Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete chloroplast genome of Viburnum schensianum (Adoxaceae).

ABSTRACT: The whole chloroplast (cp) genome sequence of Viburnum schensianum has been characterized from Illumina pair-end sequencing. The complete cp genome was 158,408 bp in length, containing a large single copy region (LSC) of 86,998 bp and a small single copy region (SSC) of 18,386 bp, which were separated by a pair of inverted repeat (IR) regions of 26,512 bp. The genome contained 130 genes, including 84 protein-coding genes, 37 tRNA genes, eight ribosomal RNA genes (four rRNA species), and a pseudogene. Most genes occur as a single copy, whereas 16 gene species are duplicated. Phylogenetic analysis revealed that V. schensianum is closely related to the species of V. utile.

SUBMITTER: Zhao Y

PROVIDER: S-EPMC7510822 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome of Viburnum dilatatum (Adoxaceae).

Project description:Viburnum dilatatum Thunb. is a large deciduous tree of Adoxaceae. In this study, the chloroplast genome sequence of V. dilatatum is 158,392 bp, consisting of a large single-copy (LSC) region with 87,070 bp, a small single-copy (SSC) region with 18,242 bp , and two inverted repeat (IR) regions with 26,540 bp. The GC content in the chloroplast genome of C. julianae is 38.1%. The chloroplast genome of V. dilatatum contains 126 genes, including 83 protein-coding genes, 39 tRNA genes, and 4 rRNA genes. Phylogenetic tree showed that V. dilatatum was clustered with V. utile.

| S-EPMC7995874 | biostudies-literature

The complete chloroplast genome sequence of Viburnum erosum (Adoxaceae).

Project description:Viburnum erosum is a deciduous shrub distributed in eastern Asia. As part of the systematic study to understand the phylogenetic relationship of V. erosum, we present the complete chloroplast genome of V. erosum. Its length is 158,624?bp and it has four subregions: 87,060?bp of large single-copy and 18,530?bp of small single-copy regions separated by a pair of inverted repeat regions of 26,517?bp each, including 129 genes (84 protein-coding genes, 8 rRNAs, and 37 tRNAs). Phylogenetic analyses show that V. erosum is sister to Viburnum japonicum, supporting morphological affinity of the two species.

| S-EPMC7707357 | biostudies-literature

The complete chloroplast genome of Viburnum sargentii Koehne (Adoxaceae).

Project description:Viburnum sargentii Koehne is widely used for garden greening and also displays excellent medicinal value in China. However, the phylogenetic relationship between V. sargentii and other Adoxaceae members remains unknown. In this research, the complete chloroplast genome of V. sargentii was obtained by the high-throughput Illumina pair-end sequencing data. The chloroplast genome shows a typically quadripartite structure with 158,524 bp in size, including a large single-copy (LSC) region of 87,087 bp and a small single-copy (SSC) region of 18,489 bp, which were separated by two inverted repeat (IR) regions (26,474 bp each). A total of 128 genes were predicted, including 8 ribosomal RNAs (rRNAs), 37 transfer RNAs (tRNAs), and 83 protein-coding genes (PCGs). Maximum-likelihood phylogenetic analysis revealed that V. sargentii was clustered in the Viburnum genus and in a sister position to Viburnum japonicum, Viburnum erosum, Viburnum fordiae, and Viburnum betulifolium. This study provides useful information for future genetic study of V. sargentii.

| S-EPMC8043549 | biostudies-literature

The complete chloroplast genome sequence of Viburnum Japonicum (Adoxaceae), an evergreen broad-leaved shrub.

Project description:The wax-leafed Viburnum japonicum (Adoxaceae) is an evergreen shrub distributed in Japan, Korea, and Taiwan. We sequenced its complete chloroplast (cp) genome to examine its phylogenetic relationship within Dipsacales. This genome is 158,614?bp long and features a large single-copy region (87,059?bp) and a small single-copy region (18,523?bp), separated by two inverted-repeat regions (26,516?bp each). It contains 128 genes, including 84 coding genes, eight rRNAs, and 36 tRNAs. The overall GC content is 38.1%. Our phylogenetic tree showed that V. japonicum is closely related to V. utile and is clustered together with four species in the family Adoxaceae.

| S-EPMC7800323 | biostudies-literature

Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae).

Project description:Phylogenetic analyses of complete chloroplast genome sequences have yielded significant improvements in our understanding of relationships in the woody flowering genus Viburnum (Adoxaceae, Dipsacales); however, these relationships were evaluated focusing only on Viburnum species within Central and South America and Southeast Asia. By contrast, despite being a hotspot of Viburnum diversity, phylogenetic relationships of Viburnum species in China are less well known. Here, we characterized the complete chloroplast (cp) genomes of 21 Viburnum species endemic to China, as well as three Sambucus species. These 24 plastomes were highly conserved in genomic structure, gene order and content, also when compared with other Adoxaceae. The identified repeat sequences, simple sequence repeats (SSRs) and highly variable plastid regions will provide potentially valuable genetic resources for further population genetics and phylogeographic studies on Viburnum and Sambucus. Consistent with previous combined phylogenetic analyses of 113 Viburnum species, our phylogenomic analyses based on the complete cp genome sequence dataset confirmed the sister relationship between Viburnum and the Sambucus-Adoxa-Tetradoxa-Sinadoxa group, the monophyly of four recognized sections in Flora of China (i.e., Viburnum sect. Tinus, Viburnum sect. Solenotinus, Viburnum sect. Viburnum and Viburnum sect. Pseudotinus) and the nonmonophyly of Viburnum sect. Odontotinus and Viburnum sect. Megalotinus. Additionally, our study confirmed the sister relationships between the clade Valvatotinus and Viburnum sect. Pseudotinus, as well as between Viburnum sect. Opulus and the Odontotinus-Megalotinus group. Overall, our results clearly document the power of the complete cp genomes in improving phylogenetic resolution, and will contribute to a better understanding of plastome evolution in Chinese Adoxaceae.

| S-EPMC7570041 | biostudies-literature

The second complete chloroplast genome sequence of the Viburnum erosum (Adoxaceae) showed a low level of intra-species variations.

