Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of monotypic Cyphotheca (Melastomataceae), an endemic genus in China.

ABSTRACT: Cyphotheca, a shrub narrowly endemic to Yunnan, southwest China, is a monotypic genus of Sonerileae in Melastomataceae. The species, Cyphotheca montana, is dwindling and is listed as 'Near Threatened (NT)' by IUCN Red List of China. Herein, we report the complete chloroplast genome (cpDNA) sequence assembled from Illumina pair-end sequencing data. The complete chloroplast genome was 156,424?bp in length, which includes two inverted repeat regions (IRs) of 26,776?bp each, which were separated by a large single copy region (LSC) 85,900?bp and a small single copy region (SSC) 16,972?bp. The chloroplast genome contained 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content in the chloroplast genome of C. montana was 37.0%. The phylogenomic analysis showed that C. montana is sister to Barthea barthei.

SUBMITTER: Wen Z

PROVIDER: S-EPMC7687601 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome sequence of monotypic Cyphotheca (Melastomataceae), an endemic genus in China.

Wen Zhenying Z Zeng Sijin S Li Tingzhang T Zhang Guoqiang G Peng Donghui D

Mitochondrial DNA. Part B, Resources 20190711 2

Cyphotheca, a shrub narrowly endemic to Yunnan, southwest China, is a monotypic genus of Sonerileae in Melastomataceae. The species, Cyphotheca montana, is dwindling and is listed as 'Near Threatened (NT)' by IUCN Red List of China. Herein, we report the complete chloroplast genome (cpDNA) sequence assembled from Illumina pair-end sequencing data. The complete chloroplast genome was 156,424 bp in length, which includes two inverted repeat regions (IRs) of 26,776 bp each, which were ...[more]

PMID: 33365512

Similar Datasets

The complete chloroplast genome sequence of Barthea barthei (Melastomataceae), a shrub endemic to southern China.

Project description:The plant genus Barthea is monotypic, comprising of only a single species (Barthea barthei), and is endemic to southern China. In this study, we report the complete chloroplast genome of B. barthei, assembled from whole-genome high-throughput sequencing data, as a resource for future studies on the taxonomy and evolution of Barthea. The chloroplast genome was 155,951 bp in length, with a large single-copy (LSC) region of 85,882 bp, a small single-copy (SSC) region of 16,445 bp, separated by two inverted repeat (IR) regions of 26,812 bp each. It was predicted to contain a total of 130 genes, with an overall GC content of 36.99%. Phylogenetic analysis placed B. barthei closest to Opisthocentra sp. in Melastomataceae.

| S-EPMC7799996 | biostudies-literature

The complete chloroplast genome sequence of an endemic monotypic genus Hagenia (Rosaceae): structural comparative analysis, gene content and microsatellite detection.

Project description:Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce) J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H. abyssinica. The genome is a circular molecule of 154,961 base pairs (bp), with a pair of Inverted Repeats (IR) 25,971 bp each, separated by two single copies; a large (LSC, 84,320 bp) and a small single copy (SSC, 18,696). H. abyssinica's chloroplast genome has a 37.1% GC content and encodes 112 unique genes, 78 of which code for proteins, 30 are tRNA genes and four are rRNA genes. A comparative analysis with twenty other species, sequenced to-date from the family Rosaceae, revealed similarities in structural organization, gene content and arrangement. The observed size differences are attributed to the contraction/expansion of the inverted repeats. The translational initiation factor gene (infA) which had been previously reported in other chloroplast genomes was conspicuously missing in H. abyssinica. A total of 172 microsatellites and 49 large repeat sequences were detected in the chloroplast genome. A Maximum Likelihood analyses of 71 protein-coding genes placed Hagenia in Rosoideae. The availability of a complete chloroplast genome, the first in the Sanguisorbeae tribe, is beneficial for further molecular studies on taxonomic and phylogenomic resolution within the Rosaceae family.

| S-EPMC5228516 | biostudies-literature

The complete chloroplast genome of Dunnia sinensis (Rubiaceae): a monotypic species endemic to Guangdong, China.

Project description:Dunnia sinensis, a monotypic genus of the Rubiaceae, is an Endangered species endemic to China. Its complete chloroplast genome was determined to be 154,909 bp in length and the GC content was 37.80%. The sequence includes a large single-copy region of 84,894 bp, a small single-copy region of 16,973 bp, and the inverted region of 26,521 bp in length. It contains 130 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The ML and BI analyses revealed D. sinensis was closely related to Galium mollugo and Leptodermis scabrida with strong bootstrap values belonging to the subfamily Rubioideae.

| S-EPMC7748692 | biostudies-literature

The complete chloroplast genome of Foonchewia coriacea (Rubioideae: Rubiaceae): a monotypic species endemic to Guangdong, China.

Project description:Foonchewia coriacea, a monotypic genus of the Rubiaceae, is endemic to China. Its complete chloroplast genome was determined to be 153,114 bp in length and the GC content was 37.90%. The sequence includes a large single-copy region of 83,978 bp, a small single-copy region of 18,290 bp, and the inverted region is 25,423 bp in length. It contains 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The maximum likelihood (ML) and Bayesian inference (BI) analyses revealed F. coriacea was closely related to Dunnia sinensis with strong bootstrap values, belonging to the subfamily Rubioideae.

| S-EPMC7832469 | biostudies-literature

The complete chloroplast genome sequence of Blastus pauciflorus (Melastomataceae).

