Characterization of <i>Angraecum</i> (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability Hotspots
<i>Angraecum</i>, commonly known as Darwin’s orchid, is the largest genus of Angraecinae (Orchidaceae). This genus exhibits a high morphological diversity, making it as a good candidate for macroevolutionary studies. In this study, four complete plastomes of <i>Angraecum</i>...
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MDPI AG
2023-12-01
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| author | Cheng-Yuan Zhou Wen-Jun Lin Ruyi Li Yuhan Wu Zhong-Jian Liu Ming-He Li |
| author_facet | Cheng-Yuan Zhou Wen-Jun Lin Ruyi Li Yuhan Wu Zhong-Jian Liu Ming-He Li |
| author_sort | Cheng-Yuan Zhou |
| collection | DOAJ |
| description | <i>Angraecum</i>, commonly known as Darwin’s orchid, is the largest genus of Angraecinae (Orchidaceae). This genus exhibits a high morphological diversity, making it as a good candidate for macroevolutionary studies. In this study, four complete plastomes of <i>Angraecum</i> were firstly reported and the potential variability hotspots were explored. The plastomes possessed the typical quadripartite structure and ranged from 150,743 to 151,818 base pair (bp), with a guanine–cytosine (GC) content of 36.6–36.9%. The plastomes all contained 120 genes, consisting of 74 protein-coding genes (CDS), 38 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes; all <i>ndh</i> genes were pseudogenized or lost. A total of 30 to 46 long repeats and 55 to 63 SSRs were identified. Relative synonymous codon usage (RSCU) analysis indicated a high degree of conservation in codon usage bias. The Ka/Ks ratios of most genes were lower than 1, indicating that they have undergone purifying selection. Based on the ranking of Pi (nucleotide diversity) values, five regions (<i>trnS<sup>GCU</sup></i>-<i>trnG<sup>GCC</sup></i>, <i>ycf1</i>-<i>trnN<sup>GGU</sup></i>, <i>trnN<sup>GUU</sup></i>-<i>rpl32</i>, <i>psaC</i>-<i>ndhE</i> and <i>trnS<sup>GCU</sup></i>-<i>trnG<sup>GCC</sup></i>) and five protein-coding genes (<i>rpl32</i>, <i>rps16</i>, <i>psbK</i>, <i>rps8</i>, and <i>ycf1</i>) were identified. The consistent and robust phylogenetic relationships of <i>Angraecum</i> were established based on a total of 40 plastomes from the Epidendroideae subfamily. The genus <i>Angraecum</i> was strongly supported as a monophyletic group and sister to Aeridinae. Our study provides an ideal system for investigating molecular identification, plastome evolution and DNA barcoding for <i>Angraecum</i>. |
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| spelling | doaj.art-64fb7ecfca134a7da375f0f5bf3e4fa12024-01-10T14:58:28ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-12-0125118410.3390/ijms25010184Characterization of <i>Angraecum</i> (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability HotspotsCheng-Yuan Zhou0Wen-Jun Lin1Ruyi Li2Yuhan Wu3Zhong-Jian Liu4Ming-He Li5Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaFujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China<i>Angraecum</i>, commonly known as Darwin’s orchid, is the largest genus of Angraecinae (Orchidaceae). This genus exhibits a high morphological diversity, making it as a good candidate for macroevolutionary studies. In this study, four complete plastomes of <i>Angraecum</i> were firstly reported and the potential variability hotspots were explored. The plastomes possessed the typical quadripartite structure and ranged from 150,743 to 151,818 base pair (bp), with a guanine–cytosine (GC) content of 36.6–36.9%. The plastomes all contained 120 genes, consisting of 74 protein-coding genes (CDS), 38 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes; all <i>ndh</i> genes were pseudogenized or lost. A total of 30 to 46 long repeats and 55 to 63 SSRs were identified. Relative synonymous codon usage (RSCU) analysis indicated a high degree of conservation in codon usage bias. The Ka/Ks ratios of most genes were lower than 1, indicating that they have undergone purifying selection. Based on the ranking of Pi (nucleotide diversity) values, five regions (<i>trnS<sup>GCU</sup></i>-<i>trnG<sup>GCC</sup></i>, <i>ycf1</i>-<i>trnN<sup>GGU</sup></i>, <i>trnN<sup>GUU</sup></i>-<i>rpl32</i>, <i>psaC</i>-<i>ndhE</i> and <i>trnS<sup>GCU</sup></i>-<i>trnG<sup>GCC</sup></i>) and five protein-coding genes (<i>rpl32</i>, <i>rps16</i>, <i>psbK</i>, <i>rps8</i>, and <i>ycf1</i>) were identified. The consistent and robust phylogenetic relationships of <i>Angraecum</i> were established based on a total of 40 plastomes from the Epidendroideae subfamily. The genus <i>Angraecum</i> was strongly supported as a monophyletic group and sister to Aeridinae. Our study provides an ideal system for investigating molecular identification, plastome evolution and DNA barcoding for <i>Angraecum</i>.https://www.mdpi.com/1422-0067/25/1/184Darwin’s orchid<i>Angraecinae</i>Orchidaceaeplastid genomephylogenetic analysis |
| spellingShingle | Cheng-Yuan Zhou Wen-Jun Lin Ruyi Li Yuhan Wu Zhong-Jian Liu Ming-He Li Characterization of <i>Angraecum</i> (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability Hotspots International Journal of Molecular Sciences Darwin’s orchid <i>Angraecinae</i> Orchidaceae plastid genome phylogenetic analysis |
| title | Characterization of <i>Angraecum</i> (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability Hotspots |
| title_full | Characterization of <i>Angraecum</i> (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability Hotspots |
| title_fullStr | Characterization of <i>Angraecum</i> (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability Hotspots |
| title_full_unstemmed | Characterization of <i>Angraecum</i> (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability Hotspots |
| title_short | Characterization of <i>Angraecum</i> (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability Hotspots |
| title_sort | characterization of i angraecum i angraecinae orchidaceae plastomes and utility of sequence variability hotspots |
| topic | Darwin’s orchid <i>Angraecinae</i> Orchidaceae plastid genome phylogenetic analysis |
| url | https://www.mdpi.com/1422-0067/25/1/184 |
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