among Orchidaceae species were reported and established. The complete chloroplast genome is 155,447 bp long, consisting of a pair of inverse duplication regions that are 26,710 bp long, a large single-copy region of 84,184 bp, and a small single-copy region of 17,843 bp. The entire genome contains 74 mRNA genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic tree of 24 Orchidaceae species revealed Cymbidium lowianum is more closely related to Cymbidium erythraeum.

SUBMITTER: Cheng L

PROVIDER: S-EPMC7782137 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of the complete chloroplast genome of a Chinese endangered species Cymbidium mannii.

Project description:Cymbidium mannii is an endangered species belonging to the first ranking in protection category in China with important ornamental value and breeding value. This study used Illumina high-throughput sequencing technologies to sequence and analyze the complete chloroplast genome of C. mannii. The genome features of C. mannii and the phylogenetic relationships among Orchidaceae species were reported and established. The complete chloroplast genome is 152,544 bp in length, consisting of a pair of inverse duplication regions 25,357 bp, a large single-copy region 86,014 bp and a small single-copy region 15,816 bp. The entire genome contains 74 mRNA genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic tree of 23 Orchidaceae species revealed C. mannii is more closely related to Cymbidium aloifolium.

| S-EPMC7782536 | biostudies-literature

Characterization of the complete chloroplast genome of a Chinese Endangered species Cymbidium mastersii.

Project description:Cymbidium mastersii is an endangered species belonging to the first ranking in protection category in China with important ornamental value and breeding value. This study used Illumina high-throughput sequencing technologies for C. mastersii of chloroplast genome sequencing. The genome features of C. mastersii and the phylogenetic relationships were reported and established. The complete chloroplast genome is 156,317 bp in length, consisting of a pair of inverse duplication regions 26,544 bp, a large single-copy region 85,360 bp and a small single-copy region 17,869 bp. The entire genome contains 73 mRNA genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic tree of 23 Orchidaceae species revealed C. mastersii is more closely related to Cymbidium eburneum.

| S-EPMC7971198 | biostudies-literature

The complete chloroplast genome of an endangered species Cymbidium mastersii (Orchidaceae).

Project description:Cymbidium mastersii Griff. & Lindl. is an endangered orchid. In this study, we report the complete chloroplast (cp) genome sequence and the cp genome features of C. mastersii. The cp genome sequence of C. mastersii was 155,362?bp in length. It included one large single-copy region (LSC, 84,465?bp), one small single-copy region (SSC, 20,647?bp), and two inverted repeat regions (IRs, 25,125?bp). The cp genome encoded 130 genes, of which 107 were unique genes (80 protein-coding genes, 23 tRNAs, and 4 rRNAs). The maximum-likelihood phylogenetic analysis showed that C. mastersii was a sister of C. erythraeum and C. nanulum.

| S-EPMC7706812 | biostudies-literature

The complete chloroplast genome of an Endangered species Cymbidium Nanulum (Orchidaceae).

Project description:Cymbidium nanulum Y.S.Wu & S.C.Chen is an IUCN Red listed Endangered species and distributes in South-Central China and Hainan. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of C. nanulum. The complete chloroplast (cp) genome sequence of C. nanulum was 149,776 bp in length. It presented a typical quadripartite structure including one large single-copy region (LSC, 85,392 bp), one small single-copy region (SSC, 14,210 bp), and two inverted repeat regions (IRs, 25,087 bp). The cp genome encoded 133 genes, of which 104 were unique genes (77 protein-coding genes, 23 tRNAs, and 4 rRNAs). The maximum-likelihood phylogenetic analysis showed that C. nanulum was closely related to other species of genus Cymbidium.

| S-EPMC7687592 | biostudies-literature

MITOGENOME ANNOUNCEMENTSCharacterization of the complete chloroplast genome of the Chinese endangered species Cymbidium iridioides D. Don.

Project description:Cymbidium iridioides D. Don 1852 is a Class I endangered species in China having important ornamental and breeding values. This study used Illumina high-throughput sequencing technology to sequence the complete chloroplast genome of C. iridioides. The genome features of C. iridioides and its phylogenetic relationships were determined. The complete chloroplast genome is 156,599 bp, containing a pair of 26,736 bp inverse duplication regions, a large 85,242 bp single-copy region, and a small 17,885 bp single-copy region. The entire genome contains 76 protein-coding genes, 37 tRNA genes, and 4 rRNA genes. A phylogenetic tree of 25 Orchidaceae species revealed that C. iridioides was grouped within Sect. Iridorchis and comprised a clade with Cymbidium tracyanum.

| S-EPMC8381904 | biostudies-literature

Characterization of the complete chloroplast genome of orchid family species Cymbidium bicolor (Orchidaceae).

