Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Reevesia thyrsoidea (Malvaceae).

ABSTRACT: Reevesia thyrsoidea Lindl. is an important ornamental plant with horticultural, industrial, and timber usages. In this study, we reported a complete chloroplast genome of R. thyrsoidea, which was quadripartite and 161,786 bp in size, including two inverted repeats (25,466 bp for each) that separated one large single-copy (90,565 bp) and one small single-copy (20,289 bp) regions. The chloroplast genome contained 131 unique genes (86 protein-coding, 37 tRNA, and 8 rRNA), and 17 of them were double copies. Phylogenetic analysis using the chloroplast genome data indicated that R. thyrsoidea was sister to the species in the family Malvaceae.

SUBMITTER: Quan G

PROVIDER: S-EPMC7720718 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome of Callianthe picta (Malvaceae).

Project description:Callianthe picta likes a warm and humid climate, is resistant to barrenness, and is easy to reproduce. Its petals and leaves can promote blood circulation and remove blood stasis, and can also be used to relax the muscles and collaterals. In this study, we sequenced the complete chloroplast genome sequence of C. picta to investigate its phylogenetic relationship in the family Abutilon. The complete chloroplast size of C. picta is 160,398 bp, including a large single-copy (LSC) region of 89,088 bp, a small single-copy (SSC) region of 20,138 bp, a pair of invert repeats (IRs) regions of 25,586 bp. The GC content of the whole complete chloroplast genome is 37.0%. We annotated 128 genes in the genome in detail, including 84 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicated that C. picta was closely related to Abutilon theophrati.

| S-EPMC8667874 | biostudies-literature

The complete chloroplast genome of Malvaviscus penduliflorus (Malvaceae)

Project description:Abstract In this study, we assembled the complete chloroplast (cp) genome of Malvaviscus penduliflorus using high-throughput Illumina sequencing reads. The resulting plastome assembly displayed a typical quadripartite structure with a total length of 160,332 bp, containing a pair of inverted repeat regions (IRs) of 26,313 bp separated by a large single-copy region (LSC) of 88,750 bp and a small single-copy region (SSC) of 18,956 bp. The M. penduliflorus cp genome contained 128 genes, and its overall GC content was 36.96%. Phylogenetic analysis among M. penduliflorus and five other Malvaceae species demonstrated that M. penduliflorus was closely related to Urena procumbens and Hibiscus cannabinus. The M. penduliflorus cp genome presented in this study will lay a good foundation for further genetic and genomic studies of the genus Malvaviscus as well as Malvaceae.

| S-EPMC10443977 | biostudies-literature

The complete chloroplast genome of Hibiscus Taiwanensis (Malvaceae).

Project description:Hibiscus taiwanensis S. Y. Hu is an ornamental plant of Hibiscus, native to Taiwan. Here, we reported the complete chloroplast genome of H. taiwanensis. The chloroplast genome of H. taiwanensis was 161,056 bp in length, containing a couple of inverted repeat (IR) regions of 26,300 bp, a large single-copy (LSC) region of 89,538 bp and a small single-copy (SSC) region of 18,918 bp. The complete chloroplast genome annotation revealed a total of 131 genes, including 85 protein-coding genes, 7 rRNA genes, and 37 tRNA genes. The entire GC content was 36.9%. Phylogenetic tree analyses indicated that H. taiwanensis was closely clustered with H. rosa-sinensis and H. syriacus.

| S-EPMC7687590 | biostudies-literature

Complete chloroplast genome sequence of Hibiscus trionum Linnaeus 1753 (Malvaceae).

Project description:Hibiscus trionum L. is an annual herbaceous plant belonging to the Malvaceae family. It is native to Central Africa, however, is now naturalized in Europe and Asia including Korea. Here, we report the complete chloroplast genome assembly of H. trionum. The complete chloroplast genome comprises 160,530 bp and is divided into four typical regions: a large single-copy region of 89,272 bp, a pair of inverse repeats of 26,152 bp each, and a small single-copy region of 18,954 bp. A total of 131 genes were identified in this chloroplast, of which 86 were protein-coding, 37 were tRNA, and 8 were rRNA genes. The results of this study will serve as a key reference for further research on Hibiscus speciation.

| S-EPMC9639535 | biostudies-literature

Complete chloroplast genome of a semi-mangrove plant Hibiscus tiliaceus (Malvaceae).

Project description:Hibiscus tiliaceus is a semi-mangrove species that is widely distributed in tropical and subtropical coastal areas around the world. Here, the complete chloroplast (cp) genome sequence of H. tiliaceus was assembled and characterized. The cp genome was 161,748 bp in length, consisting of a large single copy (LSC) region of 89,190 bp and a small single copy (SSC) region of 19,616 bp, which were separated by a pair of 26,471 bp inverted repeat (IR) regions. The overall GC content was 36.88%. A total of 131 genes, including 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes were identified. Phylogenetic tree reconstructed by 15 complete cp genomes revealed that H. tiliaceus was sister to the congeneric species H. cannabinus.

| S-EPMC8204996 | biostudies-literature

Complete chloroplast genome sequence of Heritiera angustata (Malvaceae): an endangered plant species.

