Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom
<i>Paeonia delavayi</i> var. <i>lutea</i>, <i>Paeonia delavayi</i> var. <i>angustiloba</i>, and <i>Paeonia ludlowii</i> are Chinese endemics that belong to the Paeoniaceae family and have vital medicinal and ornamental value. It is often di...
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| Format: | Article |
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MDPI AG
2023-12-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/25/1/257 |
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| author | Hanbing Cai Rong Xu Ping Tian Mengjie Zhang Ling Zhu Tuo Yin Hanyao Zhang Xiaozhen Liu |
| author_facet | Hanbing Cai Rong Xu Ping Tian Mengjie Zhang Ling Zhu Tuo Yin Hanyao Zhang Xiaozhen Liu |
| author_sort | Hanbing Cai |
| collection | DOAJ |
| description | <i>Paeonia delavayi</i> var. <i>lutea</i>, <i>Paeonia delavayi</i> var. <i>angustiloba</i>, and <i>Paeonia ludlowii</i> are Chinese endemics that belong to the Paeoniaceae family and have vital medicinal and ornamental value. It is often difficult to classify Paeoniaceae plants based on their morphological characteristics, and the limited genomic information has strongly hindered molecular evolution and phylogenetic studies of Paeoniaceae. In this study, we sequenced, assembled, and annotated the chloroplast genomes of <i>P. delavayi</i> var. <i>lutea</i>, <i>P. delavayi</i> var. <i>angustiloba</i>, and <i>P. ludlowii</i>. The chloroplast genomes of these strains were comparatively analyzed, and their phylogenetic relationships and divergence times were inferred. These three chloroplast genomes exhibited a typical quadripartite structure and were 152,687–152,759 bp in length. Each genome contains 126–132 genes, including 81–87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNAs. In addition, the genomes had 61–64 SSRs, with mononucleotide repeats being the most abundant. The codon bias patterns of the three species tend to use codons ending in A/U. Six regions of high variability were identified (<i>psbK</i>-<i>psbL</i>, <i>trnG</i>-<i>UCC</i>, <i>petN</i>-<i>psbM</i>, <i>psbC</i>, <i>rps8</i>-<i>rpl14</i>, and <i>ycf1</i>) that can be used as DNA molecular markers for phylogenetic and taxonomic analysis. The Ka/Ks ratio indicates positive selection for the rps18 gene associated with self-replication. The phylogenetic analysis of 99 chloroplast genomes from Saxifragales clarified the phylogenetic relationships of Paeoniaceae and revealed that <i>P. delavayi</i> var. <i>lutea</i>, <i>P. delavayi</i> var. <i>angustiloba</i>, and <i>P. ludlowii</i> are monophyletic groups and sisters to <i>P. delavayi</i>. Divergence time estimation revealed two evolutionary divergences of Paeoniaceae species in the early Oligocene and Miocene. Afterward, they underwent rapid adaptive radiation from the Pliocene to the early Pleistocene when <i>P. delavayi</i> var. <i>lutea</i>, <i>P. delavayi</i> var. <i>angustiloba</i>, and <i>P. ludlowii</i> formed. The results of this study enrich the chloroplast genomic information of Paeoniaceae and reveal new insights into the phylogeny of Paeoniaceae. |
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| spelling | doaj.art-f5155c82c2e14367b4d7e488c421c3c22024-01-10T14:58:45ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-12-0125125710.3390/ijms25010257Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora SubkingdomHanbing Cai0Rong Xu1Ping Tian2Mengjie Zhang3Ling Zhu4Tuo Yin5Hanyao Zhang6Xiaozhen Liu7Key Laboratory of Conservation and Utilization of Southwest Mountain Forest Resources, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory of Conservation and Utilization of Southwest Mountain Forest Resources, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory of Conservation and Utilization of Southwest Mountain Forest Resources, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory of Conservation and Utilization of Southwest Mountain Forest Resources, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory of Conservation and Utilization of Southwest Mountain Forest Resources, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory of Conservation and Utilization of Southwest Mountain Forest Resources, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory of Conservation and Utilization of Southwest Mountain Forest Resources, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory of Conservation and Utilization of Southwest Mountain Forest Resources, Ministry of Education, Southwest Forestry University, Kunming 650224, China<i>Paeonia delavayi</i> var. <i>lutea</i>, <i>Paeonia delavayi</i> var. <i>angustiloba</i>, and <i>Paeonia ludlowii</i> are Chinese endemics that belong to the Paeoniaceae family and have vital medicinal and ornamental value. It is often difficult to classify Paeoniaceae plants based on their morphological characteristics, and the limited genomic information has strongly hindered molecular evolution and phylogenetic studies of Paeoniaceae. In this study, we sequenced, assembled, and annotated the chloroplast genomes of <i>P. delavayi</i> var. <i>lutea</i>, <i>P. delavayi</i> var. <i>angustiloba</i>, and <i>P. ludlowii</i>. The chloroplast genomes of these strains were comparatively analyzed, and their phylogenetic relationships and divergence times were inferred. These three chloroplast genomes exhibited a typical quadripartite structure and were 152,687–152,759 bp in length. Each genome contains 126–132 genes, including 81–87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNAs. In addition, the genomes had 61–64 SSRs, with mononucleotide repeats being the most abundant. The codon bias patterns of the three species tend to use codons ending in A/U. Six regions of high variability were identified (<i>psbK</i>-<i>psbL</i>, <i>trnG</i>-<i>UCC</i>, <i>petN</i>-<i>psbM</i>, <i>psbC</i>, <i>rps8</i>-<i>rpl14</i>, and <i>ycf1</i>) that can be used as DNA molecular markers for phylogenetic and taxonomic analysis. The Ka/Ks ratio indicates positive selection for the rps18 gene associated with self-replication. The phylogenetic analysis of 99 chloroplast genomes from Saxifragales clarified the phylogenetic relationships of Paeoniaceae and revealed that <i>P. delavayi</i> var. <i>lutea</i>, <i>P. delavayi</i> var. <i>angustiloba</i>, and <i>P. ludlowii</i> are monophyletic groups and sisters to <i>P. delavayi</i>. Divergence time estimation revealed two evolutionary divergences of Paeoniaceae species in the early Oligocene and Miocene. Afterward, they underwent rapid adaptive radiation from the Pliocene to the early Pleistocene when <i>P. delavayi</i> var. <i>lutea</i>, <i>P. delavayi</i> var. <i>angustiloba</i>, and <i>P. ludlowii</i> formed. The results of this study enrich the chloroplast genomic information of Paeoniaceae and reveal new insights into the phylogeny of Paeoniaceae.https://www.mdpi.com/1422-0067/25/1/257Paeoniaceaechloroplast genomeselection pressurephylogenydivergence time |
| spellingShingle | Hanbing Cai Rong Xu Ping Tian Mengjie Zhang Ling Zhu Tuo Yin Hanyao Zhang Xiaozhen Liu Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom International Journal of Molecular Sciences Paeoniaceae chloroplast genome selection pressure phylogeny divergence time |
| title | Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom |
| title_full | Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom |
| title_fullStr | Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom |
| title_full_unstemmed | Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom |
| title_short | Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom |
| title_sort | complete chloroplast genomes and the phylogenetic analysis of three native species of paeoniaceae from the sino himalayan flora subkingdom |
| topic | Paeoniaceae chloroplast genome selection pressure phylogeny divergence time |
| url | https://www.mdpi.com/1422-0067/25/1/257 |
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