Project description:We presented the second complete chloroplast genome of the plant. The length of chloroplast genome is 158,587 bp, consisting of four subregions: 87,050 bp of LSC and 18,503 bp of SSC regions separated by a pair of 26,517 bp IR regions. It includes 129 genes (84 protein-coding genes, 8 rRNAs, and 37 tRNAs). A low-level of molecular variation within Viburnum erosum was found with 16 SNPs and 49 indels. The phylogenetic tree shows that the two accessions of V. erosum are clustered with Viburnum japonicum with no resolution between the species, suggesting that chloroplast genome in these species evolve slowly.

| S-EPMC7720945 | biostudies-literature

The complete chloroplast genome of Tetradoxa omeiensis (Adoxaceae) provides insights into the phylogenetic relationship of Adoxaceae.

Project description:The complete chloroplast genome of Tetradoxa omeiensis, which is endemic and endangered to the Hengduan Mountains, was sequenced and characterized in this study. The chloroplast genome is 157,502?bp in length, and it is consisted of four distinct regions: a large single-copy region (LSC, 86,526?bp), a small single-copy region (SSC, 18,682?bp) and a pair of inverted repeat regions (IRs, 26,147?bp). A total of 134 genes were annotated, including 86 protein-coding genes (80 PCG species), 40 tRNA genes (33 tRNA species) and 8 ribosomal RNA genes (4 rRNA species). We also reconstructed a comprehensive phylogenetic relationship of the family Adoxaceae, which demonstrated that the three Adoxaceae species clustered into two well-supported clades, and T. omeiensis is most closely related to the Adoxa moschatellina.

| S-EPMC7800847 | biostudies-literature

Characterization of 16 microsatellite markers for the Oreinotinus clade of Viburnum (Adoxaceae).

Project description:Microsatellite loci were isolated from four species of Viburnum (Adoxaceae) to study population structure and assess species boundaries among morphologically similar South American Viburnum species of the Oreinotinus clade. Using a microsatellite-enriched library and mining next-generation sequence data, 16 microsatellites were developed. Each locus was tested on two populations of V. triphyllum and one population of V. pichinchense. For nuclear loci, one to 13 alleles were recovered, expected heterozygosity ranged from 0 to 0.8975, Simpson diversity index ranged from 0.0167 to 1.000, and Shannon diversity index ranged from 0 to 2.3670 in a given population. For the mitochondrial locus, three to six alleles were recovered and unbiased haploid diversity values ranged from 0.756 to 0.853 in a given population. The 16 microsatellite loci developed for the Oreinotinus clade (Viburnum, Adoxaceae) will inform investigations of population structure and species boundaries within this group.

| S-EPMC5238702 | biostudies-literature

Characterization of the complete chloroplast genome of China Viburnum burejaeticum Regel et Herd and intra-species diversity.

Project description:Viburnum burejaeticum Regel et Herd is widely cultivated in botanical gardens. However, as a member of Adoxaceae, few studies have been carried out on its phylogenetic relationship with other family members. Here we report the first complete chloroplast (cp) genome sequence of V. burejaeticum collected from China. The circular cp genome is 158,381 bp in size, including a large single-copy (LSC) region of 87,067 bp and a small single-copy (SSC) region of 18,212 bp, which were separated by two inverted repeat (IR) regions (26,551 bp each). A total of 126 genes were annotated, including 8 ribosomal RNAs (rRNAs), 36 transfer RNAs (tRNAs), and 82 protein-coding genes (PCGs). The sequence comparison of two V. burejaeticum collected from Korea and China revealed 101 single nucleotide polymorphisms (SNPs) and 16 insertions/deletions (InDels). In addition, maximum-likelihood (ML) phylogenetic analysis indicated V. burejaeticum species collected in Korea and China are clustered together. This study provides useful information for future genetic study of V. burejaeticum.

| S-EPMC8032331 | biostudies-literature

Comparative wood anatomy of Korean Viburnum L. (Adoxaceae) and its taxonomic implication.

Project description:Comparative wood anatomy of Viburnum was carried out to understand the differences in wood features amongst the species which might be useful for taxonomic discrimination in the genus. Altogether, nine taxa belonging to five clades were investigated using a sliding microtome and light microscopy. The growth rings are well represented and earlywood and latewood are distinguishable in cross-section. Some of the important wood features include angular, oval and rounded vessels with scalariform perforation plates, opposite to scalariform inter-vessel pitting, rounded pits with slit-like apertures, thick-walled xylem tracheids with simple, rounded bordered pits, diffuse axial parenchyma, uni- and multiseriate rays, 2-4 cells wide. In general, there is a remarkable uniformity in the qualitative wood features in Viburnum species, although quantitative measurement showed some disparities. The most significant quantitative wood variables which might be useful for taxonomic groupings of the species comprise a frequency of vessels and rays, the diameter of the vessels and tracheids in the radial and tangential planes and height and width of rays in the tangential plane.

| S-EPMC7455588 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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