Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Catalpa 'Bairihua', a hybrid variety with multi season flowering.

ABSTRACT: The complete chloroplast genome of Catalpa 'Bairihua' a hybrid variety with multi season flowering obtained from hybrid progeny of C. bungei 'Luoqiu Sihao' (C. bungei '01' × C. bungei 'Changguo Qiu') and C. fargesii f. duclouxii was first sequenced with the Illumina HiSeq 2000 platform. Which was 158,210 bp in length with a typical quadruple structure and contained a large single copy (LSC: 84,928 bp) region and a small single copy (SSC: 12,664 bp) region that were separated by a pair of inverted repeats (IRa, b: 30,309 bp) region. The GC content of the whole chloroplast genome is 38.1%. A total of 130 genes was annotated in the complete chloroplast genome, including 85 protein-coding genes, 37 tRNA genes and 8rRNA genes. ML phylogenetic analysis by comparing with 39 chloroplast genomes of the Bignoniaceae indicated that Catalpa 'Bairihua' was close to Tecomaria capensis.

SUBMITTER: Li WQ

PROVIDER: S-EPMC7782214 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome sequence of the Alstroemeria hybrid variety 'Hanhera'.

Project description:Alstroemeria, a member of the Alstroemeriaceae family, is a species from South America. The chloroplast genome of Alstroemeria spp. was completed by de novo assembly using a small amount of whole genome sequencing data. The chloroplast genome of Alstroemeria spp. was 155,672 bp in length consisting of 84,379 bp of large single copy, 17,815 bp of small single copy, and 26,739 bp of a pair of inverted repeat regions. A total of 157 genes were annotated including 103 protein-coding genes (PCGs), 46 tRNA genes, and eight rRNA genes. Maximum likelihood phylogenetic analysis with seven species belonging to the Alstroemeriaceae or Liliaceae family revealed that Alstroemeria spp. is grouped with the species in the Alstroemeriaceae family.

| S-EPMC7759260 | 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 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 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 of agave hybrid 11648.

Project description:Agave hybrid 11648 is the most widely cultivated agave variety for sisal fiber production around the world. In the present study, we have successfully sequenced the chloroplast genome of A. H11648. The complete chloroplast genome size is 157,274 bp in length with a GC content of 37.8%. The genome contains a large single copy region (LSC) of 85,896 bp, a small single copy region (SSC) of 18,230 bp, and a pair of inverted repeat regions (IR) of 26,574 bp. 121 genes are annotated in the chloroplast genome. The numbers of protein-coding, tRNA and rRNA genes are 99, 40 and 8, respectively. Phylogenetic tree reveals that A. H11648 is closely related to A. americana.

| S-EPMC7781945 | biostudies-literature

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

Project description: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.

| S-EPMC8218834 | biostudies-literature

The complete chloroplast genome of Cannabis sativa variety Yunma 7.

Project description:Cannabis sativa variety Yunma 7 has been widely cultivated for hemp fiber production in Yunnan Province of China. In the present study, we have successfully sequenced the chloroplast genome of Yunma 7. The complete chloroplast genome size is 153,899 bp in length with a GC content of 36.67%. The genome contains a large single copy region (LSC) of 84,046 bp, a small single copy region (SSC) of 17,831 bp, and a pair of inverted repeat regions (IR) of 26,011 bp. A total of 74 protein-coding genes are annotated in the chloroplast genome, together with 37 tRNAs and 8 rRNAs. Phylogenetic tree reveals that Yunma 7 is closely related to Cannabis hybrid AK Royal Automatic reported by Matielo et al.

| S-EPMC7889209 | 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 sequence of flowering banana, Musa ornata.

Project description:Musa ornata (flowering banana) is one of more than 50 species of banana in the genus Musa of the family Musaceae. As sources of resistance to pathogens exist in germplasm, M. ornata is one of the possible hybrid parents for ameliorate commercial banana varieties. Herein, we report the complete chloroplast genome of M. ornata. The total length of the chloroplast genome is 169,989 bp with 36.82% GC content. The genome consisted of 35,426 bp of a pair of inverted repeat regions (IRs), 10,775 bp of small single copy region (SSC) and 88,362 bp of large single-copy region (LSC). A total of 136 functional genes were annotated, including 113 unique genes comprising 79 protein-coding genes, 4 ribosomal RNA (rRNA) genes and 30 transfer RNA (tRNA) genes. Maximum-likelihood phylogenetic analysis with Musaceae and Zingiberaceae species revealed that M. ornata is most closely grouped with Musa acuminata.

| S-EPMC7799988 | 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

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