Dataset Information

Genetic and phylogenetic relationships analysis of the complete chloroplast genome Cucumis sativus to China.

ABSTRACT: Cucumber, Cucumis sativus is one of the most cultivated vegetables in the world, which is mostly consumed raw in China. The complete chloroplast genome of C. sativus was assembled and annotated in this study. Its size was 155,525?bp, containing a large single-copy region of 86,878?bp, a small single-copy region of 18,269?bp and a pair of IR regions of 25,189?bp. Whole chloroplast genome of C. sativus contains 131 genes, including 77 protein-coding genes (PCGs), 46 transfer RNA genes (tRNAs), and 8 ribosome RNA genes (rRNAs). The overall nucleotide composition is: A of 31.1%, T of 31.9%, C of 18.8% and G of 18.2%, with a total GC content of the chloroplast genome 37.0% and AT of 63.0%. Genetic and phylogenetic analysis based on 10 plants species confirmed the position of C. sativus closely related to Cucurbitaceae species of Cucumis hystrix.

SUBMITTER: Xiao W

PROVIDER: S-EPMC7707661 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genetic and phylogenetic relationships analysis of the complete chloroplast genome Cucumis sativus to China.

Xiao Wei W Wang Xuanyao X Bie Mei M

Mitochondrial DNA. Part B, Resources 20191108 2

Cucumber, Cucumis sativus is one of the most cultivated vegetables in the world, which is mostly consumed raw in China. The complete chloroplast genome of C. sativus was assembled and annotated in this study. Its size was 155,525 bp, containing a large single-copy region of 86,878 bp, a small single-copy region of 18,269 bp and a pair of IR regions of 25,189 bp. Whole chloroplast genome of C. sativus contains 131 genes, including 77 protein-coding genes (PCGs), 46 transfer R ...[more]

PMID: 33366242

Similar Datasets

Project description:BackgroundThe plastome of medicinal and endangered species in Kingdom of Saudi Arabia, Barleria prionitis was sequenced. The plastome was compared with that of seven Acanthoideae species in order to describe the plastome, spot the microsatellite, assess the dissimilarities within the sampled plastomes and to infer their phylogenetic relationships.ResultsThe plastome of B. prionitis was 152,217 bp in length with Guanine-Cytosine and Adenine-Thymine content of 38.3 and 61.7% respectively. It is circular and quadripartite in structure and constitute of a large single copy (LSC, 83, 772 bp), small single copy (SSC, 17, 803 bp) and a pair of inverted repeat (IRa and IRb 25, 321 bp each). 131 genes were identified in the plastome out of which 113 are unique and 18 were repeated in IR region. The genome consists of 4 rRNA, 30 tRNA and 80 protein-coding genes. The analysis of long repeat showed all types of repeats were present in the plastome and palindromic has the highest frequency. A total number of 98 SSR were also identified of which mostly were mononucleotide Adenine-Thymine and are located at the non coding regions. Comparative genomic analysis among the plastomes revealed that the pair of the inverted repeat is more conserved than the single copy region. In addition high variation is observed in the intergenic spacer region than the coding region. The genes, ycf1and ndhF and are located at the border junction of the small single copy region and IRb region of all the plastome. The analysis of sequence divergence in the protein coding genes indicates that the following genes undergo positive selection (atpF, petD, psbZ, rpl20, petB, rpl16, rps16, rpoC, rps7, rpl32 and ycf3). Phylogenetic analysis indicated sister relationship between Ruellieae and Justcieae. In addition, Barleria, Justicia and Ruellia are paraphyletic, suggesting that Justiceae, Ruellieae, Andrographideae and Barlerieae should be treated as tribes.ConclusionsThis study sequenced and assembled the first plastome of the taxon Barleria and reported the basics resources for evolutionary studies of B. prionitis and tools for phylogenetic relationship studies within the core Acanthaceae.

Dataset Information

Genetic and phylogenetic relationships analysis of the complete chloroplast genome Cucumis sativus to China.

Publications

Genetic and phylogenetic relationships analysis of the complete chloroplast genome <i>Cucumis sativus</i> to China.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets