Browse
Submit Data
Databases
API
Help

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete chloroplast genome of Camellia chekiangoleosa (Theaceae), a shrub with gorgeous flowers and rich seed oil.

ABSTRACT: Camellia chekiangoleosa Hu is an oil-tea Camellia species with high economic and nutritional value in the south of China. In this study, the chloroplast genome of C. chekiangoleosa was determined by Illumina Miseq platform. The whole chloroplast genome is 156,971 bp in length, containing a large single-copy region (LSC, 86,673 bp), a small single-copy region (SSC, 18,394 bp), and a pair of inverted repeat regions (IRa and IRb, 25,952 bp). There is a total of 113 genes in the complete chloroplast genome of which 19 genes are repeated in the IR regions. In addition, the phylogenetic tree revealed a close relationship between C. chekiangoleosa and C. japonica. The complete chloroplast genome will contribute to further studies on phylogeny and conservation of C. chekiangoleosa and related taxa in Camellia of Theaceae.

SUBMITTER: Yin X

PROVIDER: S-EPMC7971316 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome of Camellia vietnamensis, an economic shrub producing edible seed oil.

Project description:Camellia vietnamensis is an economic woody plant producing high-value edible oils, which is commonly found and cultivated in south areas of China. To provide genetic information for future genetic research, we have sequenced and assembled the complete chloroplast (cp) genome of C. vietnamensis based on the Illumina Hiseq platform. The total genome size is 161,958 bp in length with 37% GC, which contains a large single copy (LSC, 86,657 bp) region, a small single copy (SSC, 13,347 bp) region, and a pair of inverted repeat (IRs, 30,977 bp) regions. It is comprised of 81 protein-coding genes, 44 transfer RNAs and 4 ribosomal RNAs. To obtain the phylogeny relationship, the cp genome of C. vietnamensis has been compared with other Camellia species; the results indicate that C. vietnamensis is closely related to C. taliensis. This study provides fundamental information of C. vietnamensis cp genome, and it is valuable to the molecular phylogenetic and genetic diversity analyses in future.

| S-EPMC7707582 | biostudies-literature

Characterization of the complete chloroplast genome of Camellia brevistyla, an oil-rich and evergreen shrub.

Project description:Camellia brevistyla is an economic species for its seeds with high oil content and ornamental value, which is cultivated widespreadly across southern China. In this study, the complete chloroplast (cp) genome sequence of C. brevistyla was assembled and annotated in order to future genetic research. The whole cp genome of C. brevistyla is 159,281 bp in size, composed of a small single copy (SSC) region of 15,662 bp and a large single copy (LSC) region of 86,251 bp separated by a pair of inverted repeats (IRs, IRA: 130598: 159281, IRB: 86252: 114935). The overall GC content of C. brevistyla cp genome is 37.19%, with the base content A (31.03%), T (31.78%), C (18.94%), and G (18.25%). Phylogenetic analysis of 20 species based on 74 protein-coding genes shows that C. brevistyla is evolutionarily closest to Camellia danzaiensis.

| S-EPMC7748852 | biostudies-literature

The complete chloroplast genome of Camellia fluviatilis (Theaceae), a wild oil-Camellia species.

Project description:Camellia fluviatilis is an important shrub producing edible seed oil, which is widely cultivated in South China. In this study, the complete chloroplast genome was sequenced and analyzed based on the Illumina HiSeq platform. The results showed that the complete chloroplast genome is 157,041 bp with 37.29% GC content, including a large single copy (LSC) region of 86,718 bp, a small single copy (SSC) region of 18,293 bp, and a pair of inverted repeats (IRs) regions of 26,015 bp. There are 128 genes in the chloroplast genome of C. fluviatilis, including 83 protein-coding genes, 8 ribosomal RNAs, and 37 transfer RNAs. Phylogenetic analysis revealed that C. fluviatilis is closely related to C. lanceoleosa, indicating that both belong to the Sect. Paracamellia Sealy.

| S-EPMC8635574 | biostudies-literature

The complete chloroplast genome of Camellia nitidissima (Theaceae).

Project description:Camellia nitidissima is an endangered species. This species contains two varieties. Here, we report on the chloroplast genomes of C. nitidissima var. nitidissima from Fangcheng (GenBank accession MT157617) and Nanning (MT157618), as well as one sample of C. nitidissima var. microcarpa (MT157619) from Nanning. The total chloroplast genomes of C. nitidissima var. nitidissima Fangcheng and Nanning samples are 156,596 bp and 157,567 bp in length, respectively. C. nitidissima var. microcarpa (MT157619) genome is 157,407 bp in length. The three samples possess GC contents of 37.3%, 128 genes, comprising 86 protein-coding genes, 34 tRNA genes, and 8 rRNA genes.

| S-EPMC7510655 | biostudies-literature

Complete chloroplast genome of a cultivated oil camellia species, Camellia gigantocarpa.

