Characterization of the complete chloroplast genomes of the endangered shrub species Prunus mongolica and Prunus pedunculata (Rosales: rosaceae)

Duan, Yanwu; Shen, Yehua; Kang, Furen; Wang, Jianwu

doi:10.1007/s12686-017-0979-7

Cited by 3 publications

(3 citation statements)

References 14 publications

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“…A complete cp genome is a valuable resource of information for studying plant taxonomy, phylogenetic reconstruction, and historical biogeographic inference. Next-generation sequencing (NGS) technologies have enabled a rapid expansion in the database of whole cp genomes [ 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae

Liu

Kong

Zhou

et al. 2018

IJMS

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The subfamily Caesalpinioideae of the Fabaceae has long been recognized as non-monophyletic due to its controversial phylogenetic relationships. Cercis chuniana, endemic to China, is a representative species of Cercis L. placed within Caesalpinioideae in the older sense. Here, we report the whole chloroplast (cp) genome of C. chuniana and compare it to six other species from the Caesalpinioideae. Comparative analyses of gene synteny and simple sequence repeats (SSRs), as well as estimation of nucleotide diversity, the relative ratios of synonymous and nonsynonymous substitutions (dn/ds), and Kimura 2-parameter (K2P) interspecific genetic distances, were all conducted. The whole cp genome of C. chuniana was found to be 158,433 bp long with a total of 114 genes, 81 of which code for proteins. Nucleotide substitutions and length variation are present, particularly at the boundaries among large single copy (LSC), inverted repeat (IR) and small single copy (SSC) regions. Nucleotide diversity among all species was estimated to be 0.03, the average dn/ds ratio 0.3177, and the average K2P value 0.0372. Ninety-one SSRs were identified in C. chuniana, with the highest proportion in the LSC region. Ninety-seven species from the old Caesalpinioideae were selected for phylogenetic reconstruction, the analysis of which strongly supports the monophyly of Cercidoideae based on the new classification of the Fabaceae. Our study provides genomic information for further phylogenetic reconstruction and biogeographic inference of Cercis and other legume species.

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Section: Introductionmentioning

confidence: 99%

Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae

Liu

Kong

Zhou

et al. 2018

IJMS

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“…In addition, P. pedunculata was traditionally classified as a member of genus Amygdalus (Lu & Bartholomew, 2003). However, Yazbek & Oh (2013), Yazbek & Al-Zein (2014), and Duan et al (2018) suggested that P. pendunculata should be excluded from subgenus Amygdalus , and recovered in subgenus Prunus . P. mongolica and P. davidiana were closely related to species of peach ( P. persica ), and previous studies based on molecular and morphological analysis all supported the placement of subgenus Amygdalus (Yazbek & Oh, 2013; Yazbek & Al-Zein, 2014).…”

Section: Disscussionmentioning

confidence: 99%

“…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 complete chloroplast genome of Prunus triloba var. plena and comparative analysis of Prunus species: genome structure, sequence divergence, and phylogenetic analysis

et al. 2021

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Characterization of the complete chloroplast genomes of the endangered shrub species Prunus mongolica and Prunus pedunculata (Rosales: rosaceae)

Cited by 3 publications

References 14 publications

Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae

Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae

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

The complete chloroplast genome of Prunus triloba var. plena and comparative analysis of Prunus species: genome structure, sequence divergence, and phylogenetic analysis

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