Dataset Information

The complete plastid genome of cherry plants Prunus discoidea (Rosaceae) and its phylogenetic implication.

ABSTRACT: Prunus discoidea is an endemic cherry species with ornamental value, spread in eastern China (Anhui, Jiangxi, Zhejiang provinces). Little information is available regarding its genomic, with limited phylogenetic relationship study performed on P. discoidea until now. The plastid genome was 158,024?bp in length consisting of four regions: large single-copy region (85,953?bp), small single-copy region (19,113?bp), and a pair of inverted repeat regions (26,469?bp each). The plastid genome contained a total of 129 genes, including 84 coding genes, 8 rRNA genes, and 37 tRNA genes. Phylogenetic analysis for 20 reported genomes within the Prunus sensu lato showed three main clades of Prunus s.l. with strong supports.

SUBMITTER: Li M

PROVIDER: S-EPMC7707402 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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The complete plastid genome of cherry plants Prunus discoidea (Rosaceae) and its phylogenetic implication.

Li Meng M Song Yan-Feng YF Zhu Shu-Xia SX Zhu Hong H Yi Xian-Gui XG Chen Zhang-Chi ZC Li Ming-Zhi MZ Wang Xian-Rong XR

Mitochondrial DNA. Part B, Resources 20191018 2

Prunus discoidea is an endemic cherry species with ornamental value, spread in eastern China (Anhui, Jiangxi, Zhejiang provinces). Little information is available regarding its genomic, with limited phylogenetic relationship study performed on P. discoidea until now. The plastid genome was 158,024 bp in length consisting of four regions: large single-copy region (85,953 bp), small single-copy region (19,113 bp), and a pair of inverted repeat regions (26,469 bp each). The plastid ge ...[more]

PMID: 33366121

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Project description:Prunus subgenus Cerasus (cherry) is an economically important group that distributed in temperate regions of the northern hemisphere. However, shared interspecific morphological traits and variability across taxa of Cerasus are among the impediments to taxonomic efforts to correctly delimit taxa. This is further complicated by a lack of genetic information on these taxa, with no focused genomic or phylogenetic studies being done on Cerasus. In this study, we conducted comparative analysis on the complete plastid genomes (plastomes) of 20 Cerasus species to gain a greater understanding of the attributes of the plastome of these taxa while helping resolve their phylogenetic placement in Prunus sensu lato and interspecific relationships within the subgenus. Our results displayed that (1) the plastomes of the 20 Cerasus species studied exhibited a typical quadripartite structure with conversed genome arrangement, structure, and moderate divergence. (2) The average size of complete plastomes for the Cerasus taxa studied was 157,861 bp, ranging from 157,458 to 158,024 bp. A total of 134 genes were annotated, including 86 protein-coding genes, 40 tRNAs, and 8 rRNAs across all species. In simple sequence repeat analysis, we found Cerasus had a comparable number of dispersed and tandem repeats to those identified in other angiosperm taxa, with only P. pseudocerasus found to contain trinucleotide repeats. Nucleotide diversity analysis revealed that the trnG-GCC gene and rpl32-trnL region had the highest Pi value showing potential as phylogenetic markers. (3) Two phylogenetic trees of the plastomes verified the monophyletic relationship of Cerasus and provided a more resolved species-level phylogeny. Our study provides detailed plastome information for exploring the phylogeny of subg. Cerasus taxa. We identified various types of repeats and nucleotide diversity hotspots, which can be a reference for species identification and reconstruction of phylogenetic relationships.

Dataset Information

The complete plastid genome of cherry plants Prunus discoidea (Rosaceae) and its phylogenetic implication.

Publications

The complete plastid genome of cherry plants <i>Prunus discoidea</i> (Rosaceae) and its phylogenetic implication.

Similar Datasets

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