Chloroplast characterizations and phylogenetic location of a common ornamental cherry cultivar, <i>Prunus campanulata ‘</i>Kanhizakura-plena<i>’</i> (Rosaceae)

Zhou, Yuzhen; Zheng, Yan; Chen, Bin; Wei, Ziling; Lin, Weijie; Zhao, Kai

doi:10.1080/23802359.2019.1687354

Cited by 3 publications

(1 citation statement)

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“…The PCP is native to China and is an excellent flowering cherry cultivar due to its attractive flower traits, including dark red colour, multiple petals and blossoms in early spring. Recently, PCP has been widely cultivated in central and southern China (Zhou et al., 2019). In this study, the high‐quality chromosome‐scale genome of PCP was generated with a combination of long‐ and short‐read sequencing.…”

Section: Discussionmentioning

confidence: 99%

Genome assembly, resequencing and genome‐wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry

Nie

Zhang

Zhang³

et al. 2023

The Plant Journal

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SUMMARY Flowering cherry is a very popular species around the world. High‐quality genome resources for different elite cultivars are needed, and the understanding of their origins and the regulation of key ornamental traits are limited for this tree. Here, a high‐quality chromosome‐scale genome of Prunus campanulata ‘Plena’ (PCP), which is a native and elite flowering cherry cultivar in China, was generated. The contig N50 of the genome was 18.31 Mb, and 99.98% of its contigs were anchored to eight chromosomes. Furthermore, a total of 306 accessions of flowering cherry germplasm and six lines of outgroups were collected. Resequencing of these 312 lines was performed, and 761 267 high‐quality genomic variants were obtained. The origins of flowering cherry were predicted, and these 306 accessions could be classified into three clades, A, B and C. According to phylogenetic analysis, we predicted two origins of flowering cherry. Flowering cherry in clade A originated in southern China, such as in the Himalayan Mountains, while clades B and C originated in northeastern China. Finally, a genome‐wide association study of flower colour was performed for all 312 accessions of flowering cherry germplasm. A total of seven quantitative trait loci (QTLs) were identified. One gene encoding glycosylate transferase was predicted as the candidate gene for one QTL. Taken together, our results provide a valuable genomic resource and novel insights into the origin, evolution and flower colour variations of flowering cherry.

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Section: Discussionmentioning

confidence: 99%

Genome assembly, resequencing and genome‐wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry

Nie

Zhang

Zhang³

et al. 2023

The Plant Journal

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Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species

Feng,

Zhao,

et al. 2023

BMC Genomics

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Background Prunus cistena is an excellent color leaf configuration tree for urban landscaping in the world, which has purplish red leaves, light pink flowers, plant shape and high ornamental value. Genomic resources for P. cistena are scarce, and a clear phylogenetic and evolutionary history for this species has yet to be elucidated. Here, we sequenced and analyzed the complete chloroplast genome of P. cistena and compared it with related species of the genus Prunus based on the chloroplast genome. Results The complete chloroplast genome of P. cistena is a 157,935 bp long typical tetrad structure, with an overall GC content of 36.72% and higher GC content in the in the inverted repeats (IR) regions than in the large single-copy (LSC) and small single-copy (SSC) regions. It contains 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The ycf3 and clpP genes have two introns, with the longest intron in the trnK-UUU gene in the LSC region. Moreover, the genome has a total of 253SSRs, with the mononucleotide SSRs being the most abundant. The chloroplast sequences and gene arrangements of P. cistena are highly conserved, with the overall structure and gene order similar to other Prunus species. The atpE, ccsA, petA, rps8, and matK genes have undergone significant positive selection in Prunus species. P. cistena has a close evolutionary relationship with P. jamasakura. The coding and IR regions are more conserved than the noncoding regions, and the chloroplast DNA sequences are highly conserved throughout the genus Prunus. Conclusions The current genomic datasets provide valuable information for further species identification, evolution, and phylogenetic research of the genus Prunus.

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Complete chloroplast genome sequences of the ornamental plant Prunus Cistena and comparative and phylogenetic analyses with its closely related species

Feng

Zhao

An³

et al. 2023

Preprint

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Background Prunus Cistena is an excellent color leaf configuration tree for urban landscaping in the world, which has purplish red leaves, light pink flowers, plant shape and high ornamental value. Genomic resources for P. Cistena are scarce, and a clear phylogenetic and evolutionary history for this species has yet to be elucidated. Here, we sequenced and analyzed the complete chloroplast (cp) genome of P. Cistena and compared it with related species of Prunus genus based on chloroplast genome.Results The complete chloroplast genome of P. Cistena was 157,935 bp in length, which had a typical tetrad structure. The overall GC content was 36.72%, while IR regions displayed a higher GC content than LSC and SSC regions. It encoded 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The ycf3 and clpP genes had two introns; the longest intron was trnK-UUU gene in the LSC region. There were 253 SSRs, and the mononucleotide SSRs were the most abundant. The chloroplast sequences and gene arrangements of P. Cistena were conserved, which overall structure and gene order were similar to other Prunus species. The atpE, ccsA, petA, rps8 and matK gene had significant positive selection in Prunus species. P. Cistena had a close evolutionary relationship with the P. jamasakura. The coding region and IR region were more conserved than noncoding region, and the cpDNA sequences highly conserved throughout the genus Prunus.Conclusions The current genomic datasets provide valuable information for further species identification, evolution, and phylogenetic research of genus Prunus.

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Chloroplast characterizations and phylogenetic location of a common ornamental cherry cultivar, Prunus campanulata ‘Kanhizakura-plena’ (Rosaceae)

Cited by 3 publications

References 8 publications

Genome assembly, resequencing and genome‐wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry

Genome assembly, resequencing and genome‐wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry

Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species

Complete chloroplast genome sequences of the ornamental plant Prunus Cistena and comparative and phylogenetic analyses with its closely related species

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