Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Tang L

PROVIDER: S-EPMC8008875 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

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

The complete chloroplast genome of Madhuca hainanensis (Sapotaceae), an endemic and endangered timber species in Hainan Island, China.

Project description:Madhuca hainanensis Chun & F.C.How is an endangered and endemic species in Hainan Island, and it was ranked as a VU (Vulnerable) species in China. In this study, we reported its complete chloroplast (cp) genome sequence based on high throughput sequencing data. The complete cp genome was 159,630 bp in length, containing two short inverted repeat (IRs) of 26,093 bp, a large single copy (LSC) region of 88,846 bp and a small single copy (SSC) region of 18,598 bp. Totally, the cp genome contained 131 genes, including 86 protein coding genes (PCG), eight rRNA genes and 37 tRNAs. The GC contents of this genome was 36.8%. A maximum likelihood (ML) phylogenetic analysis indicates that M. hainanensis is closely related to Sinosideroxylon wightianum.

| S-EPMC7971245 | 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

Genetic diversity and population structure in the endangered tree Hopea hainanensis (Dipterocarpaceae) on Hainan Island, China.

Project description:Hopea hainanensis Merrill & Chun (Dipterocarpaceae) is an endangered tree species restricted to Hainan Island, China and a small part of Northern Vietnam. On Hainan Island, it is an important indicator species for tropical forests. However, because of its highly valued timber, H. hainanensis has suffered from overexploitation, leading to a sharp population decline. To facilitate the conservation of this species, genetic diversity and population structure were assessed using 12 SSR markers for 10 populations sampled across Hainan Island. Compared to non-threatened Hopea species, H. hainanensis exhibited reduced overall genetic diversity and increased population differentiation (AMOVA: FST = 0.23). Bayesian model-based clustering and principal coordinate analysis consistently assigned H. hainanensis individuals into three genetic groups, which were found to be widespread and overlapping geographically. A Mantel test found no correlation between genetic and geographical distances (r = 0.040, p = 0.418). The observed genetic structure suggests that long-distance gene flow occurred among H. hainanensis populations prior to habitat fragmentation. A recent population bottleneck was revealed, which may cause rapid loss of genetic diversity and increased differentiation across populations. Based on these findings, appropriate strategies for the long-term conservation of the endangered species H. hainanensis are proposed.

| S-EPMC7703895 | 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

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

Gastrodiabawanglingensis (Orchidaceae, Epidendroideae), a new species from Hainan Island, China.

Project description:Gastrodiabawanglingensis, a new species of Orchidaceae from Hainan Island, China, is described and illustrated. It is morphologically similar to G.theana, G.albidoides and G.albida with dwarf habits, scarcely opening flowers, elongated fruit stems, curved and fleshy perianth tubes and similar columns and lips, but can be easily distinguished from them by having a pair of lateral wings bent outwards at the apex of the column and lateral wings with acuminate tips lower than the anther. According to the IUCN Red List Categories and Criteria, the new species is assessed as Endangered (EN). The plastome of G.bawanglingensis is greatly reduced and reconfigured with approximately 30876 bp in size and 25.36% in GC content. Morphological characteristics and molecular phylogenetic results based on chloroplast gene sequences support the recognition of G.bawanglingensis as a new species within Gastrodia.

| S-EPMC10209714 | biostudies-literature

Characterization of the complete plastome sequence of Torreya grandis var. jiulongshanensis (Taxaceae), a rare and endangered plant species endemic to Zhejiang province, China.

Project description:Torreya grandis var. jiulongshanensis (Taxaceae) is an evergreen tree endemic to Zhejiang province, China, and it is listed as a rare plant species with extremely small populations. In our present study, we assembled the chloroplast (CP) genome of T. grandis var. jiulongshanensis using high-throughput sequencing data generated by an Illumina Hiseq X Ten platform. The results indicate that the complete CP genome is 136,705 bp in size with an overall guanine and cytosine content of 35.5%. The plastome has lost its quadripartite structure. In the CP genome, there are a total of 119 genes, including 82 protein-coding genes, 4 ribosomal RNA genes, and 33 transfer RNA genes. Phylogenetic analysis revealed that T. grandis var. jiulongshanensis is a sister species to T. grandis.

| S-EPMC7748455 | biostudies-literature

The complete chloroplast genome of Cymbidium serratum (Orchidaceae): a rare and Endangered species endemic to Southwest China.

Project description:Cymbidium serratum is a dominant species in the large orchid family with beautiful flowers, thick petals, and long flowering periods, and has a long history of cultivation in Southwest China. However, its wild resources have been threatened with extinction due to environmental degradation and artificial exploitation. In this study, the complete chloroplast genome of C. serratum was obtained through Illumina sequencing. The size of chloroplast genome of C. serratum is 149,998 bp, including large single-copy (LSC) and small single-copy (SSC) regions over 84,854 bp and 13,926 bp, respectively, and two inverted repeats (IRs) of 25,609 bp. The total GC content was 37.11%. The chloroplast genome contains 129 genes, including 83 protein-coding genes, 8 rRNA genes, and 38 tRNA genes. The maximum-likelihood phylogenetic tree indicated that C. serratum is a sister species with the clade composed of C. faberi and C. goeringii. The complete chloroplast genome of C. serratum will contribute to protecting this highly endangered species, and provide genetic information about genetic diversity and sustainable use.

| S-EPMC7782322 | biostudies-literature

Euphorbia Section Hainanensis (Euphorbiaceae), a New Section Endemic to the Hainan Island of China From Biogeographical, Karyological, and Phenotypical Evidence.

Project description:Euphorbia hainanensis is an endangered species endemic to the tropical Hainan Island in southern China and of historical importance for Chinese medicine. It is currently the only unplaced species of the genus Euphorbia (Euphorbiaceae) due to its isolated island distribution and debated placement by a previous molecular phylogenetic study. We sequenced nuclear ITS and chloroplast rbcL and ndhF for newly collected accessions of E. hainanensis and additional Euphorbia species found in Hainan, and analyzed the sequences in the context of the entire genus together with published data. All gene regions highly supported that E. hainanensis occupied an isolated phylogenetic position, showing no close affinity with any known Euphorbia sections suggesting it was a new section. ITS placed E. hainanensis sister to sect. Crossadenia (subgenus Chamaesyce) from Brazil with an estimated divergence time of 9.3-30.6 Mya while the chloroplast markers placed E. hainanensis at a position sister to the entire New World clade of Euphorbia subgenus Chamaesyce. In addition, our karyological results suggested a close affinity between E. hainanensis and the New World species of Euphorbia subg. Chamaesyce, with which shared the same chromosome number 2n = 28 and basic chromosome number x = 7. Phenotypically, E. hainanensis is unique with no close resemblance to other species in Euphorbia subg. Chamaesyce. Based on its isolated biogeographical, karyological, and phenotypical position, we propose a new section E. subgenus Chamaesyce section Hainanensis that might origin from long distance dispersal events because collective evidences showed a close affinity between the species from the Old World with those from the New World.

| S-EPMC5968112 | 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