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

ABSTRACT: 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.

SUBMITTER: Chen S

PROVIDER: S-EPMC7706616 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

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

Chen Sheng S Yan Xiaokai X Hao Gang G Xu Yuan Y

Mitochondrial DNA. Part B, Resources 20190717 2

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 ...[more]

PMID: 33365655

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 sequence of Primula filchnerae Knuth (Primulaceae), an endangered species in China.

Project description: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.

| S-EPMC7781951 | biostudies-literature

Complete chloroplast genome of an endangered endemic tree, handeliodendron bodinieri (levl.) rehder (sapindaceae) from karst forests of southwest China.

Project description:Handeliodendron bodinieri (Sapindaceae) is an endangered monotypic species endemic to the karst forests in southwest China whose populations are now fragmented and the total number of individuals evidently decreased. In this research, we characterized the chloroplast (cp) genome of H. bodinieri using genome skimming. The whole cp genome was 155,291 bp long and comprised 137 genes, including 8 unique rRNAs, 40 tRNAs, and 89 protein-coding genes. The overall guanine-cytosine content of H. bodinieri cp genome was 37.8%. The phylogenetic analysis suggested that H. bodinieri is closely related to the genus Mangifera. This study will be useful for future studies on conservation genetics of this economically important endemic plant.

| S-EPMC7707296 | 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 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

Development of 13 microsatellite markers in the endangered Sinai primrose (Primula boveana, Primulaceae).

Project description:UNLABELLED: PREMISE OF THE STUDY:We developed microsatellite markers for the endangered plant Primula boveana, the Sinai primrose, and assessed the cross-transferability of these markers to six related taxa. • METHODS AND RESULTS:DNA sequences containing microsatellites were isolated from a microsatellite-enriched library. We obtained successful amplification of 13 microsatellite primer pairs, seven of which were polymorphic in P. boveana. Eleven of these primers successfully cross-amplified to related taxa. • CONCLUSIONS:The markers reported herein will be useful to characterize the genetic diversity of the endangered P. boveana and to evaluate its mating system, and have the potential to be useful for similar studies in close relatives.

| S-EPMC4105029 | biostudies-literature

Complete plastid genome of Primula calliantha Franch. (Primulaceae): an alpine ornamental plant endemic to Hengduan Mountain, China.

Project description:Primula calliantha Franch. is an alpine species with an ornamental value that is endemic to the Hengduan Mountains of southwest China. Here, we sequenced and assembled its plastid complete genome, which is a circular molecule of 151,954 bp and contains a large single-copy (83,820 bp) and a small single-copy (17,814 bp) region, separated by a pair of inverted repeats (25,160 bp). There are 131 genes, 86 protein-coding, 37 tRNAs, and 8 rRNAs in the plastome, of which 114 genes, 80 CDSs, 30 tRNAs, and 4 rRNAs are unique, respectively. The P. calliantha plastid genome shows a high level of synteny with its close relatives, P. chionantha, P. purdomii, and P. woodwardii. Phylogenetic analysis based on 60 complete chloroplast genomes of Primulaceae confirmed its delimitation in Primula.

| S-EPMC8366611 | 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

Polyploid evolution and Pleistocene glacial cycles: A case study from the alpine primrose Primula marginata (Primulaceae).

Project description:BACKGROUND:Recent studies highlighted the role of Pleistocene climatic cycles in polyploid speciation and of southern Alpine refugia as reservoirs of diversity during glacial maxima. The polyploid Primula marginata, endemic to the southwestern Alps, includes both hexaploid and dodecaploid cytotypes that show no ecological or morphological differences. We used flow cytometry to determine variation and geographic distribution of cytotypes within and between populations and analyses of chloroplast (cp) and nuclear ribosomal (nr) DNA sequences from the Internal Transcribed Spacer (ITS) region to infer the evolutionary history of the two cytotypes and the auto- vs. allopolyploid origin of dodecaploid populations. RESULTS:We did not detect any intermediate cytotypes or variation of ploidy levels within populations. Hexaploids occur in the western and dodecaploids in the eastern part of the distributional range, respectively. The cpDNA and nrDNA topologies are in conflict, for the former supports shared ancestry between P. marginata and P. latifolia, while the latter implies common origins between at least some ITS clones of P. marginata and P. allionii. CONCLUSIONS:Our results suggest an initial episode of chloroplast capture involving ancestral lineages of P. latifolia and P. marginata, followed by polyploidization between P. marginata-like and P. allionii-like lineages in a southern refugium of the Maritime Alps. The higher proportion of ITS polymorphisms in dodecaploid than in hexaploid accessions of P. marginata and higher total nucleotide diversity of ITS clones in dodecaploid vs. hexaploid individuals sequences are congruent with the allopolyploid hypothesis of dodecaploid origin.

| S-EPMC3444416 | biostudies-literature