Browse
Submit Data
Databases
API
Help

Dataset Information

43 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Sun HY

PROVIDER: S-EPMC7872557 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

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

Sun Hua-Ying HY Zhong Li L Guo Yong-Jie YJ Zhou Wei W Wu Zhi-Kun ZK

Mitochondrial DNA. Part B, Resources 20210208 2

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 o ...[more]

PMID: 33659689

Similar Datasets

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 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 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

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 vialii (Primulaceae), an ornamental plant.

Project description:Primula vialii Delavay ex Franch. (1905) is an alpine species with an ornamental value. In this study, we sequenced, assembled, and annotated the chloroplast genome of P. vialii. The results showed that it was a double-stranded, closed circular DNA with 154,897 bp in length, comprising a small single-copy (SSC) region of 17,766 bp, a large single-copy (LSC) region of 85,379 bp and a pair of inverted repeat (IR) regions of 25,876 bp. A total of 113 unique genes were annotated, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis revealed that P. vialii is closely related to Primula flaccida. The cp genomic data will be useful for systematics and evolutionary studies of Primula.

| S-EPMC10236967 | biostudies-literature

Development of microsatellite markers for Primula oreodoxa (Primulaceae), a distylous-homostylous species.

Project description:Premise of the studyMicrosatellite markers were developed for a distylous-homostylous species, Primula oreodoxa (Primulaceae), to investigate the mating patterns and gene flow in the species.Methods and resultsUsing RAD sequencing, 42,777 contigs were generated. A total of 1566 putative simple sequence repeat (SSR) loci were identified by MISA, and 1433 primer sets were designed. After initial screening of 107 SSR loci, 24 loci displayed polymorphism. The number of alleles per locus detected ranged from one to 11 in the sampled populations of P. oreodoxa. Levels of observed and expected heterozygosity for each locus ranged from 0 to 0.917 and 0 to 0.816, respectively. Fifteen and 13 of these loci could be successfully amplified in the two congeneric species P. obconica and P. heucherifolia, respectively.ConclusionsThe SSR markers developed here will be valuable for genetic analysis and elucidation of mating patterns in P. oreodoxa.

| S-EPMC5991559 | biostudies-literature

The complete chloroplast genome of Primula amethystina subsp. argutidens (Primulaceae).

Project description:Primula amethystina subsp. argutidens (Franchet) W. W. Smith & H. R. Fletcher (1942) is a blooming plant of the family Primulaceae. Here, we sequenced, assembled, and annotated the complete chloroplast (cp) genome of P. amethystina subsp. argutidens. The cp genome of P. amethystina subsp. argutidens is 151,560 bp in length with a GC content of 37%. The assembled genome has a typical quadripartite structure, containing a large single-copy (LSC) region of 83,516 bp, a small single-copy (SSC) region of 17,692 bp, and a pair of inverted repeat (IR) regions of 25,176 bp. The cp genome contains 115 unique genes, including 81 protein-coding genes, four rRNA genes, and 30 tRNA genes. Phylogenetic analysis showed that P. amethystina subsp. argutidens was closely related to P. amethystina.

| S-EPMC10332233 | biostudies-literature

High-throughput microsatellite marker development for the distylous herb Primula mistassinica (Primulaceae).

Project description:Twelve microsatellite markers were developed for Primula mistassinica, a distylous, diploid arctic-alpine plant. The markers will be used to investigate the landscape genetics of a disjunct population on Isle Royale, Michigan, and the phylogeographic patterns of the species. • We used Roche/454 high-throughput technology to sequence microsatellite-enriched regions in the P. mistassinica genome. We developed 12 polymorphic microsatellite primer sets. These loci contained di-, tri-, and tetranucleotide repeats with two to nine alleles per locus when assessed in 23 individuals. • Understanding the historical movements of P. mistassinica will provide insight to the survival prospects of current Arctic plant populations, which face the pressures of global, anthropogenic climate change.

| S-EPMC4103446 | biostudies-literature

Characterization of 24 microsatellite markers in Primula chungensis (Primulaceae), a distylous-homostylous species, using MiSeq sequencing.

Project description:Primula chungensis is a species with considerable floral and mating-system variation, including distylous (outcrossing), homostylous (selfing) and mixed populations that contain both outcrossing and selfing forms. We isolated 24 microsatellite markers from P. chungensis using Illumina MiSeq sequencing. Polymorphism and genetic diversity were then measured based on a sample of 24 individuals from a natural population in southern Tibet. All loci were polymorphic with the number of alleles per locus ranging from 2 to 4. The observed and expected heterozygosity ranged from 0 to 1 and 0.219 to 0.708, respectively. The microsatellite markers we have identified will serve as valuable tools for the investigation of the population genetic structure and phylogeography of P. chungensis and will inform models of the evolutionary history of mating systems in the species.

| S-EPMC6112135 | biostudies-literature

The complete chloroplast genome sequence of Primula medogensis (Primulaceae) and its phylogeny.

Project description:Primula medogensis W.B Ju, B. Xu & X.F. Gao 2023, a new species categorized under P. sect. Cordifoliae, was officially described in 2023. Given its recent classification, the genetic resources for this species are currently very limited. Here, we sequenced and assembled the first complete chloroplast genome of P. medogensis using Illumina sequencing technology. The complete chloroplast genome of P. medogensis is 151,486 bp in length, exhibiting a typical quadripartite structure. It consists of a large single-copy region (LSC; 83,407 bp) and a small single-copy region (SSC;17675 bp), separated by a pair of inverted repeat regions (IRs; 25202 bp). A total of 131 genes were annotated, including 86 protein-coding, 37 tRNA, and eight rRNA genes. The overall GC content was 37.1%. Phylogenetic analysis of 59 Primula species revealed a close relationship between P. medogensis and P. calliantha subsp. bryophila.

| S-EPMC11485687 | biostudies-literature