Browse
Submit Data
Databases
API
Help

Dataset Information

51 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete chloroplast genome of an endangered plant, Alseodaphne Hainanensis.

ABSTRACT: Alseodaphne hainanensis is an endangered species with inhabiting dense forest along valleys, and it is one of the representative species of tropical rain forest in Hainan Island. In this paper, we reported and characterized the complete chloroplast genome sequence of the species assembled from short reads generated by Illumina sequencing. The size of chloroplast was 152,829 bp, a pair of inverted repeats (IRs) separating a large single copy and a small single copy, the size of IRs, LSC and SSC were 20,036 bp, 93,872 bp and 18,885 bp, respectively. A total of 129 genes were predicted, including 81 protein-coding genes, 38 tRNA, 8 rRNA, and 2 pseudogene. Phylogenetic analysis confirmed the position of A. hainanensis within the order Laurales.

SUBMITTER: Yang Y

PROVIDER: S-EPMC7687619 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Complete chloroplast genome of an endangered plant, Alseodaphne Hainanensis.

Yang Yong Y Chen Yu-Kai YK Chen Qing Q

Mitochondrial DNA. Part B, Resources 20190710 2

Alseodaphne hainanensis is an endangered species with inhabiting dense forest along valleys, and it is one of the representative species of tropical rain forest in Hainan Island. In this paper, we reported and characterized the complete chloroplast genome sequence of the species assembled from short reads generated by Illumina sequencing. The size of chloroplast was 152,829 bp, a pair of inverted repeats (IRs) separating a large single copy and a small single copy, the size of IRs, LSC an ...[more]

PMID: 33365458

Similar Datasets

The complete chloroplast genome of the endangered species Cephalotaxus hainanensis (Cephalotaxaceae).

Project description:Cephalotaxus hainanensis is an endangered tree endemic to China with high medicinal values. In this study, the complete chloroplast genome of C. hainanensis was de novo assembled using Illumina high-throughput sequencing technology. The whole chloroplast genome was 136,877?bp long with an asymmetric base composition (32.6% A, 17.6% C, 17.4% G and 32.4% T). The genome annotation predicted a total of 114 genes, including 82 protein-coding genes, 28 tRNA genes, and four rRNA genes. The neighbour-joining phylogenetic analysis based on 41 complete chloroplast genome sequences showed that C. hainanensis was more closely related to the congeneric C. sinensis. The assembled chloroplast genome of C. hainanensis will provide useful genomic data both for the phylogenetic research of Cephalotaxus and the conservation of this endangered species.

| S-EPMC7800532 | biostudies-literature

The complete chloroplast genome of Horsfieldia hainanensis, an Endangered species with extremely small populations.

Project description:Horsfieldia hainanensis is an Endangered species with extremely small populations, inhabiting the dense forest in ravines. It has high development and utilization value in the seed oil, fatty acids, volatile oils, and liposoluble constituent. In this study, the complete chloroplast genome of Horsfieldia hainanensis was sequenced. It is 155,774 bp in size with a typical quadripartite structure: a large single-copy (LSC) region of 87,124 bp, a small single-copy (SSC) region of 20,612 bp, and 2 inverted repeat (IR) regions of 24,020 bp. The genome contains 117 genes, including 75 protein-coding genes, 34 tRNA genes, and 8 rRNA genes, 13 genes have one intron and 3 three genes have two introns. The overall GC contents of the chloroplast genome was 39.1%. The phylogenetic tree based 11 complete chloroplast genome sequences of Magnoliales shows that H. hainanensis is closely related to Horsfieldia pandurifolia.

| S-EPMC7706491 | biostudies-literature

The complete chloroplast genome of an endangered plant-Nomocharis aperta.

Project description:Nomocharis aperta is an endangered and endemic species with high ornamental value in China. In this study, we reported a complete chloroplast genome of N. aperta, which was de novo assembled using the next-generation sequencing data. The complete chloroplast genome is 152,845 in length, including a large single copy region of 70,506 bp and a small single copy region of 17,468 bp and two inverted repeat regions of 26,520 bp. A total of 130 functional genes were encoded, consisting of 84 protein-coding genes, 36 transfer RNA genes, and 8 ribosomal RNA genes. The overall AT content of the chloroplast genome is 63.00%. In addition, phylogenetic analysis with the reported chloroplast genomes showed that N. aperta is nested within Lilium and close to L. henricii, L. bakerianum and L. taliense. It indicates that the study on the relationship between Nomocharis and Lilium needs more Nomocharis and Lilium complete chloroplast genome, especially some key species like N. aperta.

| S-EPMC7720958 | 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

The complete chloroplast genome sequence of Keteleeria hainanensis (Pinaceae).

Project description:Keteleeria hainanensis is an endemic species with extremely narrow distribution. In this study, the complete genome of K._hainanensis was sequenced and analyzed. The genome size is 117,366?bp and it contains two short inverted repeat regions of 1,272?bp, which was separated by a large single-copy (LSC) region of 74,819?bp and a small single-copy (SSC) region of 40,003?bp. The GC content of this genome was 38.57%. The chloroplast genome contained 103 unique genes, including 74 protein-coding gene, 25 tRNA genes, and 4 rRNA gene. Phylogenetic analysis base on 11 chloroplast genomes indicated that K. hainanensis is closely related to K. davidiana.

| S-EPMC7706628 | biostudies-literature

The complete chloroplast genome of Aristolochia hainanensis Merr. (Aristolochiaceae).

Project description:Aristolochia hainanensis Merr. 1922, a well-known Chinese medicinal plant, is distributed in Hainan Province and Guangxi Province, China. In the current study, we sequenced the complete chloroplast genome of A. hainanensis. The complete plastome genome was 159,764 bp in length, with a GC content of 38.8%, showing a typical quadripartite organization. The genome contained a large single-copy (LSC) of 89,134 bp, a small single-copy (SSC) of 19,306 bp, and a pair of inverted repeats (IRs) of 25,662 bp. A total of 113 genes were annotated, including 79 protein-coding genes, 30 tRNAs, and four rRNAs. The trnK-UUU gene contained the longest intron (2644 bp). The topology of the maximum-likelihood tree supported a close relationship between A. hainanensis and A. kwangsiensis.

| S-EPMC9487948 | biostudies-literature

The complete chloroplast genome sequence of endangered plant Trachycarpus nanus (Arecaceae).

Project description:Trachycarpus nanus is an endangered plant that is endemic to southwest of China. In the present study, the complete chloroplast genome of this species was assembled and characterized using whole genome next-generation sequencing. The complete chloroplast genome showed a circular genome of 158,713 bp size with 36.6% GC content. The genome is of typical structure and contain a pair of inverted repeat (IR) regions with 27,240 bp, separated by one large single-copy (LSC) with 86,395 bp, and one small single-copy (SSC) regions with 17,838 bp. The genome contained 132 genes, including 86 protein-coding genes, 8 rRNA genes and 38 tRNA genes. A phylogenetic tree reconstructed based on 21 chloroplast genomes reveals that Trachycarpus nanus is most related with Chamaerops humilis. The information provides important genetic basis for the species' future studies on phylogenetic and utilization.

| S-EPMC8168733 | biostudies-literature

The complete chloroplast genome of the endangered plant Paphiopedilum wardii (Orchidaceae).

Project description:Chloroplast (cp) genome sequences provide a valuable source for phylogenetic analysis, which becomes a popular tool for population and phylogeny in a recent report. Here, the complete chloroplast genome of the Paphiopedilum wardii has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 169,820 bp in size and comprises a pair of inverted repeat (IR) regions of 33,641 bp each, a large single-copy (LSC) region of 98,872 bp and a small single-copy (SSC) region of 3666 bp. The total GC content is 33.8%, while the corresponding values of the IR regions, LSC, and SSC and are 38.7%, 31.7% and 26.7%, respectively. The chloroplast genome contains 151 genes, including 91 protein-coding genes, eight ribosomal RNA genes and 52 transfer RNA genes. Two genes (ndhA and ndhB) are pseudogenized or lost in its cpDNA. The maximum-likelihood phylogenetic analysis showed a close relationship with P. armeniacum in Orchidaceae. Our findings provide useful information for phylogenetic and evolutionary research of Paphiopedilum species.

| S-EPMC7800172 | 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

Complete chloroplast genome sequence of Annamocarya sinensis (Juglandaceae), an endangered perennial plant.

Project description:Annamocarya sinensis (Juglandaceae) is a tertiary relict tree restricted to southeastern China and northern Vietnam. Here, we first report and characterize its complete chloroplast genome based on Illumina paired-end sequencing data. The complete plastid genome was 160,065 bp, which contained inverted repeats (IR) of 25,786 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 89,759 bp and 18,734 bp, respectively. The cpDNA contains 130 genes, comprising 85 protein-coding genes, 36 tRNA genes, 8 rRNA genes, and one processed pseudogene. The overall GC content of the plastome is 36.3%. The phylogenetic analysis of 18 selected chloroplast genomes demonstrated that A. sinensis was close to the species Carya kweichowensis.

| S-EPMC7707428 | biostudies-literature