Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Nicotiana plumbaginifolia.

ABSTRACT: Nicotiana plumbaginifolia Vivianiis 1802 is an annual herb, native to Mexico and South America. It is one of the most widely distributed tobacco species. As a wild tobacco, N. plumbaginifolia has provided several economically important disease-resistance genes to cultivated tobacco. We assembled the complete chloroplast genome of N. plumbaginifolia. The chloroplast genome is 155,945 bp in length, which includes a large single copy region (86,621 bp), a small single copy region (18,528 bp) and two separated inverted repeat regions (25,398 bp). A total of 117 unique genes were annotated, consisting of 84 protein-coding genes, 29 tRNA genes and 4 rRNA genes. Based on chloroplast genomes of 17 Nicotiana species, phylogenetic analyses indicated that N. plumbaginifolia was closely related to N. suaveolens and N. amplexicaulis.

SUBMITTER: Tong Z

PROVIDER: S-EPMC8788338 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Complete chloroplast genome sequence of Nicotiana tabacum TN90 (Solanaceae).

Project description:This study reported the complete nucleotide sequence of the Nicotiana tabacum TN90 chloroplast (cp) genome. The cpDNA was 155 992 bp in length and contained 133 individual genes (79 protein encoding genes, 30 tRNA genes and four rRNA genes). Maximum-likelihood (ML) phylogenetic tree for 17 species with Arabidopsis thaliana, Oryza sativa, and Anomochloa marantoidea as an outgroup resulted in a single tree with - lnL =542 222.71, where the Nicotiana tabacum TN90 plastid was clustered with three previous reported Nicotiana species: N. tomentosiformis, N. undulata and N. tabacum. The TN90 variety of tobacco cp genome sequence reported in this study will accelerate tobacco improvement in the future.

| S-EPMC7800119 | biostudies-literature

The complete chloroplast genome sequence of Nicotiana debneyi (Solanaceae).

Project description:In present study, we report the complete chloroplast genome of Nicotiana debneyi, a species endemic to eastern coast of Australia. The total genome size of N.debneyi is 156,073 bp in length, containing a large single-copy region of 86,672 bp, a small single-copy region of 18,581 bp, and two inverted repeat regions of 25,410 bp. The all GC content of N.debneyi chloroplast genome is 38.4%. It encodes a total of 129 unique genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes, of which seven tRNA, four rRNA and seven protein-coding genes are duplicated in the IR. Sixteen genes contain a single intron, and only two genes have two introns. Phylogenetic analysis results strongly supported that N.debneyi was closely related to Nicotiana sylvestris and Nicotiana tabacum.

| S-EPMC7995905 | biostudies-literature

Complete chloroplast genome sequence of Coyote tobacco (Nicotiana attenuata, Solanaceae).

Project description:In this study, we announce the complete chloroplast genome sequence of Nicotiana attenuata. The genome sequence of 155,941?bp consists of two inverted repeat (IRa and IRb) regions of 25,438?bp each, a large single-copy (LSC) region of 86,513?bp and a small single-copy (SSC) region of 18,524?bp. The overall GC content is 37.9% and the GC contents of LSC, IRs, and SSC are 36%, 43.2%, and 32.1%, respectively. The plastome with 129 annotated unique genes includes 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Using the whole chloroplast genome sequences alignment of 16 Solanaceae species a phylogenetic hypothesis is presented validating the position of N. attenuata within Nicotianeae.

| S-EPMC7800028 | biostudies-literature

Complete Chloroplast Genome of Nicotiana otophora and its Comparison with Related Species.

Project description:Nicotiana otophora is a wild parental species of Nicotiana tabacum, an interspecific hybrid of Nicotiana tomentosiformis and Nicotiana sylvestris. However, N. otophora is least understood as an alternative paternal donor. Here, we compared the fully assembled chloroplast (cp) genome of N. otophora and with those of closely related species. The analysis showed a cp genome size of 156,073 bp and exhibited a typical quadripartite structure, which contains a pair of inverted repeats separated by small and large single copies, containing 163 representative genes, with 165 microsatellites distributed unevenly throughout the genome. Comparative analysis of a gene with known function across Nicotiana species revealed 76 protein-coding sequences, 20 tRNA sequences, and 3 rRNA sequence shared between the cp genomes. The analysis revealed that N. otophora is a sister species to N. tomentosiformis within the Nicotiana genus, and Atropha belladonna and Datura stramonium are their closest relatives. These findings provide a valuable analysis of the complete N. otophora cp genome, which can identify species, elucidate taxonomy, and reconstruct the phylogeny of genus Nicotiana.

| S-EPMC4906380 | biostudies-literature

Assembly and phylogenetic analysis of complete chloroplast genome of a wild tobacco Nicotiana Attenuata.

