Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of Catalpa fargesii (Bignoniaceae), a species endemic to China.

ABSTRACT: Catalpa fargesii Bur. is endemic to China. Its complete chloroplast genome sequence was firstly reported in this study. The whole chloroplast genome of this species was 157765 bp in length including a pair of inverted repeat (IR, 30252 bp) regions separated by a small single copy (SSC, 12662 bp) and a large single copy (LSC, 84599 bp). The genome consisted of 134 genes, including 89 protein-coding genes, 8 rRNA and 37 tRNA genes. The phylogenetic analysis strongly supported that C. fargesii was closely related to C. fargesii f. duclouxii and C. bungei.

SUBMITTER: Xu S

PROVIDER: S-EPMC8218834 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome sequence of Catalpa fargesii f. duclouxii (Bignoniaceae).

Project description:The complete chloroplast genome sequence of Catalpa fargesii f. duclouxii C.A. May was firstly assembled and analyzed in this study. The whole genome of this species was 158164 bp in length, with a typical quadripartite structure. The large single copy (LSC) was 83986 bp, the small single copy (SSC) was 12660 bp, and both of the two inverted repeats (IRs) were 30259 bp, respectively. A total of 134 genes in the chloroplast genome were annotated, including 87 protein-coding genes, 8 ribosomal RNA (rRNA) genes, and 39 transfer RNA (tRNA) genes. The phylogenetic analysis showed that C. fargesii f. duclouxii was highly clustered with C. bungei.

| S-EPMC7782581 | biostudies-literature

The complete chloroplast genome sequence of Catalpa bungei (Bignoniaceae): a high-quality timber species from China.

Project description:Catalpa bungei is an important resource of timber, belonging to the genus catalpa (Bignoniaceae). In this study, we sequenced complete chloroplast (cp) genome of C. bungei, using a NovaSeq 6000 sequencing platform. The genome of the C. bungei was 152,153 bp in length, including a large single-copy region (84,910 bp), a small single-copy region (12,664 bp), and two inverted repeats regions (30,285 bp). It encodes 126 genes, including 81 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analyses were performed based on 15 cp genomes using the maximum likelihood (ML) method, supported that C. bungei was probably more closely related to C. speciosa. This study, the cp genome of C. bungei was assembled, which will provide more theoretical basis for determine the phylogenetic relationships of the Catalpa and related species.

| S-EPMC7759281 | biostudies-literature

The complete chloroplast genome of Catalpa speciosa (Warder) Engelmann (Bignoniaceae).

Project description:Catalpa speciosa (Warder) Engelm. is a precious Catalpa tree widely used as a large ornamental shade tree. In this study, the complete chloroplast genome was assembled from Illumina sequencing data. The completed plastome was 158,239 bp in length, including a large single copy (LSC) region of 85,036 bp, a small single copy (SSC) region of 12,639 bp, and a pair of inverted repeat (IR) regions of 30,282 bp. The overall GC content of the genome was 38.09%, and the corresponding values of the LSC, SSC and IR regions were 36.44%, 33.57%, and 41.35%, respectively. A total of 129 genes were annotated, including 83 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis was carried out based on complete plastome sequences of C. speciose and 11 other species from Bignoniaceae family. The newly characterized complete chloroplast genome will provide essential data for further studies of C. speciosa.

| S-EPMC7782859 | biostudies-literature

The complete chloroplast genome of Epimedium fargesii Franch. (Berberidaceae), a rare plant species endemic to China.

Project description:Epimedium L. is a medicinally important herbaceous genus in the family Berberidaceae. Epimedium fargesii Franch. is only narrowly inhabited in the Daba Mountains in China. Here, we sequenced and assembled the first complete chloroplast genome of Epimedium fargesii Franch. The chloroplast genome of E. fargesii was 157,208 bp in length, with a total GC content of 38.77%. A total of 112 unique genes were identified, including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis indicated that E. fargesii formed a sister relationship with E. wushanense T. S. Ying. Our results provided fundamental data for further taxonomic and phylogenetic research of the genus Epimedium.

| S-EPMC8555541 | biostudies-literature

The complete chloroplast genome of Catalpa fargesii Bur. f. duclouxii (Dode) Gilmour.

