Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete chloroplast genome sequence of Hopea chinensis (Dipterocarpaceae), a rare and critically endangered species.

ABSTRACT: Hopea chinensis (Dipterocarpaceae) is a rare and critically endangered species. Here, we first report and characterize its complete chloroplast genome sequence based on Illumina paired-end sequencing data. The complete plastid genome was 152,054 bp, which contained inverted repeats (IR) of 21,702 bp separated by a large single-copy (LSC) and a small single-copy (SSC) of 20,462 bp and 88,188 bp, respectively. The cpDNA contains 129 genes, comprising 83 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC content of the plastome is 37.4%. The phylogenetic analysis of 18 selected chloroplast genomes demonstrated that H. chinensis was close to the species Parashorea macrophylla.

SUBMITTER: Shi Y

PROVIDER: S-EPMC7707529 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome of a critically endangered tree species, Hopea reticulata (Dipterocarpaceae).

Project description:Hopea reticulata Tardieu is a critically endangered tree species distributed in limited regions in Thailand, Vietnam and Hainan Island of China. In this study, we reported the complete chloroplast genome sequence of H. reticulata assembled from pair-end reads generated by Illumina sequencing. The circular chloroplast genome is 151,407 bp in length and comprises a large single copy region of 84,352 bp, a small single copy region of 19,733 bp, and a pair of inverted repeats of 23,661 bp each. The complete genome encodes 129 functional genes, including 83 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC content of the chloroplast genome was 37.4%. Phylogenetic analysis showed that H. reticulata is sister to H. hainanensis with strong bootstrap support.

| S-EPMC7782000 | biostudies-literature

Complete chloroplast genome sequence of Maytenus guangxiensis (celastraceae), a rare and critically endangered species endemic to China.

Project description:Maytenus guangxiensis (Celastraceae) is a rare and critically endangered species endemic to China. Here, we first report and characterize its complete chloroplast genome sequence based on Illumina paired-end sequencing data. The complete plastid genome was 157,102 bp, which contained inverted repeats (IR) of 26,476 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 85,559 bp and 18,591 bp, respectively. The cpDNA contains 130 genes, comprising 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. The overall GC content of the plastome is 37.3%. The phylogenetic analysis of 19 selected chloroplast genomes demonstrated that M. guangxiensis was close to the species Catha edulis.

| S-EPMC7748633 | biostudies-literature

Complete chloroplast genome sequence of Stephania kwangsiensis (Menispermaceae), a rare and critically endangered species endemic to China.

Project description:Stephania kwangsiensis (Menispermaceae) is a rare and critically endangered species endemic to China. Here, we first report and characterize its complete chloroplast genome sequence based on Illumina paired-end sequencing data. The complete plastid genome was 156,624 bp, which contained inverted repeats (IR) of 24,348 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 87,759 bp and 20,169 bp, respectively. The cpDNA contains 132 genes, comprising 85 protein-coding genes, 37 tRNA genes, eight rRNA genes, and two processed pseudogenes. The overall GC content of the plastome is 38.4%. The phylogenetic analysis of 18 selected chloroplast genomes demonstrated that S. kwangsiensis is related to the congeneric S. japonica.

| S-EPMC7748438 | biostudies-literature

Complete chloroplast genome of endangered species Dipterocarpus retusus Blume (Dipterocarpaceae) and its phylogenetic implications.

Project description:Dipterocarpus retusus Blume is an endangered species on the IUCN Red List. In this study, we reported the complete chloroplast (cp) genome of D. retusus (GenBank accession number: OP271853). The cp genome was 154,303 bp long, with a large single-copy (LSC) region of 85,586 bp and a small single-copy (SSC) region of 20,273 bp separated by a pair of inverted repeats (IRs) of 24,222 bp. It encodes 128 genes, including 84 protein-coding genes, 36 tRNA genes, and eight ribosomal RNA genes. We also reconstructed the cp genome phylogeny of Dipterocarpus, which indicated D. retusus was closely related with the sympatric species D. gracilis. This study may contribute valuable information to the phylogenetic relationships within the genus Dipterocarpus.

| S-EPMC11370694 | biostudies-literature

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

The complete chloroplast genome of Pterospermum kingtungense, a Critically Endangered species.

