Browse
Submit Data
Databases
API
Help

Dataset Information

32 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of a Citrus australasica cultivar (Rutaceae）.

ABSTRACT: Citrus australasica (F. Muell.) Swingle belongs to the family Rutaceae. Citrus australasica is native to eastern Australia and southeastern New Guinea, and is mainly concentrated in a small region of northern New South Wales and tropical rainforest areas in southern Queensland. The complete plastome length of C. australasica is 160,335 bp, with the typical structure and gene content of angiosperm plastids, including a 26,592 bp repeat B (IRB) region, 26,952 bp IRA, 87,678 bp large single copy (LSC) region and 18,756 bp small single copy (SSC) region. The plastid contains 135 genes, including 89 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The total G/C content of the C. australasica plastome is 38.4%. The complete plastome sequence of C. australasica will provide useful resources for conservation genetics research of this species and phylogenetic research of Rutaceae.

SUBMITTER: Cai QN

PROVIDER: S-EPMC8676588 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome and phylogenetic analysis of Citrus clementina (Rutaceae).

Project description:Citrus, which is widely cultivated in tropical and subtropical climates, is one of the most important crops in the world. Here, we assembled and annotated the complete chloroplast genome of Citrus clementina (C. clementina) using Illumina sequencing data. This chloroplast genome exhibited a typical quadripartite structure of 154,042 bp in length, and the overall GC content was 38.42%. A total of 134 genes (90 protein-coding genes, 36 tRNAs, and eight rRNAs) were predicted in this chloroplast genome. Phylogenetic analysis strongly supported that C. clementina was evolutionarily close to Citrus sunki.

| S-EPMC8439215 | biostudies-literature

Assembly and phylogenetic analysis of the complete chloroplast genome of Citrus aurantium (Rutaceae).

Project description:Citrus aurantium (C. aurantium), belonging to the family Rutaceae, is usually utilized as a flavoring and acidifying agent for food. This study assembled and characterized the complete chloroplast (cp) genome of C. aurantium. The cp genome was 160,140 bp in length, containing a pair of inverted repeats (IRs, 26,996 bp each), which is separated by a large single-copy (LSC, 87,763 bp) region and a small single copy (SSC, 18,385 bp) region. The cp genome has overall GC content of 38.48% and 135 genes, composing of 90 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Phylogenetic analysis based on 25 cp genomes highly supported that C. aurantium was evolutionarily close to Cirtus sinensis (C. sinensis).

| S-EPMC7510620 | biostudies-literature

The complete chloroplast genome sequence of Zanthoxylum undulatifolium Hemsl. (Rutaceae).

Project description:Zanthoxylum undulatifolium is an excellent economic tree species with important medical value. This study reports the first complete chloroplast genome sequence of Z. undulatifolium. Its whole chloroplast genome is 158,400 bp in length, including a large single-copy (LSC) region of 85,898 bp, a small single-copy (SSC) region of 17,610 bp, and two inverted repeat (IR) regions of 27,446 bp. The chloroplast genome contains a total of 132 genes, comprising 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the chloroplast genome is 38.46%, with the corresponding values in the LSC, SSC, and IR regions are 36.87%, 33.51%, and 42.55%, respectively. Phylogenetic analysis revealed the sister relationship between Z. undulatifolium and Z. bungeanum.

| S-EPMC8856060 | biostudies-literature

Complete chloroplast genome sequence of Zanthoxylum nitidum (Rutaceae), an important medicinal shrub.

Project description:Zanthoxylum nitidum (Rutaceae) is a scandent prickly shrub and widely distributed in South China. It's well known for its valuable medicinal values due to contains some important secondary metabolites. Here, we first report and characterize its complete chloroplast genome based on Illumina paired-end sequencing data. The complete plastid genome was 157,253 bp, which contained inverted repeats (IR) of 27,618 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 84,382 bp and 17,635 bp, respectively. The cpDNA contains 132 genes, comprising 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes. The overall GC content of the plastome is 38.5%. The phylogenetic analysis of 20 selected chloroplast genomes demonstrated that Z. nitidum is closely related to the congeneric Z. bungeanum.

| S-EPMC7707648 | biostudies-literature

The complete chloroplast genome sequence of a Castanea henryi cultivar.