Project description:Cymbidium bicolor belongs to Orchid family (Orchidaceae), it has high ornamental and traditional medicinal value. The complete chloroplast genome of C. bicolor was sequenced using the Illumina Hiseq platform. The size of the C. bicolor chloroplast genome is 156,528 bp, with an average GC content of 36.8%. This chloroplast genome has containing a large single copy (LSC) region of 85,907 bp, a small single copy (SSC) region of 17,215 bp, and two inverted (IRa and IRb) repeat regions of two 26,703 bp. A total of 124 genes were annotated, including 78 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. A maximum likelihood phylogenetic tree indicated that C. bicolor is closely related to C. mannii in the genus Cymbidium based on 16 whole chloroplast genome sequences.

| S-EPMC7748745 | biostudies-literature

The complete chloroplast genome of Cymbidium serratum (Orchidaceae): a rare and Endangered species endemic to Southwest China.

Project description:Cymbidium serratum is a dominant species in the large orchid family with beautiful flowers, thick petals, and long flowering periods, and has a long history of cultivation in Southwest China. However, its wild resources have been threatened with extinction due to environmental degradation and artificial exploitation. In this study, the complete chloroplast genome of C. serratum was obtained through Illumina sequencing. The size of chloroplast genome of C. serratum is 149,998 bp, including large single-copy (LSC) and small single-copy (SSC) regions over 84,854 bp and 13,926 bp, respectively, and two inverted repeats (IRs) of 25,609 bp. The total GC content was 37.11%. The chloroplast genome contains 129 genes, including 83 protein-coding genes, 8 rRNA genes, and 38 tRNA genes. The maximum-likelihood phylogenetic tree indicated that C. serratum is a sister species with the clade composed of C. faberi and C. goeringii. The complete chloroplast genome of C. serratum will contribute to protecting this highly endangered species, and provide genetic information about genetic diversity and sustainable use.

| S-EPMC7782322 | biostudies-literature

Complete chloroplast genome of an orchid species Cymbidium floribundum Lindl.

Project description:Cymbidium floribundum Lindl. is an ornamental plant and its native range is south China to north Vietnam. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of C. floribundum, which was assembled and characterized based on Illumina pair-end sequencing data. The complete chloroplast genome was 153998 bp in length. Its structure contained a large single-copy (LSC) region of 84,725 bp and a small single-copy (SSC) region of 19,009 bp, which were separated by a pair of extremely inverted repeats (IRs) of 25,132 bp each. The phylogenetic analysis indicated that C. floribundum was in the basal of subgenus Jenson.

| S-EPMC7706694 | biostudies-literature

Characterization of the complete chloroplast genome of a hybrid species Cymbidium tracyanum var 'huanghua' × Cymbidium faberi cv 'huanghui'.

Project description:Cymbidium tracyanumvar 'huanghua' × Cymbidium fabericv 'huanghui' is a hybrid species with important ornamental value. In the research, Illumina high-throughput sequencing technologies was used to sequence the chloroplastic genome of Cymbidium tracyanumvar 'huanghua' × C. fabericv 'huanghui'. The genome features of Cymbidium tracyanumvar 'huanghua' × C. fabericv 'huanghui' and the phylogenetic relationships were reported and established. The total length of the complete chloroplast genome is 154,741 bp, consisting of a pair of inverse duplication regions 26,968 bp, a large single-copy region 84,410 bp and a small single-copy region 16,395 bp. The complete genome contains 73 protein-coding genes (PCGs), The entire genome contains 73 genes that encode proteins, 30 tRNA genes and 4 rRNA genes. The phylogenetic tree revealed that Cymbidium tracyanumvar 'huanghua' × C. fabericv 'huanghui' is more closely related to Cymbidium erythraeum.

| S-EPMC8079062 | biostudies-literature

Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species.

Project description:BACKGROUND:Phoebe (Lauraceae) comprises of evergreen trees or shrubs with approximately 100 species, distributed in tropical and subtropical Asia and Neotropical America. A total of 34 species and three varieties occur in China. Despite of economic and ecological value, only limited genomic resources are available for this genus. RESULTS:We sequenced the two complete chloroplast (cp) genomes of Phoebe chekiangensis and P. bournei using Illumina sequencing technology via a combined strategy of de novo and reference-guided assembly. We also performed comparative analyses with the cp genomes of P. sheareri and P. sheareri var. oineiensis previously reported. The chloroplast genomes of P. chekiangensis and P. bournei identically contain 112 genes consisting of 78 protein coding genes, 30 tRNA genes, and 4 rRNA genes, with the size of 152,849 and 152,853 bp, respectively. From the two chloroplast genomes, 131 SSRs were identified and 12 different SSRs located in five protein coding genes. The analysis showed the extremely conserved structure of chloroplast genomes with surprisingly little variations at the LSC/IR and SSC/IR boundaries. Moreover, the mean nucleotide diversity was found to be 0.162% for 77 regions, suggesting an extraordinarily low level of sequence divergence. Four highest divergent regions (trnH-psbA, rps14-trnT, petA-psbJ, ccsA-ndhD) with the percentage of nucleotide diversity higher than 0.50% were identified, which had potential use for species identification and phylogenetic studies. CONCLUSION:This study will facilitate our understanding of population genetics, phylogenetic relationship and plant evolution of Phoebe species.

| S-EPMC5597560 | 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