Browse
Submit Data
Databases
API
Help

Dataset Information

39 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of actinidia valvata.

ABSTRACT: In this study, we first presented the complete chloroplast genome of Actinidia valvata by using Illumina Novaseq sequencing. Its complete chloroplast genome is 156,596 bp in length, containing a large single copy region of 88,477 bp and a small single copy region of 20,379 bp separated by a pair of inverted repeat regions of 23,870 bp. The chloroplast genome contains 112 unique genes, including 78 protein-coding genes, 30 tRNA, and four rRNA genes. Phylogenetic analysis based on chloroplast genome sequences of ten plants from the family Actinidiaceae showed that A. valvata is more closely related to A. polygama than other members.

SUBMITTER: Chen YT

PROVIDER: S-EPMC7782910 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome sequence of actinidia valvata.

Chen Yi-Ting YT Lai Rui-Lian RL Cheng Chun-Zhen CZ Gao Min-Xia MX Chen Wen-Guang WG Wu Ru-Jian RJ Feng Xin X

Mitochondrial DNA. Part B, Resources 20200513 3

In this study, we first presented the complete chloroplast genome of Actinidia valvata by using Illumina Novaseq sequencing. Its complete chloroplast genome is 156,596 bp in length, containing a large single copy region of 88,477 bp and a small single copy region of 20,379 bp separated by a pair of inverted repeat regions of 23,870 bp. The chloroplast genome contains 112 unique genes, including 78 protein-coding genes, 30 tRNA, and four rRNA genes. Phylogenetic analysis based on chloropla ...[more]

PMID: 33457746

Similar Datasets

The complete chloroplast genome sequence of Actinidia eriantha.

Project description:The complete chloroplast (cp) genome sequence of Actinidia eriantha was sequenced and assembled using Illumina paired-end data. The cp genome from A. eriantha is 156,964 bp in length, composed of a pair of 23,892 bp inverted repeat regions (IR) separated by a large single copy region (LSC) of 88,639 bp and a small single copy region (SSC) of 20,541 bp. The cp genome contained 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and four ribosomal RNA genes. The phylogenetic position of A. eriantha based the cp genome data was sister to the group A. rufa, A. deliciosa, and A. chinensis.

| S-EPMC7687386 | biostudies-literature

The complete chloroplast genome sequence of Actinidia styracifolia C. F. Liang.

Project description:The complete chloroplast (cp) genome sequence of Actinidia styracifolia C. F. Liang was assembled using Illumina pair-end sequencing data in this study. The assembled plastome was 156,845 bp in length, including a large single copy (LSC) region of 88,624 bp and a small single copy (SSC) region of 20,535bp, which were separated by two inverted repeat (IR) regions of 23,843 bp. The plastome contains 113 different genes, consisting of 79 unique protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis based on chloroplast genomes revealed that A. styracifolia has a close genetic relationship with A. eriantha.

| S-EPMC7721030 | biostudies-literature

The complete chloroplast genome sequence of Actinidia arguta var. giraldii.

Project description:The complete chloroplast (cp) genome sequence of Actinidia arguta var. giraldii (Diels) Vorosch. was assembled and characterized by Illumina pair-end sequencing date. The complete plastid genome was 156,729 bp in length, containing a large single-copy (LSC) of 89,647 bp, and a small single-copy (SSC) of 22,482 bp, which was separated by a pair of 22,300 bp inverted repeat regions (IR). A total of 131 unique genes were identified, including 84 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. The phylogenetic position based on the chloroplast genome of 11 species showed that A. arguta var. giraldii was sister to Actinidia kolomikta.

| S-EPMC7872529 | biostudies-literature

The complete chloroplast genome sequence of Actinidia arguta using the PacBio RS II platform.

Project description:Actinidia arguta is the most basal species in a phylogenetically and economically important genus in the family Actinidiaceae. To better understand the molecular basis of the Actinidia arguta chloroplast (cp), we sequenced the complete cp genome from A. arguta using Illumina and PacBio RS II sequencing technologies. The cp genome from A. arguta was 157,611 bp in length and composed of a pair of 24,232 bp inverted repeats (IRs) separated by a 20,463 bp small single copy region (SSC) and an 88,684 bp large single copy region (LSC). Overall, the cp genome contained 113 unique genes. The cp genomes from A. arguta and three other Actinidia species from GenBank were subjected to a comparative analysis. Indel mutation events and high frequencies of base substitution were identified, and the accD and ycf2 genes showed a high degree of variation within Actinidia. Forty-seven simple sequence repeats (SSRs) and 155 repetitive structures were identified, further demonstrating the rapid evolution in Actinidia. The cp genome analysis and the identification of variable loci provide vital information for understanding the evolution and function of the chloroplast and for characterizing Actinidia population genetics.

| S-EPMC5968424 | biostudies-literature

Assembly and phylogenetic analysis of the complete chloroplast genome sequence of Actinidia setosa.

