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 Grateloupia turuturu Yamada.

ABSTRACT: In this study, we sequenced and annotated the complete chloroplast genome of Grateloupia turuturu Yamada (GenBank accession number: MN853877). The total length of the chloroplast genome is 188,547 bps, including 196 protein-encoding genes, 23 tRNA genes and 3 rRNA. The complete chloroplast genome of G. turuturu is 30.68% C + G, which is lower than that of A + T. The phylogenetic tree, which is based on core genes, shows that G. turuturu is clustered into the Grateloupia clade and has close genetic relationships with algae Grateloupia filicina and Grateloupia taiwanensis. These data will provide more information to understand the phylogenetic status of G. turuturu.

SUBMITTER: Han H

PROVIDER: S-EPMC7748499 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete plastid genome of <i>Grateloupia filicina</i> (Rhodophyta) and phylogenetic analysis.

Project description:In this study, we obtained the complete plastid genome of Grateloupia filicina (Lamouroux) C. Agardh using the high-throughput sequencing method. It had circular mapping organization with the length of 195,990 bp and contained 265 genes including 195 protein-coding genes, three rRNA genes, one tmRNA gene, 28 tRNA genes and 38 unidentified open reading frames (ORFs). Moreover, phylogenetic analysis revealed that G. filicina firstly clustered with Grateloupia taiwanensis. The complete plastid genome obtained in this work would be useful for further understanding the evolution of Grateloupia.

| S-EPMC7800207 | biostudies-literature

Keteleeria cyclolepis complete chloroplast genome

Project description:Keteleeria cyclolepis complete chloroplast genome Raw sequence reads

| PRJNA723268 | ENA

Complete mitochondrial genome of <i>Aedes flavopictus</i> (Yamada, 1921) (Diptera: Culicidae) collected in South Korea.

Project description:In this study, we determined for the first time the mitochondrial genome sequence of an Aedes flavopictus specimen collected in South Korea. Its mitochondrial genome was 16,060 bp in length, consisting of 13 protein-coding, 22 tRNA, and 2 rRNA genes and a non-coding A + T rich region. The overall base composition in the heavy strand was 39.7, 8.6, 12.7, and 39% of A, G, C, and T, respectively, and the G + C content was 21.2%. Phylogenetic analysis revealed that Aedes spp. formed a monophyletic clade.

| S-EPMC7850365 | biostudies-literature

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

The complete chloroplast genome of solanum pimpinellifolium

Project description:The chloroplast genome were assembled and annotated for solanum pimpinellifolium

| PRJEB40533 | ENA

Complete chloroplast genome of Ophiorrhiza baviensis Drake

Project description:Ophiorrhiza baviensis chloroplast, complete genome

| PRJEB57743 | ENA

Primers for complete chloroplast genome sequencing in Magnolia.

Project description:Premise:A new set of primers was developed for sequencing of whole chloroplast genomes of Magnolia species and gap-filling of unfinished genomes. Methods and Results:Two hundred and fifty primers were newly designed based on two previously reported chloroplast genomes from two different genera in Magnoliaceae. A total of 134 primer pairs, including the ones developed in this study and 18 previously reported ones, were enough to cover the entire chloroplast genome sequences in Magnoliaceae. Four species from different sections of Magnolia (M. dealbata, M. fraseri var. pyramidata, M. liliiflora, and M. odora) were used to show the general application of these primers to chloroplast genome sequencing in Magnolia. Conclusions:Using the developed primers, four Magnolia chloroplast genomes were successfully assembled. These results show the utility of these primers across Magnolia and their potential use for phylogenetic studies, DNA barcoding, and population genetics in this group.

| S-EPMC6764489 | 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