Characterization of the Plastid Genome of the Vulnerable Endemic <i>Indosasa lipoensis</i> and Phylogenetic Analysis
<i>Indosasa lipoensis</i>, an ornamental garden plant, belongs to the <i>Indosasa</i> genus of the subfamily Bambooaceae within Poaceae. <i>Indosasa lipoensis</i> is endangered and requires protection owing to its relatively narrow distribution area. Chloroplast (...
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MDPI AG
2023-02-01
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| author | Ming-Li Wu Rong-Rong Yan Xue Xu Guang-Qian Gou Zhao-Xia Dai |
| author_facet | Ming-Li Wu Rong-Rong Yan Xue Xu Guang-Qian Gou Zhao-Xia Dai |
| author_sort | Ming-Li Wu |
| collection | DOAJ |
| description | <i>Indosasa lipoensis</i>, an ornamental garden plant, belongs to the <i>Indosasa</i> genus of the subfamily Bambooaceae within Poaceae. <i>Indosasa lipoensis</i> is endangered and requires protection owing to its relatively narrow distribution area. Chloroplast (cp) genome offers a novel awareness of the evolutionary and genetic variation of higher plants. Herein, we assembled and elucidated the complete cp genome of <i>I. lipoensis</i>, and compared it with four previously published cp genomes from this genus. The <i>I. lipoensis</i> cp genome was 139,655 bp in size, with a typical quadripartite structure, encompassing a large single-copy region (LSC, 83,256 bp), a small single-copy region (SSC, 12,809 bp), and a pair of inverted repeat regions (IR, 21,795 bp). The cp genome consisted of 130 genes with 84 protein-coding genes (CDS), 38 tRNA genes, and 8 rRNA genes. The plastomes were highly conservative, compared to other bamboo species, and exhibited similar patterns of codon usage, number of repeat sequences, and expansion and contraction of the IR boundary. Five hypervariable hotspots were identified as potential DNA barcodes, namely <i>rbcL</i>, <i>petA</i>, <i>petB</i>, <i>trnL-UAG</i>, and <i>ndhE-ndhI</i>, respectively. Phylogenetic analysis based on the complete cp genomes revealed, with high resolution, that <i>I. lipoensis</i> and <i>I. gigantea</i> were most closely related. Overall, these results provided valuable characterization for the future conservation, genetic evaluation, and the breeding of <i>I. lipoensis</i>. |
| first_indexed | 2024-03-11T08:55:45Z |
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| language | English |
| last_indexed | 2024-03-11T08:55:45Z |
| publishDate | 2023-02-01 |
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| series | Diversity |
| spelling | doaj.art-3a9b1e3254d64eb6adc0491f273077be2023-11-16T20:04:26ZengMDPI AGDiversity1424-28182023-02-0115219710.3390/d15020197Characterization of the Plastid Genome of the Vulnerable Endemic <i>Indosasa lipoensis</i> and Phylogenetic AnalysisMing-Li Wu0Rong-Rong Yan1Xue Xu2Guang-Qian Gou3Zhao-Xia Dai4Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, ChinaKey Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, ChinaKey Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, ChinaKey Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, ChinaCollege of Forestry, Guizhou University, Guiyang 550025, China<i>Indosasa lipoensis</i>, an ornamental garden plant, belongs to the <i>Indosasa</i> genus of the subfamily Bambooaceae within Poaceae. <i>Indosasa lipoensis</i> is endangered and requires protection owing to its relatively narrow distribution area. Chloroplast (cp) genome offers a novel awareness of the evolutionary and genetic variation of higher plants. Herein, we assembled and elucidated the complete cp genome of <i>I. lipoensis</i>, and compared it with four previously published cp genomes from this genus. The <i>I. lipoensis</i> cp genome was 139,655 bp in size, with a typical quadripartite structure, encompassing a large single-copy region (LSC, 83,256 bp), a small single-copy region (SSC, 12,809 bp), and a pair of inverted repeat regions (IR, 21,795 bp). The cp genome consisted of 130 genes with 84 protein-coding genes (CDS), 38 tRNA genes, and 8 rRNA genes. The plastomes were highly conservative, compared to other bamboo species, and exhibited similar patterns of codon usage, number of repeat sequences, and expansion and contraction of the IR boundary. Five hypervariable hotspots were identified as potential DNA barcodes, namely <i>rbcL</i>, <i>petA</i>, <i>petB</i>, <i>trnL-UAG</i>, and <i>ndhE-ndhI</i>, respectively. Phylogenetic analysis based on the complete cp genomes revealed, with high resolution, that <i>I. lipoensis</i> and <i>I. gigantea</i> were most closely related. Overall, these results provided valuable characterization for the future conservation, genetic evaluation, and the breeding of <i>I. lipoensis</i>.https://www.mdpi.com/1424-2818/15/2/197<i>Indosasa lipoensis</i>chloroplast genome<i>Bambooaceae</i>comparative analysis |
| spellingShingle | Ming-Li Wu Rong-Rong Yan Xue Xu Guang-Qian Gou Zhao-Xia Dai Characterization of the Plastid Genome of the Vulnerable Endemic <i>Indosasa lipoensis</i> and Phylogenetic Analysis Diversity <i>Indosasa lipoensis</i> chloroplast genome <i>Bambooaceae</i> comparative analysis |
| title | Characterization of the Plastid Genome of the Vulnerable Endemic <i>Indosasa lipoensis</i> and Phylogenetic Analysis |
| title_full | Characterization of the Plastid Genome of the Vulnerable Endemic <i>Indosasa lipoensis</i> and Phylogenetic Analysis |
| title_fullStr | Characterization of the Plastid Genome of the Vulnerable Endemic <i>Indosasa lipoensis</i> and Phylogenetic Analysis |
| title_full_unstemmed | Characterization of the Plastid Genome of the Vulnerable Endemic <i>Indosasa lipoensis</i> and Phylogenetic Analysis |
| title_short | Characterization of the Plastid Genome of the Vulnerable Endemic <i>Indosasa lipoensis</i> and Phylogenetic Analysis |
| title_sort | characterization of the plastid genome of the vulnerable endemic i indosasa lipoensis i and phylogenetic analysis |
| topic | <i>Indosasa lipoensis</i> chloroplast genome <i>Bambooaceae</i> comparative analysis |
| url | https://www.mdpi.com/1424-2818/15/2/197 |
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