Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete chloroplast genome of Camellia granthamiana (Theaceae), a Vulnerable species endemic to China.

ABSTRACT: Camellia granthamiana is a wild camellia resource endemic to China and is listed as a Vulnerable species globally. Here, we reported and characterized its complete chloroplast (cp) genome by using Illumina pair-end sequencing data. The total chloroplast genome size was 157,001?bp, including inverted repeats (IRs) of 26,042?bp, separated by a large single copy (LSC) and a small single copy (SSC) of 86,622 and 18,295?bp, respectively. A total of 131 genes, including 36 tRNA, 8 Rrna, and 87 protein-coding genes were identified. Phylogenetic analysis showed that C. granthamiana is sister to C. sinensis with 100% value support.

SUBMITTER: Li W

PROVIDER: S-EPMC7800109 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Characterization of the complete chloroplast genome of Camellia granthamiana (Theaceae), a Vulnerable species endemic to China.

Li Weixi W Shi Xianggang X Guo Wuxia W Banerjee Achyut Kumar AK Zhang Qun Q Huang Yelin Y

Mitochondrial DNA. Part B, Resources 20181029 2

Camellia granthamiana is a wild camellia resource endemic to China and is listed as a Vulnerable species globally. Here, we reported and characterized its complete chloroplast (cp) genome by using Illumina pair-end sequencing data. The total chloroplast genome size was 157,001 bp, including inverted repeats (IRs) of 26,042 bp, separated by a large single copy (LSC) and a small single copy (SSC) of 86,622 and 18,295 bp, respectively. A total of 131 genes, including 36 tRNA, 8 Rrna, and 87 ...[more]

PMID: 33474444

Similar Datasets

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

Characterization of the complete chloroplast genome of Salix magnifica, a vulnerable species endemic to China.

Project description:Salix magnifica is only sporadically distributed in the western part of Sichuan, the area of the willows is narrow. There are not many plants, and they easily fall into the endangered state. It is currently on the International Union for Conservation of Nature (IUCN) red list of threatened species. In this study, we first assembled the complete chloroplast (cp) genome of Salix magnifica by Illumina paired-end reads data. The whole genome was 154,977 bp, consisting of a pair of inverted repeats of 27,457 bp, large single-copy region, and a small single-copy region (71,119 and 16,205 bp in length, respectively). The cp genome contained 116 genes, including 80 protein-coding genes and 36 tRNA genes. The overall GC content of the whole genome was 36.7%. A neighbour-joining phylogenetic analysis demonstrated a close relationship between Salix magnifica and Salix oreinoma.

| S-EPMC7510628 | biostudies-literature

Characterization of the complete chloroplast genome of Polyspora tiantangensis (Theaceae), an endemic and endangered species in southwestern China.

Project description:Polyspora tiantangensis (Theaceae) is an endangered woody plant in southwestern China. In this study, we assembled complete chloroplast (cp) genome of P. tiantangensis based on the Illumina reads. The cp genome of P. tiantangensis is 157,057 bp in length, including a large single-copy (LSC) region of 86,593 bp and a small single-copy (SSC) region of 18,284 bp, separated by two inverted repeat (IR) regions of 26,090 bp each. The cp genome encoded 132 genes including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The GC content of cp genome of P. tiantangensis is 37.3%. A total of 68 SSRs were discovered. Phylogenetic analysis of cp genomes from 26 species of Theaceae revealed that all species of Polyspora formed one monophyletic clade and P. tiantangensis was closely related with its congeneric species P. longicarpa with 100% bootstrap value.

| S-EPMC7954410 | biostudies-literature

The complete chloroplast genome sequence of Camellia ptilophylla (Theaceae): a natural caffeine-free tea plant endemic to China.

Project description:Camellia ptilophylla is a natural caffeine-free tea plant endemic to China with high commercial and therapeutic values. Here, we report the complete chloroplast genome assembled using Illumina pair-end sequencing data. The chloroplast genome was 157,097 bp in length, with a large single copy (LSC) region of 86,631 bp, a small single copy (SSC) region of 18,286 bp, separated by two inverted repeat (IR) regions of 26,090 bp each. It contains a total of 132 genes, with an overall GC content of 37.3%. The phylogenetic analysis showed that C. ptilophylla is sister to a congeneric species, C. reticulata.

| S-EPMC7799551 | 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

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

Characterization of the complete chloroplast genome of the Camellia nitidissima, an endangered and medicinally important tree species endemic to Southwest China.

Project description:The Camellia nitidissima is an endangered tree species native to Southwest China with high economic and medicinal values. Genetic information of C. nitidissima would provide good knowledge for the conservation of this wild resource. In this article, we characterized the complete chloroplast genome of C. nitidissima using Illumina sequencing technology. The size of circular genome is 157,247 bp, containing a large single copy (LSC) region of 86,880 bp and a small single copy (SSC) region of 18,258 bp. The LSC region and SSC region are separated by a pair of inverted repeat regions (IRa and IRb), each of 26,068 bp. In total, 136 genes are encoded in this cp genome, including 89 protein-coding genes (81 species), 39 tRNA genes (30 species), and 8 rRNA genes (4 species). The overall G + C content of the chloroplast genome is 37.3%. The phylogenetic analysis suggests that C. nitidissima is closely related to C. petelotti.

| S-EPMC7800646 | 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