Project description:In this study, we reported and characterized the complete chloroplast genome sequence of Catalpa fargesii Bur. f. duclouxii (Dode) Gilmour. The chloroplast genome was determined to be 158,250 bp in length. It contained large single-copy (LSC) and small single-copy (SSC) regions of 84,929 bp and 12,663 bp, respectively, which were separated by a pair of 30,329 bp inverted repeat (IR) regions. The genome is predicted to contain 121 genes, including 78 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. The overall GC content of the genome is 38.1%. A phylogenetic tree reconstructed by 12 chloroplast genomes reveals that C. fargesii is mostly related to Catalpa. ovata and Catalpa. speciosa. This study identified the unique characteristics of the C. fargesii cp genome, which will provide a theoretical basis for species identification and biological research.

| S-EPMC7954416 | biostudies-literature

The complete chloroplast genome sequence of Sapindus delavayi, a species endemic to China.

Project description:Sapindus delavayi, widely distributed in central to southwest of China, is an economically important forest tree. The chloroplast genome is 159,861 bp in length with a typical circular quadripartite structure, containing 129 genes (84 protein-coding genes, 37 tRNAs, and eight rRNAs). Our phylogenetic result clearly showed that S. delavayi and S. mukorossi have the closest relationship.

| S-EPMC8208118 | biostudies-literature

Complete chloroplast genome sequence of Heteroplexis incana (Asteraceae), a rare species endemic to China.

Project description:Heteroplexis incana (Asteraceae) is a rare species endemic to China. Here, we report and characterize the complete chloroplast genome sequence of H. incana based on Illumina paired-end sequencing data. The complete plastid genome was 152,605 bp in length, which contained two inverted repeats (IRs) of 24,954 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 84,427 bp and 18,270 bp, respectively. The cpDNA contains 132 genes, comprising 85 protein-coding genes, 37 tRNA genes, 8 rRNA genes. The overall GC content of the plastome is 37.3%. The phylogenetic analysis of 17 selected chloroplast genomes demonstrated that Heteroplexis incana was closely related to Aster indicus.

| S-EPMC7706452 | biostudies-literature

Complete chloroplast genome sequence of Swertia mileensis (Gentianaceae): a medicinal species endemic to China.

Project description:Swertia mileensis is an important medicinal plant endemic to South-east Yunnan, China, which has been widely used to treat icteric hepatitis. The complete chloroplast genome sequence of S. mileensis is presented in this study, the total size is 153,015 bp in length with a typical quadripartite structure including a pair of inverted repeat (IRs, 25,786 bp) regions separated by a large single copy (LSC, 83,048 bp) region and a small single copy (SSC, 18,395 bp) region. The overall GC content of it is 38.2%. The cp genome has 134 annotated genes, including 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Among these genes, nine genes have one intron and two genes contain two introns. The phylogenetic tree based on 16 complete plastomes of support close relationships among two species of Swertia with 100% bootstrap value.

| S-EPMC7707743 | biostudies-literature

Complete chloroplast genome sequence of Chimonanthus praecox link (Calycanthaceae): an endemic plant species in China.

Project description:Chimonanthus praecox, a deciduous shrub tree, is endemic to China and widely cultivated in the world as a popular garden and ornamental plant. Here, we have reported its complete chloroplast genome with a length of 153,181 bp, containing a large single copy (LSC) region of 86,916 bp, a small single copy (SSC) region of 19,767 bp and two identical inverted repeat regions (IRs) of 23,249 bp. The overall GC contents of the plastome were 39.27%. A total of 114 unique genes were successfully annotated consisting of 80 protein-coding genes, 30 tRNA genes and four rRNA genes. Sixteen genes each possessed one intron and three genes had two introns. The ML phylogenetic analysis supports Chimonanthus as sister to Calycanthus. This result will be helpful for genetic breeding and population genetics of C. praecox, DNA barcoding of Chimonanthus, and phylogenetic studies of Calycanthaceae.

| S-EPMC7782217 | biostudies-literature

The complete chloroplast genome sequence of Acer cinnamomifolium (Aceraceae), a plant species endemic to China.

Project description:Acer cinnamomifolium (Aceraceae) is a plant species endemic to China. In our present study, the complete chloroplast (cp) genome sequence of Acer cinnamomifolium was assembled from Illumina pair-end sequencing data. The complete cp genome sequence of A. cinnamomifolium was 156,227 bp in size. Totally, 139 genes were identified, including 88 protein-coding genes, 40 transfer RNAs, 8 ribosomal RNA genes, and 3 pseudogenes (infA, ycf1, and rps2). Phylogenetic analysis results showed that A. cinnamomifolium is sister to Acer sino-oblongum, with a support rate of 100%.

| S-EPMC7707229 | 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