Project description:Camellia gigantocarpa Hu et T. C. Huang, belonging to the Theaceae family, is an excellent landscape tree species with high ornamental value. It is also an important woody oil-bearing plant with high economic value. This study reports the first complete chloroplast genome sequence of C. gigantocarpa (GenBank accession number: MZ054232). Its whole chloroplast genome is 156,953 bp long with an overall GC content of 37.31%, which is composed of a large single copy region (86,631 bp), a small single copy region (18,402 bp), and a pair of inverted repeat regions (25,960 bp each). A total of 135 genes were predicted in this genome, namely eight ribosomal RNA genes, 37 transfer RNA genes, and 90 protein-coding genes. Based on maximum likelihood analysis results, we found that the Camellia species are clustered into a distinct branch, and the phylogenetic relationships among C. gigantocarpa, C. crapnelliana, and C. kissii were the closest.

| S-EPMC8667929 | biostudies-literature

The complete chloroplast genome sequence of Camellia tachangensis F. C. Zhang (Theaceae).

Project description:To understand genetic background and phylogenetic position of Camellia tachangensis, we determined its complete chloroplast genome sequence which is 157,026?bp in length with overall GC content of 36.7%. It has four sub regions: a large single-copy (LSC) region (86,669?bp) and a small single-copy (SSC) region (18,253?bp) are separated by two inverted repeat (IR) regions (26,052?bp each). A total of 129 genes were annotated, containing 86 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. Phylogenetic trees showed C. tachangensis clustered with Camellia gymnogyna and Camellia taliensis and separated from Camellia sinensis and its two varieties, Camellia sinensis var. assamica and Camellia sinensis var. pubilimba.

| S-EPMC7707387 | biostudies-literature

The complete chloroplast genome sequence of Camellia sinensis var. sinensis cultivar Tieguanyin (Theaceae).

Project description:Camellia sinensis var. sinensis cultivar Tieguanyin (TGY) is an important Oolong tea variety in China. In this study, we reported a complete chloroplast (cp) genome based on the Illumina sequencing technology and combined de novo and reference-guided assembly strategies. The complete cp genome of 'TGY' displayed the regular quadripartite structure: a total of 157,126 bp in length, comprising a large single-copy (LSC, 86,904 bp) region, a small single-copy (SSC, 18,532 bp) region, and a pair of inverted repeats (IRs, 26,095 bp) regions. A lot of 132 predicted genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content is 37.3%. Maximum likelihood (ML) phylogenetic tree involving 18 cp genomes of the Camellia genus revealed a relatively independent event of local domestication among three types of cultivars. The complete cp genome of 'TGY' provides an insight into tea plants for further understanding evolutionary research on tea plants.

| S-EPMC7872547 | biostudies-literature

Characterization and phylogenetic analysis of the complete chloroplast genome of Camellia chrysanthoides (Theaceae).

Project description:Camellia chrysanthoides H.T.Chang 1979 is an economic species for its high ornamental and medicinal values. In the present work, the complete chloroplast (cp) genome sequence of C. chrysanthoides was assembled and characterized using Illumina paired-end sequencing data. The total cp genome of C. chrysanthoides is 157,439 bp in size, consisting of a small single copy (SSC) and a large single copy (LSC) separated by a pair of inverted repeats (IRs) with 18,265 bp, 88,162 bp, and 25,506 bp, respectively. Further annotation revealed the cp genome encoded 124 genes, including 82 protein-coding genes, 34 tRNA genes, and eight rRNA genes, and the overall GC content of the cp genome is 37.31%. Phylogenetic analysis based on 80 protein-coding genes shows that C. chrysanthoidesis closely related to C. azalea in the genus Camellia.

| S-EPMC8491734 | biostudies-literature

The complete chloroplast genome of Camellia semiserrata Chi. (Theaceae), an excellent woody edible oil and landscaping species in South China.

Project description:Camellia semiserrata is a woody plant that produces excellent edible oil and is a common landscaping species in South China. The complete chloroplast genome of C. semiserrata was sequenced, assembled, annotated, and characterized using the Illumina MiSeq platform in this study. The chloroplast genome is 156,968 bp (37.32% GC) and contains a large single copy (LSC) region (86,634 bp), a small single copy (SSC) region (18,272 bp), and a pair of inverted repeat (IR) regions (26,031 bp). It encodes a total of 117 genes, including 81 protein-coding genes, four ribosomal RNA genes, and 32 transfer RNA genes. The phylogenetic tree fully resolved C. semiserrata in a clade with C. reticulata, C. mairei, and C. pitardii. This study contributes to bioinformatics and further phylogeny and conservation studies as well as provides a theoretical basis for the molecular identification of C. semiserrata.

| S-EPMC8462872 | biostudies-literature

The complete chloroplast genome sequence of Camellia zhaiana (Theaceae), a critically endangered species from China.

Project description:Camellia zhaiana S.X. Yang (Theaceae) is a recently described species reported from Guangxi, China. It was proposed as a critically endangered species according to the IUCN Red List Categories and Criteria. In this study, we report and characterize the complete chloroplast (cp) genome of C. zhaiana using Illumina pair-end sequencing data. This is the first report of a cp genome of a species classified in Camellia section. Longipedicellata. The cp genome of C. zhaiana is 156,627 bp in length and includes a large single-copy region (LSC, 86,196 bp), a small single-copy region (SSC, 18,281 bp), and a pair of inverted repeat regions (IRs, 26,075 bp). The genome contains 135 genes, including 40 tRNA, eight rRNA, and 87 protein-coding genes. Phylogenetic analysis showed a strongly supported sister relationship between C. zhaiana and C. longipedicellata, which is a species classified in sect. Longipedicellata. These data support the previous systematic findings of C. zhaiana and advance the bioinformatics of the genus Camellia.

| S-EPMC8330765 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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