Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: Primula filchnerae Knuth is an endangered species endemic to China. Its complete chloroplast genome was reported in this study for the first time. The whole chloroplast genome was 151, 443 base pairs in length with 131 genes, including 66 protein-coding genes, 37 tRNAs, and 4 rRNAs. In addition, the accD was inferred to be a pseudogene. Phylogenetic analysis showed a sister relationship between P. filchnerae and P. sinensis Sabine ex Lindl.

SUBMITTER: Lu Y

PROVIDER: S-EPMC7781951 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

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 Primula obconica (Primulaceae).

Project description:We report the complete chloroplast genome of Primula obconica, a popular house-plant all over the world. The complete chloroplast genome of P. obconica was sequenced using an Illumina Miseq platform. The circular genome is 153,694?bp in length and comprises a large single copy (LSC, 84,485?bp) region and a small single copy (SSC, 17,689?bp) region, which are separated by a pair of inverted repeats (IRa and IRb, 25,760?bp each). The overall GC content is 37.2%. The P. obconica chloroplast genome encodes 113 unique genes, including 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Phylogenetic analysis based on 18 chloroplast genomes indicates that P. obconica is closely related to the clade of Primula sect. Carolinella, sect. Corusoides and sect. Monocarpicae.

| S-EPMC7687417 | biostudies-literature

The complete chloroplast genome of a distylous-homostylous species, Primula homogama (Primulaceae).

Project description:Primula homogama F. H. Chen & C. M. Hu (Primulaceae) is endemic to the Emei Mountain of China. In this study, we characterized the complete chloroplast genome of P. homogama based on next-generation sequencing (NGS). The complete chloroplast genome of P. homogama was 154,677 bp in size with a typical quadripartite structure, containing a large single-copy (LSC) region of 85,299 bp and a small single-copy (SSC) region of 17,816 bp. These two regions were separated by a pair of inverted repeat regions (IRs), each of 25,781 bp. A total of 130 functional genes were encoded, consisted of 86 protein-coding genes (PCG), 36 tRNA genes, and eight ribosomal RNA (rRNA) genes.

| S-EPMC7872557 | biostudies-literature

The complete chloroplast genome of the ornamental plant Primula violaris (Primulaceae).

Project description:Primula violaris is a perennial herb distributed throughout the western part of Hubei Province and the southern part of Shaanxi Province, China. We present on of the first reports of the complete chloroplast genome sequence for P. violaris. The complete chloroplast genome was 153,630 bp in size, including a large single-copy (LSC) region of 84,526 bp, a small single-copy (SSC) region of 17,812 bp, and a pair of inverted repeat (IR) regions of 25,646 bp. There were 130 genes in the chloroplast genome, including 86 CDSs, 36 transfer RNA (tRNA) genes, and eight rRNA genes. Phylogenetic analysis showed that P. violaris is closely related to P. oreodoxa. (NC_050848).

| S-EPMC8635539 | biostudies-literature

The complete chloroplast genome of Primula tsiangii W. W. Smith (Primulaceae): a karst endemic primrose in Southwest China.

Project description:Primula tsiangii W. W. Smith is a karst endemic species in Southwest China. Here, we report the complete chloroplast genome of P. tsiangii. The chloroplast (cp) genome was determined to be 153,281 bp and the GC contents was 37.2%. The sequence includes a large single copy (LSC) region of 84,524 bp, a small single copy (SSC) region of 17,357 bp, and two separated inverted regions of 25,700 bp each. It contains 127 unique genes, including 82 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. This is the first report of cp genomes for karst endemic primrose, and will be useful for the genetic diversity of karst plants.

| S-EPMC7706616 | biostudies-literature

The complete chloroplast genome sequence of Pellacalyx yunnanensis: an endangered species in China.

Project description:Pellacalyx yunnanensis is an endangered plant species occurring in Yunnan province of China. The first complete chloroplast genome (cpDNA) sequence of P. yunnanensis was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 163,743?bp in length, contains a large single-copy region (LSC) of 91,075?bp and a small single-copy region (SSC) of 18,668?bp, which were separated by a pair of inverted repeats (IR) regions of 27,000?bp. The genome contains 128 genes, including 83 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 35.7%, and the corresponding values of the LSC, SSC, and IR regions are 33.0%, 29.6%, and 42.3%, respectively. Further phylogenomic analysis showed that P. yunnanensis clustered in a unique clade in family Rhizophoraceae.

| S-EPMC7707691 | biostudies-literature

The complete chloroplast genome sequence of Michelia wilsonii: an endangered species in China.

Project description:The first complete chloroplast genome (cpDNA) sequence of Michelia wilsonii was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 160,100 bp in length, contains a large single-copy region (LSC) of 88,162 bp and a small single-copy region (SSC) of 18,786 bp, which were separated by a pair of inverted repeats (IR) regions of 26,576 bp. The genome contains 132 genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Further phylogenomic analysis showed that M. wilsonii closed to Michelia odora and Michelia yunnanensis in Michelieae tribe of the Magnoliaceae family.

| S-EPMC7748524 | biostudies-literature

The complete chloroplast genome of Primula helodoxa, a species endemic to China.

Project description:Primula helodoxa Balf.f. is a species endemic to southeastern China distributed in Tengchong county of Yunnan Province. Here is the first time to report the complete chloroplast genome sequence of P. helodoxa. The complete chloroplast genome was 151,909 bp in length, containing a large single-copy (LSC) region of 83192 bp, a small single-copy (SSC) region of 17,797 bp, and a pair of inverted repeats (IRs) regions of 25,460 bp. There are 137 genes in total, 91 protein-coding genes, eight rRNA genes, and 38 transfer RNA genes. The phylogenetic tree showed relative relationship of P. helodoxa and P. chrysochlora.

| S-EPMC7748870 | 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 sequence of Abies chensiensis (Pinaceae: Abietoideae), an endangered species endemic to China.

Project description:Chloroplast (cp) genome sequences became a widely used tool for evolutionary and phylogenetic studies in plants. Abies chensiensis (Pinaceae: Abietoideae) is an endangered species endemic to China. To understand its evolutionary characteristics, the complete chloroplast genome of the A. chensiensis has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 121,784?bp in length and without a typical quadripartite structure due to the loss of IR region. The total GC content of whole genome sequence is 38.3%. The chloroplast genome encodes 109 genes, including 75 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Among them, 35 genes involved in photosynthesis, while 58 genes involved in self-replication. The Maximum-Likelihood phylogenetic analysis showed a strong sister relationship with A. nephrolepis and A. koreana in Abietoideae. Our findings provide fundamental information for further evolutionary and phylogenetic researches of Abietoideae.

| S-EPMC7800204 | 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