Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete plastome sequence of Nephelium topengii (Merr.) H. S. Lo (Sapindaceae): an endemic species in Hainan.

ABSTRACT: Nephelium topengii is an evergreen tree of the Sapindaceae family, which can be used as timber. Here, we report and characterize the complete plastome of N. topengii. The complete plastome is 162,944 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 30,092 bp, a large single-copy (LSC) region of 85,909 bp and a small single-copy (SSC) region of 16,851bp. The plastome contains 130 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA gene, 4 unique rRNA genes (5S rRNA, 4.5S rRNA, 23S rRNA and 16S rRNA). The overall A/T content in the plastome of N. topengii is 62.30%. The complete plastome sequence of N. topengii will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Sapindaceae.

SUBMITTER: Zhu ZX

PROVIDER: S-EPMC7781924 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Complete plastome sequence of Monoon laui (Merr.) B. Xue and R.M.K. Saunders, 2012: an endemic species in Hainan.

Project description:Monoon laui (Merr.) B. Xue and R.M.K. Saunders 2012 is produced in Hainan province. The trunk is straight, the wood texture is straight, and the material is slightly soft, which is suitable for furniture and building materials. In our study, we report and characterize the complete plastome of M. laui The complete length of the plastome of M. laui possesses 161,181 bp, including a large single-copy (LSC) of 89,556 bp, small single-copy (SSC) of 18,977 bp, and two inverted repeats (IRs) of 26,313 bp. The overall G/C content in the plastome of M. laui is 39.13%. The plastome contains 257 genes, consisting of 130 protein-coding genes (16 of which are duplicated in the IR), 37 tRNA genes (seven of which are duplicated in the IR), and eight rRNA genes (5S rRNA, 4.5S rRNA, 16S rRNA, and 23S rRNA). Here, we explore the phylogenetic relationships and make contributions to the conservation genetics of the specie of M. laui using the complete plastome sequence.

| S-EPMC9467546 | biostudies-literature

Complete plastome sequences of Diospyros maclurei Merr. and Diospyros hainanensis Merr. (Ebenaceae): two endemic species in Hainan Province, China.

Project description:Diospyros is the largest genus (about 485 species) in Ebenaceae. It is a deciduous or evergreen tree or shrub. It grows in pantropical and extending into temperate regions. Here, we report and characterize the complete plastid genome sequences of D. maclurei Merr. and D. hainanensis Merr. in an effort to provide genomic resources useful for promoting their systematics research and potential economic development. The complete plastome of D. maclurei is 157,946?bp in length, including two Inverted Repeat (IR) regions of 26,081?bp, a Large Single-Copy (LSC) region of 87,387?bp, and a Small Single-Copy (SSC) region of 18,397?bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes, and four unique rRNA genes. The overall A/T content in the plastome of D. maclurei is 62.60%. The complete plastome of D. hainanensis is 157,999?bp in length, including two Inverted Repeat (IR) regions of 26,077?bp, a Large Single-Copy (LSC) region of 87,523?bp, and a Small Single-Copy (SSC) region of 18,322?bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes, and four unique rRNA genes. The overall A/T content in the plastome of D. hainanensis is 62.60%. The complete plastome sequences of D. Maclurei and D. hainanensis will provide a useful resource for the conservation genetics of the two species as well as for the phylogenetic studies of Diospyros.

| S-EPMC7799653 | biostudies-literature

Complete plastome sequence of Croton laevigatus Vahl (Euphorbiaceae): an endemic species in Hainan, China.

