Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Akebia longeracemosa (Lardizabalaceae).

ABSTRACT: The complete chloroplast genome of Akebia longeracemosa, a monoecious woody vine endemic to China, was determined. The total genome size is 158,020 bp, containing a large single copy region of 86,659 bp, a small single copy region of 19,059 bp, and a pair of inverted repeats of 26,151 bp. The chloroplast genome encodes 113 unique genes, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Among them, fifteen genes have one intron each, and three genes contain two introns. The overall GC content is 38.7%, while the corresponding values of LSC, SSC, and IR regions are 37.1, 33.6, and 43.1%, respectively. Phylogenetic analysis showed that A. longeracemosa was closely related to A. trifoliata.

SUBMITTER: Xiao X

PROVIDER: S-EPMC7954470 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome of Akebia trifoliata (Lardizabalaceae), a traditional herb in China.

Project description:Akebia trifoliata, commonly known as 'Bayuezha' in China, has been widely used as traditional Chinese medicinal herbs with a long history. In the present study, the complete chloroplast genome of A. trifoliata was sequenced using Illumina high-throughput sequencing approach. The length of the complete chloroplast genome is 157,952 bp with 38.7% GC content. It contains 131 genes, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicated that A. trifoliata was closely related to another Lardizabalaceae species, Akebia quinata, which further confirms traditional species classification.

| S-EPMC7782334 | biostudies-literature

The complete chloroplast genome of Akebia trifoliata subsp. australis (Lardizabalaceae), a medicinal plant in China.

Project description:Akebia trifoliata subsp. australis (Diels) T.Shimizu is a medicinal plant in China. Here, the complete chloroplast (cp) genome sequence of A. trifoliata subsp. australis was assembled and characterized as a resource for future genetic studies. The whole cp genome was 157,952 bp in length, containing of a large single-copy (LSC) region of 86,596 bp, a small single-copy (SSC) region of 19,060 bp, and two inverted repeat (IR) regions of 26,148 bp. The new sequence possessed total 113 unique genes, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The nucleotide composition was asymmetric (30.3% A, 19.7% C, 19.0% G and 31.0% T) with an overall GC content of 38.7%. The maximum likelihood phylogenetic analysis based on 10 cp genomes indicated that A. trifoliata subsp. australis was closely related to Akebia trifoliata subsp. trifoliata. However, Akebia quinata was closely related to Stauntonia obovatifoliola.

| S-EPMC7782757 | biostudies-literature

The complete chloroplast genome of Holboellia angustifolia (Ranales: Lardizabalaceae), a traditional herbal species.

Project description:The complete chloroplast genome of Holboellia angustifolia was 157,797 bp in length, displayed a typical quadripartite structure, composed of a LSC region of 86,543 bp and a SSC region of 18,972 bp, separated by a pair of IRs of 26,141 bp each. The chloroplast genome contains 130 genes, consisting of 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Fifteen genes have one intron, and 3 genes contain two introns. The overall A/T content in the chloroplast genome of H. angustifolia was 61.31%. Phylogenetic analysis showed that H. angustifolia was closely related to Holboellia latifolia.

| S-EPMC7707227 | biostudies-literature

Complete chloroplast genome sequence of Stauntonia hexaphylla (Ranunculales: Lardizabalaceae), a species endemic to Korea.

Project description:The complete chloroplast (cp) genome of Stauntonia hexaphylla, a monotypic genus native to Korea, was determined. The whole cp genome is 158,390 bp in size, containing a large single-copy (LSC) region of 87,115 bp and a small single-copy region (SSC) of 18,928 bp, separated by a pair of inverted repeats (IRs) of 26,174 bp. The cp genome encodes 117 genes, including 79 protein-coding, 38 tRNA-coding, and 8 rRNA-coding genes. The overall GC content is 37.8%. A phylogenetic analysis demonstrated a close relationship between S. hexaphylla and S. obovatifoliola subsp. urophylla. The cp genome will provide new insight into the evolution of Lardizabalaceae.

| S-EPMC7971286 | biostudies-literature

Complete chloroplast genome of Holboellia grandiflora Reaubourg (Lardizabalaceae), a plant with an edible fruit.

