Browse
Submit Data
Databases
API
Help

Dataset Information

44 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Elaeocarpus japonicus Sieb. et Zucc. (Elaeocarpaceae).

ABSTRACT: The complete chloroplast genome of Elaeocarpus japonicus Sieb. et Zucc. was reported in this study. The cp genome was 157,639 bp in length including two inverted repeats (IRs) of 27,437 bp, which were separated by large single copy (LSC) and small single copy (SSC) of 85,784 bp and 16,981 bp, respectively. The GC content was 37.2%. The genome encoded 111 functional genes, including 77 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic tree showed that E. japonicus representing Elaeocarpaceae is sister to Averrhoa carambola representing Oxalidaceae with strong support.

SUBMITTER: Wang Y

PROVIDER: S-EPMC7889153 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome sequence of Elaeocarpus decipiens (Elaeocarpaceae).

Project description:Elaeocarpus decipiens F. B. Forbes and Hemsl is an evergreen tree native to East Asia. Here, we sequenced and reported the complete chloroplast genome of E. decipiens for the first time. In the present work, the complete chloroplast (cp) genome sequence of E. decipiens was characterized by Illumina pair-end sequencing. The genome was 158,148 bp in total length, including a large single-copy (LSC) region of 85,702 bp, a small single-copy (SSC) region of 17,672 bp, and a pair of invert repeats (IR) regions of 27,387 bp. The plastid genome contained 142 genes including 97 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on 13 chloroplast genomes indicates that E. decipiens is closely related to Elaeocarpus bracean in Elaeocarpacea.

| S-EPMC8510590 | biostudies-literature

The complete chloroplast genome of Laportea bulbifera (Sieb. et Zucc.) Wedd. and its phylogenetic analysis.

Project description:The circle complete chloroplast genome of Laportea bulbifera (Sieb. et Zucc.) Wedd. was sequenced for the first time. The genome length of L. bulbifera is 150,042 bp with 36.80% of GC content. The genome consists of a large single copy (LSC) region of 82,414 bp, a small single copy (SSC) region of 17,714 bp, and two inverted repeat (IRa and IRb) regions of 24,957 bp each. A total of 129 genes were annotated, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis was conducted by 29 species from the Rosales, the results presented a closed relationship between the species Laportea bulbifera and Poikilospermum lanceolatum.

| S-EPMC9009949 | biostudies-literature

The complete chloroplast genome of Epimedium sagittatum (Sieb. Et Zucc.) Maxim. (Berberidaceae), a traditional Chinese herb.

Project description:Epimedium sagittatum is an important traditional medicinal plant in China. In this study, we assembled the complete chloroplast (cp) genome of E. sagittatum. The whole cp genome of E. sagittatum is 157,114?bp in length, comprising a pair of inverted repeat (IR) regions (25,775?bp) separated by a large single copy (LSC) region (88,507?bp) and a small single copy (SSC) region (17,057?bp). The E. sagittatum cp genome contains 133 genes, of which 82 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 5 pseudogenes. Phylogenetic analysis shows that E. sagittatumis closely clustered with E. lishihchenii. This genome provides a wealth of information for distinguishing of Epimedium species.

| S-EPMC7706818 | biostudies-literature

The complete chloroplast genome sequence of Zanthoxylum ailanthoides Sieb. et. Zucc (Rutaceae): an important medicinal plant.

Project description:Zanthoxylum ailanthoides is a deciduous tree, with important medicinal and economic values. The complete chloroplast genome sequence of Z. ailanthoides was assembled and the phylogenetic relationship to other species was inferred in this study. The chloroplast genome is 157,209 bp in length, including two inverted repeats of 26,408 bp, a large single-copy of 86,099 bp and a small single copy of 18,294 bp. Moreover, the chloroplast genome contains 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of the chloroplast genome is 38.4%. The phylogenetic analysis indicated that Z. ailanthoides was grouped with a clade containing the species of Z. multijugum, Z. calcicola, Z. oxyphyllum, Z. stenophyllum, and the genus was closely related to Phellodendron. This study contributes to a better understanding of the phylogenetic relationships among Zanthoxylum species.

| S-EPMC11018064 | biostudies-literature

The complete chloroplast genome of Castanea crenata Sieb. & Zucc.

Project description:The complete chloroplast genome sequence of Castanea crenata was sequenced and assembled using PacBio Sequel data. The cpDNA was 160,787?bp in length, containing a pair of inverted repeats (IRs) of 25,654?bp each separated by a large and small single copy (LSC and SSC) regions of 90,645?bp and 18,836?bp, respectively. The cpDNA contained 102 genes, including 65 protein-coding genes, 8 ribosomal RNA genes and 37 transfer RNA genes. Phylogenetic analysis indicated that C. crenata was closest to C. pumila var. pumila, which is known as a typical variety of American chinquapin or dwarf chestnut.

| S-EPMC7707651 | biostudies-literature

The complete chloroplast genome sequence of Trapa incisa Sieb. & Zucc. (Lythraceae).

Project description:Trapa L., an annual floating-leaved herb, is widely distributed in the old world and has important edible and medicinal values. However, the taxonomy and phylogeny of Trapa are unclear. Here, we reported the complete chloroplast genome of a wild species with small nuts, T. incisa. The complete chloroplast genome size of T. incisa was 155, 453 bp, consisting of two inverted repeat (IR) regions (24, 388 bp), one large single copy (LSC) region (88, 398 bp) and one small single copy (SSC) region (18, 279 bp). A total of 129 genes were annotated, including 83 protein-coding genes, 38 tRNA genes and 8 rRNA genes. Among them, 19 genes were duplicated (6 protein-coding genes, 9 tRNA genes and 4 rRNA genes). The phylogenomic analysis suggested a close relationship between T. incisa and T. maximowiczii.

| S-EPMC8174476 | biostudies-literature

The complete chloroplast genome of Petasites japonicus (Siebold & Zucc.) Maxim. (Asteraceae).

