Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete plastid genome of the endangered species Paraisometrum mileense (Gesneriaceae) endemic to China.

ABSTRACT: Paraisometrum mileense is a unique species of Paraisometrum endemic to south-west China, which is a "100-years-lost" plant and was rediscovered in 2006. In this paper, complete plastid genome of P. mileense is firstly assembled and characterized. The length of total plastid genome is 153,259 bp consisting of a large single-copy region (LSC) of 84,293 bp, a small single-copy region (SSC) of 18,162 bp, and two inverted repeat regions (IRs) of 25,402 bp. In total, 113 genes are predicted, including 80 protein-coding genes (PCGs), four rRNA genes and 29 tRNA genes. Phylogenetic analysis indicated that P. mileense with the other eight Gesneriaceae species formed a clade with a 100% bootstrap support.

SUBMITTER: Meng J

PROVIDER: S-EPMC7707429 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Complete plastid genome sequence of the rare and endangered medicinal herb Psammosilene tunicoides, endemic to China.

Project description:Psammosilene tunicoides W.C. Wu et C.Y. Wu, a monotypic species and endemic to Southwest China, is a rare and endangered traditional medicinal herb with satisfactory effects on multifold pathology. In order to provide crucial data for protection, we reported and analyzed the complete plastid genome of P. tunicoides as the foundation of germplasm conservation. The complete plastid genome is a typical quadripartite circular molecule of 153,957 bp in length, including a large single copy (LSC) region of 83,972 bp and a small single copy (SSC) region of 17,495 bp separated by two inverted repeat (IR) regions of 26,245 bp. In total of 111 unique genes were predicted, including 78 protein-coding genes (PCGs), 29 transfer RNA genes, and four ribosomal RNA genes. The overall GC content of P. tunicoides is 36.5%. The phylogenetic analysis revealed that P. tunicoides and Dianthus caryophyllus formed an independent clade with a 100% bootstrap support.

| S-EPMC7687624 | biostudies-literature

Complete plastid genome of Litsea honghoensis Liou 1933, an endangered evergreen species in China.

Project description:Litsea honghoensis Liou is an endangered tree endemic to south China. In this study, the first complete plastid genome of L. honghoensis was presented, which had a length of 152,605 base pairs (bp) with a GC content of 39.20%. The genome consisted of a large single-copy (LSC) region of 93,560 bp, a small single-copy (SSC) region of 18,905 bp, and two inverted repeat regions (IRa and IRb) of 20,070 bp. There were 125 genes in the plastid genome, including 81 protein-coding genes, 36 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Phylogenomic analysis based on 52 complete plastomes of Laureae in the family Lauraceae supports the close relationships among L. honghoensis, Lindera communis, Lindera nacusua, Lindera angustifolia, and Lindera glauca.

| S-EPMC9518278 | biostudies-literature

The complete chloroplast genome of Zelkova schneideriana (Rosales: Ulmaceae), an Endangered species endemic to China.

Project description:Zelkova schneideriana Hand.-Mazz. (Ulmaceae) is an endangered species endemic to China. In this study, we reported its complete chloroplast (cp) genome based on Illumina pair-end sequencing. The whole genome was 158,999?bp long, consisting of a pair of inverted repeat (IR) regions of 26,427?bp, a large single copy (LSC) region of 87,397?bp and a small single copy (SSC) region of 18,748?bp. The cp genome contained 133 genes, including 88 protein-coding genes (80 PCG species), 37 tRNA genes (30 tRNA species), and eight rRNA genes (4 rRNA species). The overall G+C content of the whole genome was 35.6%, and the corresponding values of the LSC, SSC, and IR regions were 33.0, 28.3, and 42.4%, respectively. The maximum likelihood phylogenetic analysis of 25 selected chloroplast genomes demonstrated that Z. schneideriana was closely related to Ulmus macrocarpa and Ulmus pumila.

| S-EPMC7800157 | biostudies-literature

The complete chloroplast genome of Sauvagesia rhodoleuca, an endangered species endemic to China.

Project description:Sauvagesia rhodoleuca is an endangered and national key protected species of China, with limited natural distribution in Guangdong and Guangxi, Southern China. Here we reported the first complete chloroplast genome of S. rhodoleuca using genome skimming approach. The chloroplast genome is 157,300 bp in length, with a large single-copy region (LSC) of 86,021 bp and a small single-copy region (SSC) of 18,137 bp separated by a pair of inverted repeats (IRs) of 26,571 bp. It encodes 112 unique genes, including 80 protein-coding genes, 28 transfer RNA genes, and four ribosomal RNA genes. Phylogenetic analysis results strongly supported that S. rhodoleuca was closely related to Medusagyne oppositifolia.

| S-EPMC8284140 | biostudies-literature

Characterization of the complete plastid genome of Psammosilene tunicoides (Caryophyllaceae), an endangered medical herb endemic to south-western China.