Project description:The complete chloroplast (cp) genome sequence of Actinidia setosa (A. setosa) was sequenced and assembled into a circular genome of 156,728 bp length using Illumina paired-end data. The cp genome composed of a pair of 24,090 bp inverted repeat (IR) regions separated by a large single copy region (LSC) of 88,256 bp and a small single copy region (SSC) of 20,292 bp. Additionally, a total of 131 genes, including 85 protein-coding genes, 38 tRNA genes and 8 rRNA genes, were identified in the A. setosa cp genome. Phylogenetic analysis showed that A. setosa was evolutionarily close to other two kiwifruits A. deliciosa and A. chinensis.

| S-EPMC7707611 | biostudies-literature

The complete chloroplast genome of Actinidia fulvicoma.

Project description:The species of genus Actinidia are economically and nutritionally important fruits with remarkably high vitamin C content. Here, we assembled and characterized the complete chloroplast (cp) genome sequence of Actinidia fulvicoma (A. fulvicoma) using Illumina paired-end sequencing data. The cp genome is 157,339 bp in length, including a large single-copy region (LSC) of 88,741 bp, a small single-copy region (SSC) of 20,512 bp, and a pair of 24,043 bp inverted repeat (IR) regions. A total of 131 genes, consisting of 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes, were annotated in the A. fulvicoma cp genome. Phylogenetic analysis confirmed the evolutionary position of A. fulvicoma within the genus Actinidia.

| S-EPMC7707750 | biostudies-literature

The complete chloroplast genome of Actinidia macrosperma.

Project description:Actinidia macrosperma (A. macrosperma) is a medicinal plant in China, which has been well known for its activities against leprosy and cancers. In this study, we assembled and characterized the complete chloroplast (cp) genome sequence of A. macrosperma in an effort to provide genomic resources for promoting its conservation. The cp genome is 156,231 bp in length, containing a pair of 23,720 bp inverted repeat (IR) regions, which is separated by a large single copy region (LSC) of 88,214 bp and a small single copy region (SSC) of 20,577 bp. A total of 132 genes were annotated in this cp genome, including 85 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Phylogenetic analysis highly supported that A. macrosperma was evolutionarily close to another Actinidia species Actinidia deliciosa.

| S-EPMC7707781 | biostudies-literature

The complete chloroplast genome of Actinidia rubus (Actinidiaceae).

Project description:A complete chloroplast genome of Actinidia rubus, an endemic shrub in China, was sequenced and identified. The length of genome is 156,573 bp, and the GC content is 37.3%. This genome contains a large single copy (LSC; 88,473 bp) region, a small single copy (SSC; 20,492) region, a pair of inverted repeat (IR; 23,804) regions. A total of 113 unique genes were identified, including 78 protein-coding genes, 31 tRNA genes and 4 rRNA genes. The phylogenetic analysis based on complete chloroplast genome of 10 species showed that Actintdia eriantha was sister to A. rubus.

| S-EPMC7748799 | biostudies-literature

Characterization of the complete chloroplast genome of Actinidia hemsleyana.

Project description:The completed chloroplast genome sequence of Actinidia hemsleyana, collected from eastern China, was firstly determined using next-generation sequencing (NGS) and bioinformatic analysis. The length of cp genome was 156,845 bp, including a large single-copy (LSC) region of 88,666 bp and a small single-copy (SSC) region of 20,543 bp, which were separated by a pair of inverted repeats (IRs) of 23,818 bp. The cp genome contained 132 genes, including 83 protein-coding genes, 41 tRNA genes, and 8 rRNA genes. The overall GC content was 37.19%, whereas the corresponding values of the LSC, SSC, and IR regions were 35.46%, 31.09%, and 43.06%, respectively. Phylogenetic analysis based on whole cp genome sequences of 20 Actinidia species showed that A. hemsleyana has the closest relationship with A.latifolia.

| S-EPMC8530474 | biostudies-literature

Characterization of the complete chloroplast genome of Actinidia Melanandra (Actinidiaceae).

Project description:The whole chloroplast (cp) genome sequence of Actinidia melanandra has been characterized from Illumina pair-end sequencing. The complete cp genome was 156,124 bp in length, containing a large single-copy region (LSC) of 88,006 bp and a small single-copy region (SSC) of 20,332 bp, which were separated by a pair of inverted repeat (IR) regions of 23,893 bp. The genome contained 131 genes, including 84 protein-coding genes, 39 tRNA genes, and 8 ribosomal RNA genes (4 rRNA species). Most genes occur as a single copy, while 17 gene species are duplicated. Phylogenetic analysis revealed that A. melanandra is closely related to the species of A. deliciosa and A. chinensis.

| S-EPMC7687634 | biostudies-literature