The Complete Chloroplast Genomes of <i>Blepharoglossum elegans</i> and <i>B. grossum</i> and Comparative Analysis with Related Species (Orchidaceae, Malaxideae)
<i>Blepharoglossum</i> is a rare orchid genus of the Malaxidinae primarily distributed in tropical Pacific islands, with several species occurring in the Taiwan and Hainan Islands of China. Currently, the monophyletic status of <i>Blepharoglossum</i> has been challenged, and...
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MDPI AG
2023-05-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/5/1069 |
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| author | Wenting Yang Kunlin Wu Lin Fang Songjun Zeng Lin Li |
| author_facet | Wenting Yang Kunlin Wu Lin Fang Songjun Zeng Lin Li |
| author_sort | Wenting Yang |
| collection | DOAJ |
| description | <i>Blepharoglossum</i> is a rare orchid genus of the Malaxidinae primarily distributed in tropical Pacific islands, with several species occurring in the Taiwan and Hainan Islands of China. Currently, the monophyletic status of <i>Blepharoglossum</i> has been challenged, and the phylogenetic relationships among its allied groups have remained unresolved with traditional DNA markers. In this study, we initially sequenced and annotated the chloroplast (cp) genomes of two <i>Blepharoglossum</i> species, <i>Blepharoglossum elegans</i> (Lindl.) L. Li and <i>Blepharoglossum grossum</i> (Rchb.f.) L. Li. These cp genomes of <i>Blepharoglossum</i> share the typical quadripartite and circular structure. Each of the genomes encodes a total of 133 functional genes, including 87 protein-coding genes (CDS), 38 tRNA genes and 8 rRNA genes. By comparing the sequence differences between these two cp genomes, it was found that they are relatively conserved in terms of overall gene content and gene arrangement. However, a total of 684 SNPs and 2664 indels were still identified, with <i>ycf</i>1, <i>clp</i>P, and <i>trn</i>K-UUU protein-coding genes having the highest number of SNPs and indels. In further comparative analyses among the six cp genomes in Malaxidinae, significant sequence divergences were identified in the intergenic regions, namely <i>rps</i>16–<i>trn</i>Q-UUG, <i>trn</i>S-GCU–<i>trn</i>G-GCC, <i>rpo</i>B–<i>trn</i>C-GCA, <i>trn</i>E-UUC–<i>trn</i>T-GGU, <i>trn</i>F-GAA–<i>trn</i>V-UAC, <i>atp</i>B–<i>rbc</i>L, <i>pet</i>A–<i>psb</i>J, <i>psb</i>E–<i>pet</i>L, <i>psb</i>B–<i>psb</i>T, <i>trn</i>N-GUU–<i>rpl</i>32, <i>trn</i>V-GAC–<i>rps</i>7, and <i>rps</i>7–<i>trn</i>L-CAA, and five coding regions, including <i>mat</i>K, and <i>rpo</i>C2, <i>ycf</i>1, and two <i>ycf</i>2 genes. Phylogenetic analysis indicated that <i>Blepharoglossum</i> and <i>Oberonia</i> form a highly supported sister group relationship. Our results are consistent with previous studies and present increased resolution among major clades. |
| first_indexed | 2024-03-11T03:42:13Z |
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| publishDate | 2023-05-01 |
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| spelling | doaj.art-1a0ec343be154b01b4e3dab4d9dbd3f32023-11-18T01:30:03ZengMDPI AGGenes2073-44252023-05-01145106910.3390/genes14051069The Complete Chloroplast Genomes of <i>Blepharoglossum elegans</i> and <i>B. grossum</i> and Comparative Analysis with Related Species (Orchidaceae, Malaxideae)Wenting Yang0Kunlin Wu1Lin Fang2Songjun Zeng3Lin Li4Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaKey Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaKey Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaKey Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaKey Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China<i>Blepharoglossum</i> is a rare