Project description:Heritiera angustata (Malvaceae) is an evergreen tree distributed in the Chinese provinces of Hainan and Yunnan and in Cambodia. In China, it is listed as 'Endangered' (EN) China Red List of Higher Plants, although it is not protected by law. The complete chloroplast (cp) genome sequence of this threatened species is reported in this study, based on high-throughput sequencing (Illumina). The complete cp genome is 168, 953?bp in length, containing a pair of inverted repeat regions (IRs) of 34,491?bp, a large single copy (LSC) region of 89,054?bp, and a small single copy (SSC) region of 10,917?bp. The cp genome contains 129 genes, consisting of 85 protein-coding genes, 36 tRNA genes and eight rRNA genes. The overall AT content in the cp genome of H. angustata is 63.2%. The phylogenetic analyses indicate that there is a close relationship between H. angustata and Firmiana pulcherrima.

| S-EPMC7800114 | biostudies-literature

The complete chloroplast genome of a medicinal plant, Abutilon theophrasti Medik. (Malvaceae).

Project description:Abutilon theophrasti Medik. is an annual weed, widely distributed in Asia and Europe. The complete chloroplast genome reported here is 160,446 bp in length, including two inverted repeats (IRs) of 25,064 bp, which are separated by a large single-copy (LSC) and a small single-copy (SSC) of 89,089 and 21,229 bp, respectively. The whole chloroplast genome of A. theophrasti contains 113 distinct genes, including 79 protein-coding genes, 30 transfer RNA, and four ribosome RNA. Phylogenetic analysis indicated that A. theophrasti is located in the basal position in Malveae.

| S-EPMC7703700 | biostudies-literature

Complete Chloroplast Genome Sequence of Hibiscus cannabinus and Comparative Analysis of the Malvaceae Family.

Project description:Kenaf (Hibiscus cannabinus) is one of the most fast-growing bast in the world and belongs to the family Malvaceae. However, the systematic classification and chloroplast (cp) genome of kenaf has not been reported to date. In this study, we sequenced the cp genome of kenaf and conducted phylogenetic and comparative analyses in the family of Malvaceae. The sizes of H. cannabinus cp genomes were 162,903 bp in length, containing 113 unique genes (79 protein-coding genes, four rRNA genes, and 30 tRNA genes). Phylogenetic analysis indicated that the cp genome sequence of H. cannabinus has closer relationships with Talipariti hamabo and Abelmoschus esculentus than with Hibiscus syriacus, which disagrees with the taxonomical relationship. Further analysis obtained a new version of the cp genome annotation of H. syriacus and found that the orientation variation of small single copy (SSC) region exists widely in the family of Malvaceae. The highly variable ycf1 and the highly conserved gene rrn32 were identified among the family of Malvaceae. In particular, the explanation for two different SSC orientations in the cp genomes associated with phylogenetic analysis is discussed. These results provide insights into the systematic classification of the Hibiscus genus in the Malvaceae family.

| S-EPMC7090147 | biostudies-literature

The complete chloroplast genome and phylogenetic analysis of Sida szechuensis matsuda (Malvaceae).

Project description:Sida szechuensis Matsuda is an economically and medicinally important plant. Here, we report the first chloroplast (cp) genome of the genus Sida (S. szechuensis). The complete cp genome is 159,878 bp in length with an overall GC content of 36.9% and consists of a large single copy region (LSC, 89,426 bp), a small single copy region (SSC, 114,715 bp), and a pair of inverted repeat regions (IRa and IRb, 25,288 bp). The genome encodes 111 unique genes, including 78 protein-coding genes, 29 tRNA genes, 4 rRNA genes, and 1 pseudogene. Phylogenetic analysis constructed using the maximum likelihood (ML) method showed that Sida was closely related to Malvastrum and Malva.

| S-EPMC8567882 | biostudies-literature

The complete chloroplast genome of Diplodiscus trichospermus and phylogenetic position of Brownlowioideae within Malvaceae.

Project description:BackgroundMalvaceae is an economically important plant family of 4,225 species in nine subfamilies. Phylogenetic relationships among the nine subfamilies have always been controversial, especially for Brownlowioideae, whose phylogenetic position remains largely unknown due to the lack of samples in previous analysis datasets. To greatly clarify the phylogenetic relationship of Malvaceae, we newly sequenced and assembled the plastome of Diplodiscus trichospermus taxonomically located in Brownlowioideae, and downloaded the allied genomes from public database to build a dataset covering all subfamily members of Malvaceae.ResultsThe annotation results showed that the plastome of Diplodiscus trichospermus has a typical quadripartite structure, comprising 112 unique genes, namely 78 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The total length was 158,570 bp with 37.2% GC content. Based on the maximum likelihood method and Bayesian inference, a robust phylogenetic backbone of Malvaceae was reconstructed. The topology showed that Malvaceae was divided distinctly into two major branches which were previously recognized as Byttneriina and Malvadendrina. In the Malvadendrina clade, Malvoideae and Bombacoideae formed, as always, a close sister clade named as Malvatheca. Subfamily Helicteroideae occupied the most basal position and was followed by Sterculioideae which was sister to the alliance of Malvatheca, Brownlowioideae, Dombeyoideae, and Tilioideae. Brownlowioideae together with the clade comprising Dombeyoideae and Tilioideae formed a sister clade to Malvatheca. In addition, one specific conservation SSR and three specific palindrome sequences were observed in Brownlowioideae.ConclusionsIn this study, the phylogenetic framework of subfamilies in Malvaceae has been resolved clearly based on plastomes, which may contribute to a better understanding of the classification and plastome evolution for Malvaceae.

| S-EPMC10521492 | 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