Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Zhao Y

PROVIDER: S-EPMC7687634 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

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

Zhao Yuemei Y Zhao Zhixin Z Tang Weili W Li Xiaoling X Zhao Yongping Y Gao Baoyun B Xie Xiaodan X Zhang Xiaobin X

Mitochondrial DNA. Part B, Resources 20190711 2

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 gen ...[more]

PMID: 33365471

Similar Datasets

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 and phylogenetic analysis of the complete chloroplast genome of Actinidia latifolia (Actinidiaceae).

Project description:The complete chloroplast (cp) genome of Actinidia latifolia was sequenced and assembled using Illumina pair-end sequencing data. The cp genome is 157,021 bp in length and comprises a large single copy (LSC) region of 88,557 bp and a small single copy (SSC) region of 21,562 bp separated by two inverted repeat (IR) regions of 23,451 bp. A total of 113 unique genes were identified, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis based on cp genomes of 20 Actinidiaceae species revealed that A. latifolia was evolutionarily close to A. eriantha, A. styracifolia, and A. fulvicoma.

| S-EPMC7928189 | biostudies-literature

The First Complete Chloroplast Genome Sequences in Actinidiaceae: Genome Structure and Comparative Analysis.

Project description:Actinidia chinensis is an important economic plant belonging to the basal lineage of the asterids. Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement. We report here the complete nucleotide sequences of the chloroplast genomes for Actinidia chinensis and A. chinensis var deliciosa obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The total genome size ranges from 155,446 to 157,557 bp, with an inverted repeat (IR) of 24,013 to 24,391 bp, a large single copy region (LSC) of 87,984 to 88,337 bp and a small single copy region (SSC) of 20,332 to 20,336 bp. The genome encodes 113 different genes, including 79 unique protein-coding genes, 30 tRNA genes and 4 ribosomal RNA genes, with 16 duplicated in the inverted repeats, and a tRNA gene (trnfM-CAU) duplicated once in the LSC region. Comparisons of IR boundaries among four asterid species showed that IR/LSC borders were extended into the 5' portion of the psbA gene and IR contraction occurred in Actinidia. The clap gene has been lost from the chloroplast genome in Actinidia, and may have been transferred to the nucleus during chloroplast evolution. Twenty-seven polymorphic simple sequence repeat (SSR) loci were identified in the Actinidia chloroplast genome. Maximum parsimony analyses of a 72-gene, 16 taxa angiosperm dataset strongly support the placement of Actinidiaceae in Ericales within the basal asterids.

| S-EPMC4457681 | 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 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 valvata.

Project description: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.

| S-EPMC7782910 | 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 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

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

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