Characterization of the complete chloroplast genome of the Chinese cherry Prunus pseudocerasus (Rosaceae)

Feng, Ying; Liu, Tao; Wang, Xiaoyu; Li, Binbin; Liang, Chengcheng; Cai, Yuliang

doi:10.1007/s12686-017-0770-9

Cited by 19 publications

(15 citation statements)

References 8 publications

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“…Our data assume P. mira as the most closely related to P. mongolica and P. dulcis, and support the hypothesis of the hybrid origin of peach with almond [3,34]. Furthermore, the current analyses strongly support the monophyly of P. pseudocerasus as the rootstock for Chinese cherry species [35].…”

Section: Discussionsupporting

confidence: 84%

ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels in Prunus persica

Amar

2020

Journal of Genetic Engineering and Biotechnology

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Background: Chloroplast genome sequencing is becoming a valuable process for developing several DNA barcodes. At present, plastid DNA barcode for systematics and evolution in flowering plant rely heavily on the use of non-coding genes. The present study was performed to verify the novelty and suitability of the two hotspot barcode plastid coding gene ycf1 and ndhF, to estimate the rate of molecular evolution in the Prunus genus at low taxonomic levels. Results: Here, 25 chloroplast genomes of Prunus genus were selected for sequences annotation to search for the highly variable coding DNA barcode regions. Among them, 5 genera were of our own data, including the ornamental, cultivated, and wild haplotype, while 20 genera have been downloaded from the GenBank database. The results indicated that the two hotspot plastid gene ycf1 and ndhF were the most variable regions within the coding genes in Prunus with an average of 3268 to 3416 bp in length, which have been predicted to have the highest nucleotide diversity, with the overall transition/transversion bias (R = 1.06). The ycf1-ndhF structural domains showed a positive trend evident in structure variation among the 25 specimens tested, due to the variant overlap ' s gene annotation and insertion or deletion with a broad trend of the full form of IGS sequence. As a result, the principal component analysis (PCA) and the ML tree data drew an accurate monophyletic annotations cluster in Prunus species, offering unambiguous identification without overlapping groups between peach, almond, and cherry. Conclusion: To this end, we put forward the domain of the two-locus ycf1-ndhF genes as the most promising coding plastid DNA barcode in P. persica at low taxonomic levels. We believe that the discovering of further variable loci with high evolutionary rates is extremely useful and potential uses as a DNA barcode in P. persica for further phylogeny study and species identification.

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Section: Discussionsupporting

confidence: 84%

ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels in Prunus persica

Amar

2020

Journal of Genetic Engineering and Biotechnology

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“…The cp genome normally has a circular structure, and it is composed of a LSC region, a SSC region and two IR regions. From the results, the genome structure, gene order and GC content of P. avium ‘Summit’ were much similar to those reported Prunus cp genomes (Cho et al, 2016; Feng et al, 2018; Luan et al, 2018). Through comparative analysis of complete cp genome sequences, much genetic information could be discovered.…”

Section: Disscussionsupporting

confidence: 82%

“…As the plastid genome provides more accurate proofs to estimate genetic affinities and phylogenetic relationships, several plastomes of Prunus plants have been sequenced and reported, such as P. persica (Jansen et al, 2011), P. yedoensis (Cho et al, 2016), P. mume (Wang, Gao & Gao, 2016), Amygdalus mira (Amar et al, 2018), P. tomentosa (Chen et al, 2018b), P. takesimensis (Cho, Yang & Kim, 2018), P. mongolica (Duan et al, 2018), P. pedunculata (Duan et al, 2018; Wang et al, 2018a), P. pseudocerasus (Feng et al, 2018), P. serotina (Luan et al, 2018), Cerasus humilis (Mu et al, 2018), P. cerasoides (Xu et al, 2018), P. davidiana (Zhang et al, 2018), and P. speciosa (Sun, Katsuki & Liu, 2019).…”

Section: Introductionmentioning

confidence: 99%

Characterization and comparative analysis of the complete chloroplast genome sequence from Prunus avium ‘Summit’

Zhao

Yan

Ding

et al. 2019

PeerJ

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BackgroundSweet cherry (Prunus avium) is one of the most popular of the temperate fruits. Previous studies have demonstrated that there were several haplotypes in the chloroplast genome of sweet cherry cultivars. However, none of chloroplast genome of a sweet cherry cultivar were yet released, and the phylogenetic relationships among Prunus based on chloroplast genome data were unclear.MethodsIn this study, we assembled and annotated the complete chloroplast genome of a sweet cherry cultivar P. avium ‘Summit’ from high-throughput sequencing data. Gene Ontology (GO) terms were assigned to classify the function of the annotated genes. Maximum likelihood (ML) trees were constructed to reveal the phylogenetic relationships within Prunus species, using LSC (large single-copy) regions, SSC (small single-copy) regions, IR (inverted repeats) regions, CDS (coding sequences), intergenic regions, and whole cp genome datasets, respectively.ResultsThe complete plastid genome was 157, 886 bp in length with a typical quadripartite structure of LSC (85,990 bp) and SSC (19,080 bp) regions, separated by a pair of IR regions (26,408 bp). It contained 131 genes, including 86 protein-coding genes, 37 transfer RNA genes and 8 ribosomal RNA genes. A total of 77 genes were assigned to three major GO categories, including molecular function, cellular component and biological process categories. Comparison with other Prunus species showed that P. avium ‘Summit’ was quite conserved in gene content and structure. The non-coding regions, ndhc-trnV, rps12-trnV and rpl32-trnL were the most variable sequences between wild Mazzard cherry and ‘Summit’ cherry. A total of 73 simple sequence repeats (SSRs) were identified in ‘Summit’ cherry and most of them were mononucleotide repeats. ML phylogenetic tree within Prunus species revealed four clades: Amygdalus, Cerasus, Padus, and Prunus. The SSC and IR trees were incongruent with results using other cp data partitions. These data provide valuable genetic resources for future research on sweet cherry and Prunus species.

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“…The GC content is 36.7%, while the IR region has a GC content of 42.5%, significantly higher than that of the LSC and SSC regions, which are 34.6% and 30.2%, respectively. This is a sequence attribute that is seen more often in published Eurosids chloroplast genomes (Cho et al 2016;Feng et al 2017;Gichira et al 2017). Furthermore, while most repeats in chloroplast genomes are AT rich, a low number of repeats occur within the IR regions.…”

mentioning

confidence: 93%

The chloroplast genome of Cerasus campanulata (Maxim.) A.N. Vassiljeva

Cheng

Weng

Yang

et al. 2018

Mitochondrial DNA Part B

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The complete chloroplast genome of Cerasus campanulata was obtained by using 454 pyrosequencing technology. Cerasus campanulata chloroplast genome is 157,906 base pairs containing 115 unique genes, including 79 protein-coding genes, 39 tRNAs and eight rRNAs. Phylogenetic analysis of the protein-coding genes indicates that C. campanulata is clearly a member of the Rosaceae order.

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Characterization of the complete chloroplast genome of the Chinese cherry Prunus pseudocerasus (Rosaceae)

Cited by 19 publications

References 8 publications

ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels in Prunus persica

ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels in Prunus persica

Characterization and comparative analysis of the complete chloroplast genome sequence from Prunus avium ‘Summit’

The chloroplast genome of Cerasus campanulata (Maxim.) A.N. Vassiljeva

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