Project description:Holboellia grandiflora Réaubourg (Lardizabalaceae) is an evergreen twining perennial woody vine. To our knowledge, this is the first report on the complete chloroplast genome sequence of H. grandiflora. The complete chloroplast genome sequence was 157,811 bp in length and contained a large single-copy region of 86,554 bp and a small single-copy region of 18,975 bp. A pair of inverted repeats of 26,141 bp were included. It contained 130 genes, comprising 37 transfer RNA genes, and eight ribosomal RNA genes, as well as 85 coding sequences (CDSs). The GC content of the complete chloroplast genome sequence was 38.7%. The phylogenetic tree showed a close relationship among the three species of Holboellia (H. grandiflora, H. angustifolia, and H. latifolia). These findings provide a reference for phylogenetic relationships and assessment of the genetic structure of the Lardizabalaceae family.

| S-EPMC9246023 | biostudies-literature

Keteleeria cyclolepis complete chloroplast genome

Project description:Keteleeria cyclolepis complete chloroplast genome Raw sequence reads

| PRJNA723268 | ENA

Complete chloroplast genome of Sedum sarmentosum and chloroplast genome evolution in Saxifragales.

Project description:Comparative chloroplast genome analyses are mostly carried out at lower taxonomic levels, such as the family and genus levels. At higher taxonomic levels, chloroplast genomes are generally used to reconstruct phylogenies. However, little attention has been paid to chloroplast genome evolution within orders. Here, we present the chloroplast genome of Sedum sarmentosum and take advantage of several available (or elucidated) chloroplast genomes to examine the evolution of chloroplast genomes in Saxifragales. The chloroplast genome of S. sarmentosum is 150,448 bp long and includes 82,212 bp of a large single-copy (LSC) region, 16.670 bp of a small single-copy (SSC) region, and a pair of 25,783 bp sequences of inverted repeats (IRs).The genome contains 131 unique genes, 18 of which are duplicated within the IRs. Based on a comparative analysis of chloroplast genomes from four representative Saxifragales families, we observed two gene losses and two pseudogenes in Paeonia obovata, and the loss of an intron was detected in the rps16 gene of Penthorum chinense. Comparisons among the 72 common protein-coding genes confirmed that the chloroplast genomes of S. sarmentosum and Paeonia obovata exhibit accelerated sequence evolution. Furthermore, a strong correlation was observed between the rates of genome evolution and genome size. The detected genome size variations are predominantly caused by the length of intergenic spacers, rather than losses of genes and introns, gene pseudogenization or IR expansion or contraction. The genome sizes of these species are negatively correlated with nucleotide substitution rates. Species with shorter duration of the life cycle tend to exhibit shorter chloroplast genomes than those with longer life cycles.

| S-EPMC3799696 | biostudies-literature

The complete chloroplast genome of Agave angustifolia

Project description:Abstract Agave angustifolia is commonly used for the production of bacanora, a kind of fermented and distilled beverage in Mexico. In the present study, we have successfully assembled its chloroplast genome. The full length of the genome is 157,274 bp with the GC content of 37.84%. There is a large single copy region (LSC) of 85,895 bp, a pair of inverted repeat regions (IR) of 26,575 bp and a small single copy region (SSC) of 18,229 bp in the genome. A total of 132 genes are annotated in the cp genome. Among these, there are 86 protein-coding genes, 38 tRNAs and 8 rRNAs. Phylogenetic analysis reveals that A. angustifolia is closely related with A. H11648.

| S-EPMC8547807 | biostudies-literature

Complete chloroplast genome comparisons for Pityopsis (Asteraceae).

Project description:Pityopsis includes several regionally and one federally endangered species of herbaceous perennials. Four species are highly localized, including the federally endangered P. ruthii. The genus includes several ploidy levels and interesting ecological traits such as drought tolerance and fire-dependent flowering. Results from previous cladistic analyses of morphology and from initial DNA sequence studies did not agree with one another or with the infrageneric taxonomic classification, with the result that infrageneric relationships remain unresolved. We sequenced, assembled, and compared the chloroplast (cp) genomes of 12 species or varieties of Pityopsis to better understand generic evolution. A reference cp genome 152,569 bp in length was assembled de novo from P. falcata. Reads from other sampled species were then aligned to the P. falcata reference and individual chloroplast genomes were assembled for each, with manual gapfilling and polishing. After removing the duplicated second inverted region, a multiple sequence alignment of the cp genomes was used to construct a maximum likelihood (ML) phylogeny for the twelve cp genomes. Additionally, we constructed a ML phylogeny from the nuclear ribosomal repeat region after mapping reads to the Helianthus annuus region. The chloroplast phylogeny supported two clades. Previously proposed clades and taxonomic sections within the genus were largely unsupported by both nuclear and chloroplast phylogenies. Our results provide tools for exploring hybridity and examining the physiological and genetic basis for drought tolerance and fire-dependent flowering. This study will inform breeding and conservation practices, and general knowledge of evolutionary history, hybridization, and speciation within Pityopsis.

| S-EPMC7769439 | biostudies-literature

Complete chloroplast genome of Ophiorrhiza baviensis Drake

Project description:Ophiorrhiza baviensis chloroplast, complete genome

| PRJEB57743 | ENA