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>...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-12-01
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| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/25/1/184 |
| Summary: | <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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| ISSN: | 1661-6596 1422-0067 |