Project description:Blastus pauciflorus, a shrub endemic to Hong Kong and Guangdong, south China, growing on low-altitude hillsides, under the forest. The species is controversial in classification. Herein, we report the complete chloroplast genome sequence assembled from Illumina pair-end sequencing data, with aims to resolve its relationship with the related species. The complete chloroplast genome was 155,983?bp in length, includes two inverted repeat regions (IRs) of 26,716?bp each, which were separated by a large single copy region (LSC) 86,101?bp and a small single copy region (SSC) 16,450?bp. The chloroplast genome contained 129 genes, including 82 protein-coding genes, 2 pseudogenes, 37 tRNA genes and 8 rRNA genes. The overall GC content in the chloroplast genome of B. pauciflorus was 37.0%. Phylogenetic analysis showed that B. pauciflorus is closed to B. cochinchinensis.

| S-EPMC7707767 | biostudies-literature

The complete chloroplast genome sequence of Melastoma candidum (Melastomataceae).

Project description:The plant genus Melastoma is comprised of members estimated to have formed through recent species radiation. Natural hybridization among member species further complicates taxonomy within the genus. Herein, we report the complete chloroplast genome of M. candidum, assembled from partial data obtained from a parallel whole-genome Illumina paired-end sequencing effort on the species. The chloroplast genome was 156,682 bp in length, with a large single-copy (LSC) region of 86,084 bp, a small single-copy (SSC) region of 17,094 bp, separated by two inverted repeat (IR) regions of 26,752 bp each. It was predicted to contain a total of 129 genes, with an overall GC content of 37.17%. Phylogenetic analysis placed M. candidum in the same clade as species within the Melastomeae tribe of Melastomataceae.

| S-EPMC7800422 | biostudies-literature

The complete chloroplast genome of the monotypic genus of Bulleyia Schltr. (Orchidaceae).

Project description:Bulleyia Schltr. is monotypic and represented only by Bulleyia yunnanensis Schltr., native to the Yunnan of China, Bhutan, and northeast India. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of B. yunnanensis. The cp genome sequence of B. yunnanensis was 159,581 bp in length and presented a typical quadripartite structure consisting of one large single-copy region (LSC, 87,563 bp), one small single-copy region (SSC, 18,714 bp), and two inverted repeat regions (IR, 26,652 bp). Besides, the cp genome encoded 132 genes, including 113 unique genes (79 protein-coding genes, 30 tRNA genes, and four rRNA genes). The phylogenetic analysis suggested that B. yunnanensis be closely related to Pholidota in tribe Arethuseae.

| S-EPMC7646580 | biostudies-literature

Characterization of the complete chloroplast genome sequence of Blastus cochinchinensis (Melastomataceae).

Project description:Blastus Lour. belongs to tribe Sonerileae (Melastomataceae), comprising about 18 species worldwide. Herein, we presented, assembled, and annotated the first complete chloroplast genome of Blastus (B. cochinchinensis). The complete chloroplast genome (cp) size of B. cochinchinensis was 156,005 bp in length, containing a pair of 26,812 bp inverted repeat (IR) regions, which were separated by a large single-copy region (LSC) 85,926 bp and a small single-copy (SSC) region 16,455 bp. The overall GC content of the genome was 37.0%. The whole genome contained 129 unique genes, including 81 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis showed that B. cochinchinens was sister to Barthea barthei. The present study provided B. cochinchinensis genomic information that may be found useful in conservation and molecular phylogenetic studies on Blastus.

| S-EPMC7687533 | biostudies-literature

Characterization of the complete chloroplast genome of Scorpiothyrsus erythrotrichus (Melastomataceae), an endemic to Hainan.

Project description:Scorpiothyrsus erythrotrichus belongs to Melastomataceae. Here, we present its complete plastome. To our knowledge, this is the first reported complete chloroplast genome of S. erythrotrichus. The complete plastome of S. erythrotrichus is 160,731 bp in length with a typical quadripartite structure, consisting of four regions: large single-copy (LSC) region (85,483 bp), small single-copy (SSC) region (17,007 bp), and two inverted repeat regions (IRs, 26,780 bp). It contains 128 genes (79 coding genes, four rRNAs, and 30 tRNAs). The overall GC content is 36.9% and in the LSC, SSC, and IR regions are 34.70%, 30.40%, and 42.50%, respectively. Our study contributes to the molecular phylogenetic studies of Scorpiothyrsus and Melastomataceae.

| S-EPMC8604445 | biostudies-literature

The complete chloroplast genome sequence of Phyllagathi hainanensis (Melastomataceae) and phylogenetic analysis.

Project description:Phyllagathi hainanensis (Merr. et Chun) C. Chen is a small shrubs of Melastomataceae. It is only distributed in Hainan provinces of China. The complete chloroplast genome of P. hainanensis is reported in this study. The complete chloroplast genome of P. hainanensis is 156,123 bp in length with a typical quadripartite structure, consisting of a large single-copy region (LSC, 85,497 bp), a single-copy region (SSC, 17,076 bp), and a pair of inverted repeats (IRs, 26,775 bp). There are 129 genes annotated, including 37 transfer RNA genes, 8 ribosomal RNA genes, and 84 proteincoding genes. The complete plastome sequence of P. hainanensis will provide a useful resource for phylogenetic studies in Melastomataceae.

| S-EPMC8635600 | biostudies-literature