Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species
Abstract 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 histor...
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BMC
2023-12-01
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| Cyfres: | BMC Genomics |
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| Mynediad Ar-lein: | https://doi.org/10.1186/s12864-023-09838-9 |
| _version_ | 1827590749945856000 |
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| author | Lijuan Feng Guopeng Zhao Mengmeng An Chuanzeng Wang Yanlei Yin |
| author_facet | Lijuan Feng Guopeng Zhao Mengmeng An Chuanzeng Wang Yanlei Yin |
| author_sort | Lijuan Feng |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-03-09T01:21:10Z |
| format | Article |
| id | doaj.art-1558abb891364752a4831689bbfd0e35 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-09T01:21:10Z |
| publishDate | 2023-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-1558abb891364752a4831689bbfd0e352023-12-10T12:08:39ZengBMCBMC Genomics1471-21642023-12-0124111310.1186/s12864-023-09838-9Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related speciesLijuan Feng0Guopeng Zhao1Mengmeng An2Chuanzeng Wang3Yanlei Yin4Shandong Institute of PomologyYantai Testing Center for Food and DrugZibo Academy of Agricultural SciencesShandong Academy of Agricultural SciencesShandong Institute of PomologyAbstract 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.https://doi.org/10.1186/s12864-023-09838-9Prunus cistenaChloroplast genomeGenetic diversityPhylogenetic analysis |
| spellingShingle | Lijuan Feng Guopeng Zhao Mengmeng An Chuanzeng Wang Yanlei Yin Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species BMC Genomics Prunus cistena Chloroplast genome Genetic diversity Phylogenetic analysis |
| title | Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species |
| title_full | Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species |
| title_fullStr | Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species |
| title_full_unstemmed | Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species |
| title_short | Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species |
| title_sort | complete chloroplast genome sequences of the ornamental plant prunus cistena and comparative and phylogenetic analyses with its closely related species |
| topic | Prunus cistena Chloroplast genome Genetic diversity Phylogenetic analysis |
| url | https://doi.org/10.1186/s12864-023-09838-9 |
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