Project description:The complete chloroplast (cp) genome sequence of Petasites japonicus (Asteraceae) was determined. The cp genome is 150,445 bp and consists of a large single-copy region (82,910 bp), a small single-copy region (17,907 bp), and a pair of inverted repeats (24,814 bp). It encodes a set of 114 genes, consisting of 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic inference confirmed that P. japonicus is sister to the genus Ligularia in the tribe Senecioneae of Asteraceae.

| S-EPMC8635567 | biostudies-literature

Genome-wide DNA polymorphisms in two cultivars of mei (Prunus mume sieb. et zucc.).

Project description:BackgroundMei (Prunus mume Sieb. et Zucc.) is a famous ornamental plant and fruit crop grown in East Asian countries. Limited genetic resources, especially molecular markers, have hindered the progress of mei breeding projects. Here, we performed low-depth whole-genome sequencing of Prunus mume 'Fenban' and Prunus mume 'Kouzi Yudie' to identify high-quality polymorphic markers between the two cultivars on a large scale.ResultsA total of 1464.1 Mb and 1422.1 Mb of 'Fenban' and 'Kouzi Yudie' sequencing data were uniquely mapped to the mei reference genome with about 6-fold coverage, respectively. We detected a large number of putative polymorphic markers from the 196.9 Mb of sequencing data shared by the two cultivars, which together contained 200,627 SNPs, 4,900 InDels, and 7,063 SSRs. Among these markers, 38,773 SNPs, 174 InDels, and 418 SSRs were distributed in the 22.4 Mb CDS region, and 63.0% of these marker-containing CDS sequences were assigned to GO terms. Subsequently, 670 selected SNPs were validated using an Agilent's SureSelect solution phase hybridization assay. A subset of 599 SNPs was used to assess the genetic similarity of a panel of mei germplasm samples and a plum (P. salicina) cultivar, producing a set of informative diversity data. We also analyzed the frequency and distribution of detected InDels and SSRs in mei genome and validated their usefulness as DNA markers. These markers were successfully amplified in the cultivars and in their segregating progeny.ConclusionsA large set of high-quality polymorphic SNPs, InDels, and SSRs were identified in parallel between 'Fenban' and 'Kouzi Yudie' using low-depth whole-genome sequencing. The study presents extensive data on these polymorphic markers, which can be useful for constructing high-resolution genetic maps, performing genome-wide association studies, and designing genomic selection strategies in mei.

| S-EPMC3851432 | biostudies-literature

A New Megastigmane Sesquiterpenoid from Zanthoxylum Schinifolium Sieb. et Zucc.

Project description:Zanthoxylum schinifolium Sieb. et Zucc. (Rutaceae), a dioecious shrub with hooked prickly branches, has been used as folk medicine for the treatment of the common cold, stomach ache, diarrhea, and jaundice in China, Korea, and Japan. In our phytochemical investigations on this genus, a new megastigmane sesquiterpenoid, which is referred to as schinifolenol A (1), was isolated from Z. schinifolium. The stereochemistry was characterized via the analyses of extensive spectra. The absolute configuration was established by the application of a modified Mosher's experiment and assisted by a time-dependent density functional theory (TD-DFT) on calculated electronic circular dichroism (ECD). Bioactivity screenings showed that compound 1 exhibited a safe hypotoxicity and a better selectivity on anti-Kaposi's sarcoma associated herpes virus (KSHV).

| S-EPMC6273384 | biostudies-literature

Proanthocyanidin Synthesis in Chinese Bayberry (Myrica rubra Sieb. et Zucc.) Fruits.

Project description:Proanthocyanidins (PAs) are distributed widely in Chinese bayberry fruit and have been associated with human health benefits, but molecular and biochemical characterization of PA biosynthesis remains unclear. Here, two genes encoding key PA biosynthetic enzymes, anthocyanidin reductase (ANR) and leucoanthocyanidin reductase (LAR) were isolated in bayberry fruit. MrANR was highly expressed at the early stage of fruit development when soluble PAs accumulated at high levels. Meanwhile, the transcript abundance of both MrANR and MrLAR observed at the late stage was paralleled with the high amounts of insoluble PAs. LC-MS/MS showed that PAs in developing Chinese bayberry fruits were comprised predominantly of epigallocatechin-3-O-gallate terminal subunits, while the extension subunits were a mixture of epigallocatechin-3-O-gallate, epigallocatechin and catechin. Recombinant MrANR protein converted cyanidin to a mixture of epicatechin and catechin, and delphinidin to a mixture of epigallocatechin and gallocatechin in vitro. Recombinant MrLAR was active with leucocyanidin as substrate to produce catechin. Ectopic expression of MrANR in tobacco reduced anthocyanin levels but increased PA accumulation. The catechin and epicatechin contents in transgenic flowers overexpressed MrANR were significantly higher than those of wild-type. However, overexpression of MrLAR in tobacco led to an increase in catechin levels but had no impact on PA contents. Quantitative real time PCR revealed that the loss of anthocyanin in transgenic flowers overexpressed MrANR or MrLAR is probably attributed to decreased expression of tobacco chalcone isomerase (CHI) gene. Our results not only reveal in vivo and in vitro functions for ANR and LAR but also provide a resource for understanding the mechanism of PA biosynthesis in Chinese bayberry fruit.

| S-EPMC5835688 | 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