Project description:Nicotiana attenuata (N. attenuata) is an annual herb that induces nicotine, volatiles and phenolics in response to damage. In this study, we assembled the complete chloroplast (cp) genome of N. attenuata with the length of 155,886 bp, which was composed of a large single copy region (LSC) of 86,602 bp, a small copy (SSC) region of 18,518 bp and a pair of inverted repeats (IR) of 25,383 bp. This typical cp genome contains 112 unique genes, including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Phylogenetic analysis of 32 plant cp genomes based on 76 conserved protein-coding genes shows that N. attenuata is evolutionarily close to N. tabacum, then Capsicum annuum. The complete cp genome sequence of N. attenuata may provide a crucial foundation for the study of evolution, molecular biology and genetic engineering in Nicotiana species.

| S-EPMC7800318 | biostudies-literature

Keteleeria cyclolepis complete chloroplast genome

Project description:Keteleeria cyclolepis complete chloroplast genome Raw sequence reads

| PRJNA723268 | ENA

Complete chloroplast genome of Sedum sarmentosum and chloroplast genome evolution in Saxifragales.

Project description:Comparative chloroplast genome analyses are mostly carried out at lower taxonomic levels, such as the family and genus levels. At higher taxonomic levels, chloroplast genomes are generally used to reconstruct phylogenies. However, little attention has been paid to chloroplast genome evolution within orders. Here, we present the chloroplast genome of Sedum sarmentosum and take advantage of several available (or elucidated) chloroplast genomes to examine the evolution of chloroplast genomes in Saxifragales. The chloroplast genome of S. sarmentosum is 150,448 bp long and includes 82,212 bp of a large single-copy (LSC) region, 16.670 bp of a small single-copy (SSC) region, and a pair of 25,783 bp sequences of inverted repeats (IRs).The genome contains 131 unique genes, 18 of which are duplicated within the IRs. Based on a comparative analysis of chloroplast genomes from four representative Saxifragales families, we observed two gene losses and two pseudogenes in Paeonia obovata, and the loss of an intron was detected in the rps16 gene of Penthorum chinense. Comparisons among the 72 common protein-coding genes confirmed that the chloroplast genomes of S. sarmentosum and Paeonia obovata exhibit accelerated sequence evolution. Furthermore, a strong correlation was observed between the rates of genome evolution and genome size. The detected genome size variations are predominantly caused by the length of intergenic spacers, rather than losses of genes and introns, gene pseudogenization or IR expansion or contraction. The genome sizes of these species are negatively correlated with nucleotide substitution rates. Species with shorter duration of the life cycle tend to exhibit shorter chloroplast genomes than those with longer life cycles.

| S-EPMC3799696 | biostudies-literature

The complete chloroplast genome of Agave angustifolia

Project description:Abstract Agave angustifolia is commonly used for the production of bacanora, a kind of fermented and distilled beverage in Mexico. In the present study, we have successfully assembled its chloroplast genome. The full length of the genome is 157,274 bp with the GC content of 37.84%. There is a large single copy region (LSC) of 85,895 bp, a pair of inverted repeat regions (IR) of 26,575 bp and a small single copy region (SSC) of 18,229 bp in the genome. A total of 132 genes are annotated in the cp genome. Among these, there are 86 protein-coding genes, 38 tRNAs and 8 rRNAs. Phylogenetic analysis reveals that A. angustifolia is closely related with A. H11648.

| S-EPMC8547807 | biostudies-literature

Complete chloroplast genome comparisons for Pityopsis (Asteraceae).

Project description:Pityopsis includes several regionally and one federally endangered species of herbaceous perennials. Four species are highly localized, including the federally endangered P. ruthii. The genus includes several ploidy levels and interesting ecological traits such as drought tolerance and fire-dependent flowering. Results from previous cladistic analyses of morphology and from initial DNA sequence studies did not agree with one another or with the infrageneric taxonomic classification, with the result that infrageneric relationships remain unresolved. We sequenced, assembled, and compared the chloroplast (cp) genomes of 12 species or varieties of Pityopsis to better understand generic evolution. A reference cp genome 152,569 bp in length was assembled de novo from P. falcata. Reads from other sampled species were then aligned to the P. falcata reference and individual chloroplast genomes were assembled for each, with manual gapfilling and polishing. After removing the duplicated second inverted region, a multiple sequence alignment of the cp genomes was used to construct a maximum likelihood (ML) phylogeny for the twelve cp genomes. Additionally, we constructed a ML phylogeny from the nuclear ribosomal repeat region after mapping reads to the Helianthus annuus region. The chloroplast phylogeny supported two clades. Previously proposed clades and taxonomic sections within the genus were largely unsupported by both nuclear and chloroplast phylogenies. Our results provide tools for exploring hybridity and examining the physiological and genetic basis for drought tolerance and fire-dependent flowering. This study will inform breeding and conservation practices, and general knowledge of evolutionary history, hybridization, and speciation within Pityopsis.

| S-EPMC7769439 | biostudies-literature

The complete chloroplast genome of Ormosia ferruginea

Project description:Chloroplast genome of Ormosia ferruginea

| PRJEB51808 | ENA