Browse
Submit Data
Databases
API
Help

Dataset Information

31 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Scurrula chingii (W.C. Cheng) H.S. Kiu (Loranthaceae), a hemiparasitic shrub.

ABSTRACT: Scurrula chingii (W.C. Cheng) H.S. Kiu is a stem hemiparasite of the genus Scurrula in the family Loranthaceae distributed in southwest China and northern Vietnam. Here, we report and characterize the complete plastid genome sequence of S. chingii to provide genomic resources useful for the phylogenetic studies of Santalales. The plastome of S. chingii is 122,764 bp in length, consisted of a large single-copy region (70,726 bp), a small single-copy region (6,091 bp), and a pair of inverted repeat regions (22,974 bp). The GC content of the whole plastome is 37.2%. It contains 109 genes, including 69 CDS (protein-coding genes), eight rRNAs, and 32 tRNAs. The alignment of 14 species complete chloroplast genomes of Loranthaceae was implemented and a phylogenetic tree was constructed using maximum-likelihood (ML) method, which revealed that S. chingii clustered with Scurrula parasitica and Taxillus thibetensis as a monophyletic group.

SUBMITTER: Li M

PROVIDER: S-EPMC7850402 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome of Elytranthe Albida (Loranthaceae), a hemiparasitic shrub.

Project description:The complete chloroplast genome (plastome) of Elytranthe albida (Blume) Blume (Loranthaceae) was sequenced. The plastome is 128,658?bp in length, which encodes 96 unique genes, including 64 protein-coding genes, 4 rRNAs, and 28 tRNAs. The complete plastome-based phylogeny indicated that E. albida is sister to remaining Loranthaceae species.

| S-EPMC7706827 | biostudies-literature

Complete chloroplast genome sequence of Scurrula notothixoides (Loranthaceae): a hemiparasitic shrub in South China.

Project description:Scurrula notothixoides (Loranthaceae) is a hemiparasitic shrub distributed in forest margins of Southeast Asian countries. Here, we report and characterize the complete plastid genome sequence of S. notothixoides in an effort to provide genomic resources useful for the phylogenetic studies for Santalales. The complete plastome is 123,810?bp in length and contains the typical structure and gene content of angiosperm plastomes, including two inverted repeat (IR) regions of 23,101?bp, a large single copy (LSC) region of 71,448?bp and a small single copy (SSC) region of 6160?bp. The plastome contains 88 genes, consisting of 61 unique protein-coding genes, 23 unique tRNA genes and four unique rRNA genes. The overall A/T content in the plastome of S. notothixoides is 62.7%. Phylogenetic analyses were performed using the entire plastome, including spacers, introns, etc. and we recovered that S. notothixoides and Taxillus sutchuenensis was closely related. The complete plastome sequence of S. notothixoides will provide a useful resource for the phylogenetic studies for Santalales.

| S-EPMC7799537 | biostudies-literature

Complete chloroplast genome sequence of Taxillus chinensis (Loranthaceae): a hemiparasitic shrub in South China.

Project description:Taxillus chinensis (DC) Danser, which is a hemiparasitic shrub distributed in southern China and Southeast Asian countries, is wildly used in various traditional Chinese medicine prescriptions. In this study, the complete chloroplast genome of the T. chinensis was assembled from the whole genome Illumina sequencing data. The complete plastome is a typical quadripartite structure with a length of 121,305 bp, which contained two inverted repeats (IRs) of 22,460 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 70,295 bp and 6090 bp, respectively. The plastome contains 106 genes, comprising 66 protein-coding genes, 28 tRNA genes, eight rRNA genes, and four processed pseudogenes. The overall GC content of the plastome is 37.4%, which is unevenly distributed across the whole chloroplast genome. The phylogenetic analysis shows that T. chinensis was closely related to the congeneric species T. sutchuenensis.

| S-EPMC7706901 | biostudies-literature

The complete chloroplast genome sequence of Taxillus yadoriki (Loranthaceae): a hemi-parasitic evergreen shrub in East Asia.

Project description:Taxillus yadoriki (Loranthaceae) is a hemiparasitic evergreen shrub distributed in Korea and Japan. We report the complete chloroplast genome of T. yadoriki to provide insight into the phylogenetic relationship of Loranthaceae. This genome is 122,192 bp long, with two IR regions (22,756 bp each) that separate a large single-copy (LSC) region (70,628 bp) and a small single-copy (SSC) region (6052 bp). It contains 109 genes that encode 68 proteins, 8 rRNAs, and 33 tRNAs. All of ndh genes have been lost and the SSC region consists of only four genes similar to other Taxillus species. In ML phylogenetic, monophyly of Taxillus was strongly supported with high bootstrap value and formed a sister group with Scurrula.

| S-EPMC7781972 | biostudies-literature

The complete plastome of Taxillus vestitus (Loranthaceae), a hemiparasitic plant.

Project description:Taxillus vestitus (Wallich) Danser (Loranthaceae) is a stem hemiparasite occurring in southwest China and Himalayas. In this study, we report the first complete plastome of this species. The plastome is 122,200?bp in size, which encodes 94 unique genes (64 protein-encoding gens, 4 ribosomal RNAs, and 26 tRNAs). Compared to the plastomes of the autotrophic relatives, the T. vestitus plastome is significantly reduced. A total of 15 protein-coding genes, and 4 tRNAs were deleted from the plastome.

| S-EPMC7706843 | biostudies-literature

The complete chloroplast genome sequence of Helixanthera parasitica (Loranthaceae).