Project description:Castanea henryi（Skam）Rehd. et Wils is an important woody plant producing nuts in China. In this study, the complete chloroplast genome sequence of C. henryi was reported by using the Illumina Hiseq 2500 platform. The complete chloroplast sequence is 160,807 bp, including large single-copy (LSC) region of 90,394 bp, small single-copy (SSC) region of 18,963 bp, and a pair of invert repeats (IR) regions of 25,725 bp. Plastid genome contains 112 genes, 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Based on 26 chloroplast genomes, phylogenetic analysis indicates that C. henryi is closely related to C. mollissima in Fagaceae.

| S-EPMC7748877 | biostudies-literature

Complete Chloroplast Genome Sequence and Annotation of the Saccharum Hybrid Cultivar RB867515.

Project description:Here, we present the chloroplast genome sequence of the Saccharum hybrid cultivar RB867515, the most planted sugarcane cultivar in Brazil.

| S-EPMC5064122 | biostudies-literature

Complete chloroplast genome sequence of Murraya paniculata (Rutaceae): a widely used folk medicinal herb.

Project description:Murraya paniculate, is traditionally used for management of gut, air way and cardiovascular disorders. In this study, we sequenced the complete chloroplast genome of M. paniculata based on next-generation sequencing and used the data to assess genomic resources. The chloroplast genome of M. paniculata is 160,280 bp in length consisting of large and small single-copy regions of length 87,605 and 18,609 bp, separated by two IR regions of 27,033 bp. The overall GC content was 38.61%. De novo assembly and annotation showed the presence of unique genes with 85 protein-coding genes, 29 tRNA genes, and eight rRNA genes. A maximum-likelihood phylogenomic analysis showed that M. paniculata was closely related to M. caloxylon.

| S-EPMC7671698 | biostudies-literature

The complete chloroplast genome sequence of a hybrid blackberry (Rubus spp.) cultivar.

Project description:Blackberry (Rubus spp.) is an important hybrid fruit crop popular in the US Pacific Northwest and the European region with complex origins. In this study, we report the complete chloroplast genome sequence of a hybrid blackberry cultivar 'Arapohol' using next-generation sequencing technology. The complete chloroplast genome size is 156,621 bp. The genome contains 134 genes, including 40 tRNA genes, 86 protein-coding genes, and 8 rRNA genes. Phylogenetic analysis based on 11 complete chloroplast genomes revealed that taxa is closely related to Rubus niveus. The complete chloroplast genome of this Rubus sp. provides valuable information for understanding the origination of this crop species.

| S-EPMC8245066 | biostudies-literature

The complete chloroplast genome sequence of Citrus maxima (Burm.) Merr. 'Guanximiyou'.

Project description:Citrus maxima (Burm.) Merr. 'Guanximiyou' is a major citrus tree largely cultivated in China. A previous study has reported the complete chloroplast genome of C. maxima, but there may be some differences between wild species and cultivating variety. In this study, the complete chloroplast genome sequence of 'Guanximiyou' pummelo was characterized using BGISEQ-500 sequencing. The chloroplast genome was 160,186 bp in length and separated into four distinct regions such as large single-copy region (87,939 bp), small single-copy region (18,395 bp), and a pair of inverted repeat regions (26,926 bp). The genome contained a total of 109 genes including 79 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. Phylogenetic maximum-likelihood analysis revealed that 'Guanximiyou' pummelo was clustered with other Rutaceae species with high bootstrap values.

| S-EPMC7748689 | biostudies-literature

The complete chloroplast genome of Dictamnus dasycarpus Turcz. (Rutaceae).

Project description:Dictamnus dasycarpus Turcz. 1842 is a medicinal plant of China. Its dry root bark is called BAIXIANPI, which is a common traditional Chinese medicine. Here, we report the complete chloroplast genome of D. dasycarpus. The length of the genome, large single-copy (LSC), small single-copy (SSC), inverted repeat (IR), and GC content was 157,056 bp, 84,497 bp, 18,487 bp, 27,036 bp, and 38.5%, respectively. A total of 132 genes were annotated, including 87 protein coding, eight rRNA, and 37 tRNA genes. Interestingly, 15 genes contained single intron while two others contained two introns. The phylogenetic tree showed the two D. dasycarpus (D. albus) clustered in a clade, which was sister to clade formed by the species of Melicope, Tetradium, Phellodendron, and Zanthoxylum.

| S-EPMC9415454 | 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