Project description:Pterospermum kingtungense (Pterospermum, Sterculiaceae) is a Critically Endangered species. In this study, we reported a complete chloroplast genome of P. kingtungense based on high-throughput sequencing data. The size of chloroplast genome was 162,929 bp, including a large single-copy region (LSC: 91,535 bp) and a small single-copy region (SSC: 20,464 bp), separated by a pair of inverted repeats (IRa and IRb: 25,465 bp). The genome encoded 126 genes in total, including 81 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the P. kingtungense chloroplast genome is 36.39%. The phylogenetic tree showed P. kingtungense clustered together with the family Sterculiaceae.

| S-EPMC7801019 | biostudies-literature

Complete chloroplast genome sequence of Semiliquidambar cathayensis (hamamelidaceae), a rare and endangered species endemic to China.

Project description:Semiliquidambar cathayensis (Hamamelidaceae) is a rare and endangered species endemic to China. Here, we first report and characterize the complete chloroplast genome sequence of S. cathayensis based on Illumina paired-end sequencing data. The complete plastid genome was 160,406 bp in length, which contained two inverted repeats (IRs) of 26,282 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 88,920 bp and 18,922 bp, respectively. The cpDNA contains 132 genes, comprising 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes and one processed pseudogene. The overall GC content of the plastome is 37.9%. The phylogenetic analysis of 20 selected chloroplast genomes demonstrated that S. cathayensis was close to the species Liquidambar formosana.

| S-EPMC7707359 | 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

Isolation and characterization of twelve polymorphic microsatellite markers in the endangered Hopea hainanensis (Dipterocarpaceae).

Project description:Microsatellite markers were isolated and characterized for Hopea hainanensis Merrill & Chun, an endangered tree species with scattered distribution in Hainan Island and northern Vietnam. Twenty-six microsatellite markers were developed based on next-generation sequencing data and were genotyped by capillary electrophoresis on an ABI 3730xl DNA Analyzer. Twelve markers were found to be polymorphic in H. hainanensis. GENODIVE analyses indicated that the number of alleles ranged from 2 to 6 per locus, and the observed and expected heterozygosity varied from 0 to 0.755 and from 0.259 to 0.779, respectively. Primer transferability was tested with Hopea chinensis Hand.-Mazz. and Hopea reticulata Tardieu, in which 3 and 7 microsatellite markers were found to be polymorphic, separately. The results showed that H. reticulata and H. hainanensis had similar levels of genetic diversity. A neighbor joining dendrogram clustered all individuals into two major groups, one of which was exclusively constituted by H. hainanensis, while the other consisted of two subgroups, corresponding to H. reticulata and H. chinensis, respectively. The 12 polymorphic microsatellite markers could be applied to study genetic diversity, population differentiation, mating system, and fine-scale spatial genetic structures of H. hainanensis as well as its close relatives, facilitating the conservation and restoration of these endangered but valuable Hopea species.

| S-EPMC7790650 | biostudies-literature

Intraspecific Variation of Samara Dispersal Traits in the Endangered Tropical Tree Hopea hainanensis (Dipterocarpaceae).

Project description:Propagule dispersal is a crucial life history stage, which affects population recruitment and regeneration as well as community structure and functions. The windborne process of samara dispersal is affected not only by samara traits and other plant traits, but also by environmental factors. Therefore, studying samara traits related to its dispersal and intraspecific variation in relation to other plant traits and environmental factors could help to understand population distribution and dynamics. Hopea hainanensis, a Dipterocarpaceae tree species dominant in lowland rainforests in Hainan (China) but endangered due to anthropogenic disturbances, is dispersed mainly by wind because of its sepal-winged samara. Here, we measured dispersal-related intraspecific samara traits of H. hainanensis, and analyzed their variation and correlation in relation to plant height, DBH (diameter at breast height), and elevation plant location. Great variations in the samara traits existed, and the variations were larger within than among individuals, which indicated a "bet-hedging" strategy of this species. Plant height, DBH, and elevation explained slight variation in the samara traits. Samara dispersal potential is mainly affected by the samara mass and morphological traits. Samara settling velocity was significantly positively correlated with fruit mass, seed mass, length and width, as well as samara wing loading, and negatively correlated with wing mass ratio, wing area, and wing aspect ratio. Substantial proportions of intraspecific variation in samara dispersal are explained by the samara mass and morphological traits. Natural regeneration with human-aided dispersal is necessary for recovering the H. hainanensis population. This finding contributes to the generalization of trait-based plant ecology, modeling of seed dispersal in tropical forests, and conservation and recovery of rare and endangered species such as H. hainanensis.

| S-EPMC7691252 | 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