Project description:Croton laevigatus grows as an evergreen tree or shrub with 15 meters height. It is distributed in the dense or open forests of Hainan province, China. Here, we report and characterize the complete plastome of C. laevigatus in an effort to provide genomic resources useful for promoting its systematics research. The plastome of C. laevigatus is found to possess a total length 162,515 bp with the typical quadripartite structure of angiosperms, contains two Inverted Repeats (IRs) of 26,866 bp, a Large Single-Copy (LSC) region of 90,234 bp and a Small Single-Copy (SSC) region of 18,549 bp. The plastome contains 113 genes, consisting of 79 unique protein-coding genes, 30 unique tRNA genes and four unique rRNA genes. The overall A/T content in the plastome of C. laevigatus is 64.10%. The phylogenetic analysis indicated that C. laevigatus is close to C. tiglium within Euphorbiaceae in this study. The complete plastome sequence of C. laevigatus will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies of Euphorbiaceae.

| S-EPMC7748857 | biostudies-literature

Complete plastome sequence of Ardisia bullata G. H. Huang & G. Hao, an endemic species in Hainan.

Project description:Ardisia bullata G. H. Huang & G. Hao is a small shrubs of Primulaceae. It is only distributed in Hainan provinces of China. It is a plant medicinal value. There is no study on the genome of A. bullata so far. Here, we report and characterize the complete plastid genome sequence of A. bullata in an order to provide genomic resources useful for promoting its conservation. The complete chloroplast genome of A. bullata is 160,176 bp in length with a typical quadripartite structure, consisting of a large single-copy region (LSC, 89,710 bp), a single-copy region (SSC, 18,357 bp), and a pair of inverted repeats (IRs, 26,054 bp). There are 133 genes annotated, including 83 unique protein-coding genes, eight unique ribosomal RNA genes, and 37 transfer RNA genes. The overall G/C content in the plastome of A. bullata is 36.0%. The complete plastome sequence of A. bullata will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Apocynaceae.

| S-EPMC7782065 | biostudies-literature

Complete plastome sequence of Hydnocarpus hainanensis Merr (Achariaceae): an endemic 'vulnerable' tree in South China.

Project description:Hydnocarpus hainanensis Merr. is an evergreen tree with a height of 6-12 m and a diameter at breast height of 50 cm. It is distributed in Guangxi, Guizhou, Hainan, South of Yunnan Province of China. Here, we report and characterize the complete plastid genome sequence of H. hainanensis in an effort to provide genomic resources useful for promoting its conservation and systematics research. The plastome of H. hainanensis is found to possess a total length 163,330 bp with the typical quadripartite structure of angiosperms, containing two inverted repeats (IRs) of 26,870 bp, a large single copy (LSC) region of 91,510 bp and a small single copy (SSC) region of 18,080 bp. The plastome contains 111 genes, consisting of 78 unique protein-coding genes (seven of which are duplicated in the IR: rps 12, rps7, ndhB, ycf2, rpl23, rpl2, and rps 19), 29 unique tRNA genes (seven of which are duplicated in the IR, i.e. trnNGUU , trnRACG, trnAUGC, trnlGAU, trnVGAC, trnLCAA , and trnlCAU ) and four unique rRNA genes (5S rRNA, 4.55S rRNA, 23S rRNA, and 16S rRNA). The overall A/T content in the plastome of H. hainanensis is 63.70%. The phylogenetic analysis indicated that H. hainanensis is close to Salix rorida within Malpighiales. The complete plastome sequence of H. hainanensis will provide a useful resource for the conservation genetics of the one species as well as for the phylogenetic studies of Achariaceae.

| S-EPMC7800351 | biostudies-literature

Complete plastome sequence of Elaeagnus glabra (Elaeagnaceae): an Asian endemic plant species.

Project description:Elaeagnus glabra is an evergreen vine or climbing shrub with 5 m height. It is widespread in southern China. It grows in the sunny forests or forest margins below 1000 m a.s.l. In this paper, we report and describe the complete plastome of E. glabra in order to provide useful genomic data for its systematic research. The complete plastome of E. glabra is 152,555 bp with a typical quadripartite structure of angiosperms. It contains two Inverted Repeats (IRs) of 25,918 bp, a large single-copy (LSC) of 82,408 bp, and a small single-copy (SSC) region of 18,311 bp. The complete plastome contains 129 genes, including 83 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The overall A/T content in the chloroplast genome of E. glabra is 62.90%. The phylogenetic analysis indicated that E. glabra is close to E. loureirii within Elaeagnaceae. The complete plastome of E. glabra will provide useful resources for the development and utilization of this species and the phylogenetic study of Rosales.

| S-EPMC7748609 | biostudies-literature

Complete plastome sequence of Piper laetispicum (Piperaceae): An endemic plant species in South China.

