Dataset Information

Characterization of complete chloroplast genome and phylogenetic analysis of sweet cherry Cerasus avium (L.) Moench (Prunoideae, Rosaceae).

ABSTRACT: Sweet cherry (Cerasus avium (L.) Moench) belonging to family Rosaceae, is an important economical fruit crop worldwide. In this study, the complete chloroplast (cp) genome of sweet cherry was generated by De novo assembly with low coverage whole-genome sequencing data. The genome size was 157,987?bp in length consisting of a typical quadripartite structure; a large single-copy region (LSC, 85,975?bp), a small single-copy region (SSC, 19,121?bp) and a pair of inverted repeat regions (IRs, 26,445?bp each). A total of 115 genes were predicted including 82 protein-coding genes, 29 tRNA genes and four rRNA genes. Phylogenetic analysis based on 12 reported complete chloroplast genome indicated the monophyly of the genus Creasus including newly sequenced C. avium, which is conform to the traditional classification.

SUBMITTER: Chen T

PROVIDER: S-EPMC7800472 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Publications

Characterization of complete chloroplast genome and phylogenetic analysis of sweet cherry Cerasus avium (L.) Moench (Prunoideae, Rosaceae).

Chen Tao T Hu Guo-Ping GP Wang Yan Y Chen Qing Q Wang Lei L Zhang Jing J Tang Hao-Ru HR Wang Xiao-Rong XR

Mitochondrial DNA. Part B, Resources 20181031 2

Sweet cherry (Cerasus avium (L.) Moench) belonging to family Rosaceae, is an important economical fruit crop worldwide. In this study, the complete chloroplast (cp) genome of sweet cherry was generated by De novo assembly with low coverage whole-genome sequencing data. The genome size was 157,987 bp in length consisting of a typical quadripartite structure; a large single-copy region (LSC, 85,975 bp), a small single-copy region (SSC, 19,121 bp) and a pair of inverted repeat regions ...[more]

PMID: 33474490

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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

Characterization of complete chloroplast genome and phylogenetic analysis of sweet cherry Cerasus avium (L.) Moench (Prunoideae, Rosaceae).

Publications

Characterization of complete chloroplast genome and phylogenetic analysis of sweet cherry <i>Cerasus avium</i> (L.) Moench (Prunoideae, Rosaceae).

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