Complete Chloroplast Genome of <i>Hypericum perforatum</i> and Dynamic Evolution in <i>Hypericum</i> (Hypericaceae)
<i>Hypericum perforatum</i> (St. John’s Wort) is a medicinal plant from the Hypericaceae family. Here, we sequenced the whole chloroplast genome of <i>H. perforatum</i> and compared the genome variation among five <i>Hypericum</i> species to discover dynamic chang...
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MDPI AG
2023-11-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/22/16130 |
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| author | Xinyu Liu Yuran Bai Yachao Wang Yifeng Chen Wenpan Dong Zhixiang Zhang |
| author_facet | Xinyu Liu Yuran Bai Yachao Wang Yifeng Chen Wenpan Dong Zhixiang Zhang |
| author_sort | Xinyu Liu |
| collection | DOAJ |
| description | <i>Hypericum perforatum</i> (St. John’s Wort) is a medicinal plant from the Hypericaceae family. Here, we sequenced the whole chloroplast genome of <i>H. perforatum</i> and compared the genome variation among five <i>Hypericum</i> species to discover dynamic changes and elucidate the mechanisms that lead to genome rearrangements in the <i>Hypericum</i> chloroplast genomes. The <i>H. perforatum</i> chloroplast genome is 139,725 bp, exhibiting a circular quadripartite structure with two copies of inverted repeats (IRs) separating a large single-copy region and a small single-copy region. The <i>H. perforatum</i> chloroplast genome encodes 106 unique genes, including 73 protein-coding genes, 29 tRNAs, and 4 rRNAs. <i>Hypericum</i> chloroplast genomes exhibit genome rearrangement and significant variations among species. The genome size variation among the five <i>Hypericum</i> species was remarkably associated with the expansion or contraction of IR regions and gene losses. Three genes—<i>trnK</i>-UUU, <i>infA</i>, and <i>rps16</i>—were lost, and three genes—<i>rps7</i>, <i>rpl23</i>, and <i>rpl32</i>—were pseudogenized in <i>Hypericum</i>. All the <i>Hypericum</i> chloroplast genomes lost the two introns in <i>clpP</i>, the intron in <i>rps12</i>, and the second intron in <i>ycf3</i>. <i>Hypericum</i> chloroplast genomes contain many long repeat sequences, suggesting a role in facilitating rearrangements. Most genes, according to molecular evolution assessments, are under purifying selection. |
| first_indexed | 2024-03-09T16:45:39Z |
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| language | English |
| last_indexed | 2024-03-09T16:45:39Z |
| publishDate | 2023-11-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-1d05749fc8484edfa37720f14785a5462023-11-24T14:46:07ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-11-0124221613010.3390/ijms242216130Complete Chloroplast Genome of <i>Hypericum perforatum</i> and Dynamic Evolution in <i>Hypericum</i> (Hypericaceae)Xinyu Liu0Yuran Bai1Yachao Wang2Yifeng Chen3Wenpan Dong4Zhixiang Zhang5School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaSchool of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaSchool of Life Sciences, Fudan University, Shanghai 200437, ChinaSchool of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaSchool of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaSchool of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China<i>Hypericum perforatum</i> (St. John’s Wort) is a medicinal plant from the Hypericaceae family. Here, we sequenced the whole chloroplast genome of <i>H. perforatum</i> and compared the genome variation among five <i>Hypericum</i> species to discover dynamic changes and elucidate the mechanisms that lead to genome rearrangements in the <i>Hypericum</i> chloroplast genomes. The <i>H. perforatum</i> chloroplast genome is 139,725 bp, exhibiting a circular quadripartite structure with two copies of inverted repeats (IRs) separating a large single-copy region and a small single-copy region. The <i>H. perforatum</i> chloroplast genome encodes 106 unique genes, including 73 protein-coding genes, 29 tRNAs, and 4 rRNAs. <i>Hypericum</i> chloroplast genomes exhibit genome rearrangement and significant variations among species. The genome size variation among the five <i>Hypericum</i> species was remarkably associated with the expansion or contraction of IR regions and gene losses. Three genes—<i>trnK</i>-UUU, <i>infA</i>, and <i>rps16</i>—were lost, and three genes—<i>rps7</i>, <i>rpl23</i>, and <i>rpl32</i>—were pseudogenized in <i>Hypericum</i>. All the <i>Hypericum</i> chloroplast genomes lost the two introns in <i>clpP</i>, the intron in <i>rps12</i>, and the second intron in <i>ycf3</i>. <i>Hypericum</i> chloroplast genomes contain many long repeat sequences, suggesting a role in facilitating rearrangements. Most genes, according to molecular evolution assessments, are under purifying selection.https://www.mdpi.com/1422-0067/24/22/16130St. John’s wortphylogenycodon usagesubstitution rateintron lossrearrangement |
| spellingShingle | Xinyu Liu Yuran Bai Yachao Wang Yifeng Chen Wenpan Dong Zhixiang Zhang Complete Chloroplast Genome of <i>Hypericum perforatum</i> and Dynamic Evolution in <i>Hypericum</i> (Hypericaceae) International Journal of Molecular Sciences St. John’s wort phylogeny codon usage substitution rate intron loss rearrangement |
| title | Complete Chloroplast Genome of <i>Hypericum perforatum</i> and Dynamic Evolution in <i>Hypericum</i> (Hypericaceae) |
| title_full | Complete Chloroplast Genome of <i>Hypericum perforatum</i> and Dynamic Evolution in <i>Hypericum</i> (Hypericaceae) |
| title_fullStr | Complete Chloroplast Genome of <i>Hypericum perforatum</i> and Dynamic Evolution in <i>Hypericum</i> (Hypericaceae) |
| title_full_unstemmed | Complete Chloroplast Genome of <i>Hypericum perforatum</i> and Dynamic Evolution in <i>Hypericum</i> (Hypericaceae) |
| title_short | Complete Chloroplast Genome of <i>Hypericum perforatum</i> and Dynamic Evolution in <i>Hypericum</i> (Hypericaceae) |
| title_sort | complete chloroplast genome of i hypericum perforatum i and dynamic evolution in i hypericum i hypericaceae |
| topic | St. John’s wort phylogeny codon usage substitution rate intron loss rearrangement |
| url | https://www.mdpi.com/1422-0067/24/22/16130 |
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