orchid genus of the Malaxidinae primarily distributed in tropical Pacific islands, with several species occurring in the Taiwan and Hainan Islands of China. Currently, the monophyletic status of <i>Blepharoglossum</i> has been challenged, and the phylogenetic relationships among its allied groups have remained unresolved with traditional DNA markers. In this study, we initially sequenced and annotated the chloroplast (cp) genomes of two <i>Blepharoglossum</i> species, <i>Blepharoglossum elegans</i> (Lindl.) L. Li and <i>Blepharoglossum grossum</i> (Rchb.f.) L. Li. These cp genomes of <i>Blepharoglossum</i> share the typical quadripartite and circular structure. Each of the genomes encodes a total of 133 functional genes, including 87 protein-coding genes (CDS), 38 tRNA genes and 8 rRNA genes. By comparing the sequence differences between these two cp genomes, it was found that they are relatively conserved in terms of overall gene content and gene arrangement. However, a total of 684 SNPs and 2664 indels were still identified, with <i>ycf</i>1, <i>clp</i>P, and <i>trn</i>K-UUU protein-coding genes having the highest number of SNPs and indels. In further comparative analyses among the six cp genomes in Malaxidinae, significant sequence divergences were identified in the intergenic regions, namely <i>rps</i>16–<i>trn</i>Q-UUG, <i>trn</i>S-GCU–<i>trn</i>G-GCC, <i>rpo</i>B–<i>trn</i>C-GCA, <i>trn</i>E-UUC–<i>trn</i>T-GGU, <i>trn</i>F-GAA–<i>trn</i>V-UAC, <i>atp</i>B–<i>rbc</i>L, <i>pet</i>A–<i>psb</i>J, <i>psb</i>E–<i>pet</i>L, <i>psb</i>B–<i>psb</i>T, <i>trn</i>N-GUU–<i>rpl</i>32, <i>trn</i>V-GAC–<i>rps</i>7, and <i>rps</i>7–<i>trn</i>L-CAA, and five coding regions, including <i>mat</i>K, and <i>rpo</i>C2, <i>ycf</i>1, and two <i>ycf</i>2 genes. Phylogenetic analysis indicated that <i>Blepharoglossum</i> and <i>Oberonia</i> form a highly supported sister group relationship. Our results are consistent with previous studies and present increased resolution among major clades.https://www.mdpi.com/2073-4425/14/5/1069<i>Blepharoglossum</i>chloroplast genomecomparative genomicOrchidaceaephylogeny |
| spellingShingle | Wenting Yang Kunlin Wu Lin Fang Songjun Zeng Lin Li The Complete Chloroplast Genomes of <i>Blepharoglossum elegans</i> and <i>B. grossum</i> and Comparative Analysis with Related Species (Orchidaceae, Malaxideae) Genes <i>Blepharoglossum</i> chloroplast genome comparative genomic Orchidaceae phylogeny |
| title | The Complete Chloroplast Genomes of <i>Blepharoglossum elegans</i> and <i>B. grossum</i> and Comparative Analysis with Related Species (Orchidaceae, Malaxideae) |
| title_full | The Complete Chloroplast Genomes of <i>Blepharoglossum elegans</i> and <i>B. grossum</i> and Comparative Analysis with Related Species (Orchidaceae, Malaxideae) |
| title_fullStr | The Complete Chloroplast Genomes of <i>Blepharoglossum elegans</i> and <i>B. grossum</i> and Comparative Analysis with Related Species (Orchidaceae, Malaxideae) |
| title_full_unstemmed | The Complete Chloroplast Genomes of <i>Blepharoglossum elegans</i> and <i>B. grossum</i> and Comparative Analysis with Related Species (Orchidaceae, Malaxideae) |
| title_short | The Complete Chloroplast Genomes of <i>Blepharoglossum elegans</i> and <i>B. grossum</i> and Comparative Analysis with Related Species (Orchidaceae, Malaxideae) |
| title_sort | complete chloroplast genomes of i blepharoglossum elegans i and i b grossum i and comparative analysis with related species orchidaceae malaxideae |
| topic | <i>Blepharoglossum</i> chloroplast genome comparative genomic Orchidaceae phylogeny |
| url | https://www.mdpi.com/2073-4425/14/5/1069 |
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