Project description:Piper laetispicum is dioecious climbers woody with 10 m tall, which is an endemic species in China. It grows on trees or rocks in forests (100-600 m) in Guangdong and Hainan Province of China. Here, we report and characterize the complete plastid genome sequence of P. laetispicum in an effort to provide genomic resources useful for promoting its conservation. The complete plastome is 161,721?bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 27,125?bp, a large single copy (LSC) region of 89,224?bp and a small single copy (SSC) region of 18,247?bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA gene, and four unique rRNA genes. The overall A/T content in the plastome of P. laetispicum is 61.70%. The complete plastome sequence of P. laetispicum will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for Piper.

| S-EPMC7800576 | biostudies-literature

Complete plastome sequence of Prunus hypoxantha (Rosaceae), a species endemic in west of China.

Project description:The Chinese endemic species Prunus hypoxantha is of great importance biogeographically, and is distributed in the edge of the Qinghai-Tibetan Plateau. Here, the complete chloroplast genome sequence of P. hypoxantha was assembled based on the Illumina reads. The complete plastome is 158,740 bp in length, with a large single-copy (87,206 bp) region, a small single-copy (18,884 bp) region, and two inverted repeat (26,325 bp) regions. The plastome contains 134 genes. Complete chloroplast genome sequence of P. hypoxantha will provide irreplaceable information in rebuilding the evolutionary history of the Maddenia clade.

| S-EPMC7832505 | biostudies-literature

The plastome of Phaius hainanensis (Orchidaceae): an endangered species endemic to Hainan province, China.

Project description:Phaius hainanensis C. Z. Tang et S. J. Cheng is a species with extremely small populations and is endemic to China. Genetic data of this orchid species is minimal. With the aim to identify appropriate chloroplast markers for the use in conservation biology studies, the plastome of P. hainanenisis was assembled. The plastome of P. hainanensis is 158,314 bp in length and contains a large single copy region of 86,700 bp in length, a small single copy region of 18,452 bp, and a pair of inverted repeats of 26,581 bp. The annotation predicted 114 unique genes, including 80 protein-coding, 30 tRNAs, and four rRNAs. Seventeen genes contained a single intron and two genes (clpP and ycf3) have two introns. The GC content of P. hainanensis is 36.9%. Phylogenetic analysis indicated P. hainanensis is closely related to P. tancarvilleae, and it also supported that Phaius and Calanthe are sister groups. The plastome data reported in this study will contribute to further studies of phylogeny and conservation of Phaius species.

| S-EPMC8008875 | biostudies-literature

Complete plastome sequence of Changiostyrax dolichocarpa (Styracaeae): An endangered (EN) plant species endemic to China.

Project description:Changiostyrax dolichocarpa is a critically endangered plant species occurring in central and southeastern China. Although the systematic position of Changiostyrax was still unclear, morphological characters, plastid and nSSR evidence supported that C. dolichocarpa should be separated from Sinojackia (Styracaceae). Here, we report and characterize the complete plastid genome sequence of C. dolichocarpa in an effort to provide genomic resources useful for promoting its conservation. The complete plastome is 158,821?bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 26,000?bp, a large single copy (LSC) region of 88,038?bp and a small single copy (SSC) region of 18,784?bp. The plastome contains 120 genes, consisting of 83 unique protein-coding genes, 37 unique tRNA gene, and eight unique rRNA genes. The overall A/T content in the plastome of C. dolichocarpa is 62.70%. The complete plastome sequence of C. dolichocarpa will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for Changiostyrax.

| S-EPMC7800059 | 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