Project description:The complete chloroplast genome of Helixanthera parasitica from China was analyzed using next-generation sequencing. The plastome of H. parasitica is a typical quadripartite structure with a length of 125,021 bp, which contained inverted repeats (IR) of 22,752 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 73,151 bp and 6,366 bp, respectively. The cpDNA contains 105 genes, comprising 67 protein-coding genes, 30 tRNA genes, and 8 rRNA genes. The overall GC content of the plastome is 36.5%. Phylogenetic analysis showed that H. parasitica was closely related to the Tolypanthus maclurei.

| S-EPMC7707008 | biostudies-literature

The complete chloroplast genome of hemiparasitic flowering plant Schoepfia jasminodora.

Project description:The complete chloroplast genome hemiparasitic plant Schoepfia jasminodora (Schoepfiaceae), was determined in this study by de novo assembly with whole-genome sequence data. The chloroplast genome is 118,743?bp in length with a typical quadripartite structure containing a pair of inverted repeats of 12,406?bp, separated by a large and a small single copy fragments of 84,168?bp and 9763?bp, respectively. The chloroplast genome contains 112 genes that consisting of 69 protein-coding, 27 tRNA, 4 rRNA and 3 pseudolized genes. All of the ndh (except for ndhA) and two tRNA (trnV-UAG and trnG-UCC) genes were found to be lost. The three pseudogenes are ndhA, ycf15 and trnL-CAA. Schoepfia represents the early stages of chloroplast genome degradation along with its transition to heterotrophy in related taxa.

| S-EPMC7799538 | biostudies-literature

The complete chloroplast genome of a medicinal plant Viscum articulatum Burm.f. (Loranthaceae).

Project description:Viscum articulatum is usually used as famous ethno-medicinal plant and popular drink in many provinces of China. In this study, the characterization of the complete chloroplast genome of V. articulatum was analyzed using the Illumina NovaSeq platform. The whole chloroplast genome sequence of V. articulatum is 131,825 including a large single-copy region (LSC, 76,069 bp), a small single-copy region (SSC, 8990 bp), and a pair of repeated regions (IRs, 23,383 bp, each). Further gene annotation in our study revealed the chloroplast genome contains 114 genes, including 36 tRNA genes, 8 rRNA genes and 70 protein-coding genes. A total of 118 simple sequence repeats (SSRs) were identified in the chloroplast genome. Phylogenetic development was analyzed based on V. articulatum with other species of Loranthaceae, the phylogenetic tree in our study revealed that V. articulatum is a lineage independent of other species in genus Viscum.

| S-EPMC8381967 | biostudies-literature

The complete chloroplast genome sequence of the relict woody plant Metasequoia glyptostroboides Hu et Cheng.

Project description:Metasequoia glyptostroboides Hu et Cheng is the only species in the genus Metasequoia Miki ex Hu et Cheng, which belongs to the Cupressaceae family. There were around 10 species in the Metasequoia genus, which were widely spread across the Northern Hemisphere during the Cretaceous of the Mesozoic and in the Cenozoic. M. glyptostroboides is the only remaining representative of this genus. Here, we report the complete chloroplast (cp) genome sequence and the cp genomic features of M. glyptostroboides. The M. glyptostroboides cp genome is 131,887 bp in length, with a total of 117 genes comprised of 82 protein-coding genes, 31 tRNA genes and four rRNA genes. In this genome, 11 forward repeats, nine palindromic repeats, and 15 tandem repeats were detected. A total of 188 perfect microsatellites were detected through simple sequence repeat (SSR) analysis and these were distributed unevenly within the cp genome. Comparison of the cp genome structure and gene order to those of several other land plants indicated that a copy of the inverted repeat (IR) region, which was found to be IR region A (IRA), was lost in the M. glyptostroboides cp genome. The five most divergent and five most conserved genes were determined and further phylogenetic analysis was performed among plant species, especially for related species in conifers. Finally, phylogenetic analysis demonstrated that M. glyptostroboides is a sister species to Cryptomeria japonica (L. F.) D. Don and to Taiwania cryptomerioides Hayata. The complete cp genome sequence information of M. glyptostroboides will be great helpful for further investigations of this endemic relict woody plant and for in-depth understanding of the evolutionary history of the coniferous cp genomes, especially for the position of M. glyptostroboides in plant systematics and evolution.

| S-EPMC4468836 | biostudies-literature

Characterization of the complete chloroplast genome of Carya hunanensis W. C. Cheng & R. H. Chang.

Project description:Carya hunanensis W. C. Cheng & R. H. Chang is a tree of great economic importance in China. In this study, the complete chloroplast genome of C. hunanensis was determined and analyzed phylogenetically. The whole genome was determined to be 159,892 bp in length, presenting a typical quadripartite structure with a large single copy (LSC) region (89,466 bp), a small single copy (SSC) region (18,714 bp), and a pair of inverted repeat (IR) regions (25,856 bp each). There were 132 genes annotated in the genome, including 84 protein-coding genes, 40 tRNA genes, and eight rRNA genes. The overall GC content of C. hunanensis chloroplast genome was 36.24%. Phylogenetic analysis indicated that C. hunanensis was closely related to C. kweichowensis and Annamocarya sinensis.

| S-EPMC7832538 | 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