Browse
Submit Data
Databases
API
Help

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Tanacetum coccineum.

ABSTRACT: Tanacetum coccineum, a perennial plant of the Tanacetum genus, cultivated as a natural pesticide or ornamental plant widely distributed in many countries. In this research, the complete chloroplast genome sequence of T. coccineum was determined to comprise a 150,143 bp double-stranded circular DNA, including a pair of 24,416 bp inverted repeat regions (IRs), small single copy (SSC) region of 18,389 bp and large single copy (LCS) region of 82,922 bp. An overall GC content was 37.49%, and the corresponding values in IRs, SSC, and LSC regions are 43.16%, 30.88%, and 35.61%, respectively. A total of 129 genes include 84 protein-coding genes, 37 tRNA, and eight rRNA. Four rRNA genes and seven tRNA genes were duplicated in IRs. A phylogenetic tree reconstructed by 38 Composite family chloroplast genomes sequence reveals that T. coccineum is mostly related to Ismelia carinata.

SUBMITTER: Zeng T

PROVIDER: S-EPMC7510654 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Draft Genome of Tanacetum Coccineum: Genomic Comparison of Closely Related Tanacetum-Family Plants.

Project description:The plant Tanacetum coccineum (painted daisy) is closely related to Tanacetum cinerariifolium (pyrethrum daisy). However, T. cinerariifolium produces large amounts of pyrethrins, a class of natural insecticides, whereas T. coccineum produces much smaller amounts of these compounds. Thus, comparative genomic analysis is expected to contribute a great deal to investigating the differences in biological defense systems, including pyrethrin biosynthesis. Here, we elucidated the 9.4 Gb draft genome of T. coccineum, consisting of 2,836,647 scaffolds and 103,680 genes. Comparative analyses of the draft genome of T. coccineum and that of T. cinerariifolium, generated in our previous study, revealed distinct features of T. coccineum genes. While the T. coccineum genome contains more numerous ribosome-inactivating protein (RIP)-encoding genes, the number of higher-toxicity type-II RIP-encoding genes is larger in T. cinerariifolium. Furthermore, the number of histidine kinases encoded by the T. coccineum genome is smaller than that of T. cinerariifolium, suggesting a biological correlation with pyrethrin biosynthesis. Moreover, the flanking regions of pyrethrin biosynthesis-related genes are also distinct between these two plants. These results provide clues to the elucidation of species-specific biodefense systems, including the regulatory mechanisms underlying pyrethrin production.

| S-EPMC9267051 | biostudies-literature

Tanacetum coccineum

Project description:Tanacetum coccineum genome project

| PRJDB12537 | ENA

Tanacetum coccineum

Project description:The complete chloroplast genome of Tacacetum coccineum

| PRJNA606816 | ENA

Tanacetum coccineum

Project description:Tanacetum coccineum overview

| PRJNA811292 | ENA

Complete genome sequence of Ilumatobacter coccineum YM16-304(T.).

Project description:Ilumatobacter coccineum YM16-304(T) (=NBRC 103263(T)) is a novel marine actinobacterium isolated from a sand sample collected at a beach in Shimane Prefecture, Japan. Strain YM16-304(T) is the type strain of the species. Phylogenetically, strain YM16-304(T) is close to Ilumatobacter nonamiense YM16-303(T) (=NBRC 109120(T)), Ilumatobacter fluminis YM22-133(T) and some uncultured bacteria including putative marine sponge symbionts. Whole genome sequence of these species has not been reported. Here we report the complete genome sequence of strain YM16-304(T). The 4,830,181 bp chromosome was predicted to encode a total of 4,291 protein-coding genes.

| S-EPMC3910706 | biostudies-literature

Transcriptional Responses and GCMS Analysis for the Biosynthesis of Pyrethrins and Volatile Terpenes in Tanacetum coccineum.

Project description:Natural pyrethrins have been widely used as natural pesticides due to their low mammalian toxicity and environmental friendliness. Previous studies have mainly focused on Tanacetumcinerariifolium, which contains high levels of pyrethrins and volatile terpenes that play significant roles in plant defense and pollination. However, there is little information on T. coccineum due to its lower pyrethrin content and low commercial value. In this study, we measured the transcriptome and metabolites of the leaves (L), flower buds (S1), and fully blossomed flowers (S4) of T. coccineum. The results show that the expression of pyrethrins and precursor terpene backbone genes was low in the leaves, and then rapidly increased in the S1 stage before decreasing again in the S4 stage. The results also show that pyrethrins primarily accumulated at the S4 stage. However, the content of volatile terpenes was consistently low. This perhaps suggests that, despite T. coccineum and T. cinerariifolium having similar gene expression patterns and accumulation of pyrethrins, T. coccineum attracts pollinators via its large and colorful flowers rather than via inefficient and metabolically expensive volatile terpenes, as in T. cinerariifolium. This is the first instance of de novo transcriptome sequencing reported for T. coccineum. The present results could provide insights into pyrethrin biosynthetic pathways and will be helpful for further understanding how plants balance the cost-benefit relationship between plant defense and pollination.

| S-EPMC8657971 | biostudies-literature

The complete chloroplast genome of dalmatian pyrethrum (<i>Tanacetum cinerariifolium</i> (Trevir.) Sch. Bip. (Asteraceae)), the source of the natural insecticide pyrethrin.

Project description:Tanacetum cinerariifolium is an endemic species of the eastern Adriatic coast that synthesizes the natural insecticide pyrethrin. We have characterized the complete chloroplast genome of the species and analyzed its phylogeny within the Asteraceae family. The complete chloroplast genome of T. cinerariifolium has a size of 150,136 bp, including a large single-copy (LSC) region of 82,717 bp, a small single-copy (SSC) region of 18,411bp, and a pair of inverted repeats (IRs) of 24,504 bp. The chloroplast genome of T. cinerariifolium encodes 108 genes, including 77 protein-coding genes (PCGs), 27 tRNA genes, and 4 rRNA genes. Phylogenetic analyses based on the complete chloroplast genomes placed T. cinerariifolium in a sister position to species of the genera Artemisia and Chrysanthemum.

| S-EPMC9090375 | 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

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