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The complete chloroplast genome of Prunus verecunda, and phylogenetic analysis with amygdaleae species.

ABSTRACT: We assembled complete chloroplast (cp) genome of Prunus verecunda based on Illumina sequencing. The cp genome of P. verecunda is 157,917?bp in length with 129 genes comprising 84 protein-coding genes, 37 tRNA genes and 8 rRNA ribosomal genes. The overall GC content of cp genome is 36.7%. A maximum likelihood phylogenetic analysis revealed that P. verecunda is sister to P. serrulata var. spontanea and P. maximowiczii.

SUBMITTER: Jiang D

PROVIDER: S-EPMC7707214 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of Prunus verecunda, and phylogenetic analysis with amygdaleae species.

Jiang Dongyue D Liu Xinhong X Shen Xin X

Mitochondrial DNA. Part B, Resources 20191004 2

We assembled complete chloroplast (cp) genome of Prunus verecunda based on Illumina sequencing. The cp genome of P. verecunda is 157,917 bp in length with 129 genes comprising 84 protein-coding genes, 37 tRNA genes and 8 rRNA ribosomal genes. The overall GC content of cp genome is 36.7%. A maximum likelihood phylogenetic analysis revealed that P. verecunda is sister to P. serrulata var. spontanea and P. maximowiczii. ...[more]

PMID: 33365982

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Project description:BackgroundThe large genus Ficus comprises approximately 800 species, most of which possess high ornamental and ecological values. However, its evolutionary history remains largely unknown. Plastome (chloroplast genome) analysis had become an essential tool for species identification and for unveiling evolutionary relationships between species, genus and other rank groups. In this work we present the plastomes of ten Ficus species.ResultsThe complete chloroplast (CP) genomes of eleven Ficus specimens belonging to ten species were determined and analysed. The full length of the Ficus plastome was nearly 160 kbp with a similar overall GC content, ranging from 35.88 to 36.02%. A total of 114 unique genes, distributed in 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, were annotated in each of the Ficus CP genome. In addition, these CP genomes showed variation in their inverted repeat regions (IR). Tandem repeats and mononucleotide simple sequence repeat (SSR) are widely distributed across the Ficus CP genome. Comparative genome analysis showed low sequence variability. In addition, eight variable regions to be used as potential molecular markers were proposed for future Ficus species identification. According to the phylogenetic analysis, these ten Ficus species were clustered together and further divided into three clades based on different subgenera. Simultaneously, it also showed the relatedness between Ficus and Morus.ConclusionThe chloroplast genome structure of 10 Ficus species was similar to that of other angiosperms, with a typical four-part structure. Chloroplast genome sizes vary slightly due to expansion and contraction of the IR region. And the variation of noncoding regions of the chloroplast genome is larger than that of coding regions. Phylogenetic analysis showed that these eleven sampled CP genomes were divided into three clades, clustered with species from subgenus Urostigma, Sycomorus, and Ficus, respectively. These results support the Berg classification system, in which the subgenus Ficus was further decomposed into the subgenus Sycomorus. In general, the sequencing and analysis of Ficus plastomes, especially the ones of species with no or limited sequences available yet, contribute to the study of genetic diversity and species evolution of Ficus, while providing useful information for taxonomic and phylogenetic studies of Ficus.

Dataset Information

The complete chloroplast genome of Prunus verecunda, and phylogenetic analysis with amygdaleae species.

Publications

The complete chloroplast genome of <i>Prunus verecunda</i>, and phylogenetic analysis with amygdaleae species.

Similar Datasets

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