Project description:Psammosilene tunicoides is an endangered medical herb endemic to south-western China. In this study, the complete plastid genome of the species was characterized and assembled using the next-generation DNA sequencing method. The plastid genome is 153,978?bp in length, including a large single copy (LSC) region of 83,981?bp and a small single copy (SSC) region of 17,489?bp, which were separated by a pair of inverted repeat (IR) regions of 26,254?bp. The genome encoded 112 unique genes, including 78 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA genes. The overall GC content of the whole genome is 36.49%. The phylogenetic analysis based on 17 plastid genome of Caryophyllaceae revealed that P. tunicoides nested within the tribe Caryophylleae with strong support value.

| S-EPMC7706586 | biostudies-literature

The complete chloroplast genome of an endangered endemic herb species in China, Primula filchnerae (Primulaceae).

Project description:Primula filchnerae (Primulaceae) is an endangered endemic herb species in China. In this study, we characterized the complete chloroplast genome of P. filchnerae based on next generation sequencing (NGS). The chloroplast genome of P. filchnerae was 151,547 bp in size, containing a large single-copy (LSC) region of 82, 662 bp and a small single-copy (SSC) region of 17,749 bp. These two regions were separated by a pair of inverted repeat regions (IRs), each of 25,568 bp. A total of 130 functional genes were encoded, consisted of 86 protein-coding genes, 36 tRNA genes, and eight rRNA genes.

| S-EPMC7706512 | biostudies-literature

The complete chloroplast genome of Fritillaria yuminensis, a rare and endangered species endemic to China.

Project description:Fritillaria yuminensis is a medicinal species endemic to northwest Xinjiang, China. The complete chloroplast genome sequence of F. yuminensis was sequenced by Illumina Hiseq platform. The complete cp genome was 151,813?bp in length, containing a pair of inverted repeats (IRa and IRb) of 26,377?bp, a large single copy (LSC) of 81,533 bp and a small single copy (SSC) of 17,526?bp, respectively. The overall GC contents was 36.9%. A total of 114 genes were annotated, including 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. A maximum-likelihood phylogenetic analysis indicated that F. yuminensis was closely related to F. tortifolia and F. verticillata.

| S-EPMC7800183 | biostudies-literature

The complete chloroplast genome of Gymnospermium kiangnanense (Berberidaceae): an endangered species endemic to Eastern China.

Project description:Gymnospermium kiangnanense is an endangered species in the family Berberidaceae. In this study, we assembled the chloroplast (cp) genome of G. kiangnanense and reconstructed the phylogenetic tree of Berberidaceae based on the complete cp genome. The cp genome of G. kiangnanense is 160,136?bp in length, comprising a pair of inverted repeat (IR) regions (26,424?bp) separated by a large single-copy (LSC) region (87,580?bp) and a small single-copy (SSC) region (19,708bp). The genome encodes 111 unique genes, consisting of 77 different protein-coding genes, 30 transfer RNA, and 4 ribosomal RNA genes, with 18 duplicated genes in the inverted repeats. Phylogenetic analysis indicates that G. kiangnanense is sister to G. microrrhynchum, and the Gymnospermium clade is closely related with Nandina.

| S-EPMC7799652 | biostudies-literature

Characterization of the complete chloroplast genome of Alsophila spinulosa, an endangered species endemic to China.

Project description:Tree fern Alsophila spinulosa is an endangered relic plant in the world. It is currently on the International Union for Conservation of Nature (IUCN) red list of threatened species. In this study, we first assembled the complete chloroplast (cp) genome of A. spinulosa by Illumina paired-end reads data. The whole genome was 156,661 bp, consisting of a pair of inverted repeats of 24,364 bp, large single copy region and a small single copy region (70,352 and 21,624 bp in length, respectively). The cp genome contained 133 genes, including 92 protein-coding genes, 33 trRNA genes, and eight rRNA genes. The overall GC content of the whole genome was 40.4%. A neighbour-joining phylogenetic analysis demonstrated a close relationship between A. spinulosa and Cystoathyrium chinense Ching.

| S-EPMC7510675 | biostudies-literature

The complete chloroplast genome of Epimedium elachyphyllum Stearn (Berberidaceae), an endangered species endemic to China.

Project description:Epimedium elachyphyllum, which belongs to Berberidaceae, is only distributed in Guizhou province of China. In this study, the complete chloroplast (cp)genome of E. elachyphyllum was sequenced and assembled. The circular genome is 157,201 bp in length, which comprises of a large single-copy region (LSC, 88,519 bp), a small single-copy region (SSC, 17,042 bp), and a pair of inverted repeat regions (IRa and IRb, 25,820 bp). The genome of E. elachyphyllum contains 112 unique genes, of which 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 18 complete cp genome sequences indicated that E. elachyphyllum was closely related to E. dolichostemon.

| S-EPMC7748844 | 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