Chloroplast Genomic Variation in <i>Euonymus maackii</i> Rupr. and Its Differentiation Time in <i>Euonymus</i>
<i>Euonymus maackii</i> Rupr. is a small deciduous tree belonging to family Celastraceae. It is an important ornamental tree and a potential medicinal plant resource. Here, we assembled and annotated the chloroplast (cp) genome of <i>E. maackii</i>. By combining this genome w...
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| Format: | Article |
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MDPI AG
2022-02-01
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| Series: | Forests |
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| Online Access: | https://www.mdpi.com/1999-4907/13/2/265 |
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| author | Yu-Cheng Wang Hao-Yang Zhou Xiu-Qun Liu |
| author_facet | Yu-Cheng Wang Hao-Yang Zhou Xiu-Qun Liu |
| author_sort | Yu-Cheng Wang |
| collection | DOAJ |
| description | <i>Euonymus maackii</i> Rupr. is a small deciduous tree belonging to family Celastraceae. It is an important ornamental tree and a potential medicinal plant resource. Here, we assembled and annotated the chloroplast (cp) genome of <i>E. maackii</i>. By combining this genome with seven available cp genomes from <i>Euonymus</i> species, we performed plastome variation analysis of <i>E. maackii</i> and <i>Euonymus</i>. Furthermore, we reconstructed a phylogenetic tree and estimated the differentiation time of <i>E. maackii</i>. The newly assembled cp genome of <i>E. maackii</i> was 157,551 bp in size and had a typical quadripartite structure, which consisted of one large single-copy (LSC 86,524 bp) region, one small single-copy (SSC 18,337 bp) region, and a pair of inverted repeat regions (26,345 bp). A total of 652 single nucleotide polymorphisms (SNPs) and 65 insertions/deletions (indels) were detected between the two cp genomes of <i>E. maackii</i>, with overall genetic variation of 4.1 SNPs per kb or a π value of 0.00443, reflecting a high level of intraspecific variation. Some coding and noncoding regions with higher variation were identified, including <i>trnV-UAC</i>, <i>petN</i>, <i>ycf1-ndhF</i>, <i>trnM<sup>-CAU</sup>-atpE</i>, <i>rpl2-rpl23</i>, <i>psbZ-trnG<sup>-GCC</sup></i>, <i>trnY<sup>-GUA</sup>-trnE<sup>-UUC</sup></i>, <i>trnW<sup>-CCA</sup>-trnP<sup>-UGG</sup></i>, <i>rps16-trnQ<sup>-UUG</sup></i>, and <i>psbC-trnS<sup>-UGA</sup></i>. The hypervariable coding and noncoding regions in <i>E. maackii</i> were not the same as those in <i>Euonymus</i>. The phylogenetic tree and divergence time based on the whole cp genomes showed that the seven <i>Euonymus</i> species formed a clade, which was sister to that formed with <i>Catha edulis</i> and <i>Maytenus guangxiensis</i>, and they separated 24.74 million years ago. <i>E. maackii</i> and <i>E. hamiltonianus</i> were most closely related, having separated from each other only approximately 2.68 million years ago. Our study provides important genetic information for further studies of <i>E. maackii</i>, such as studies on its phylogeography, population genetics and molecular ecology, and provides new insights into the evolution of the cp genome in <i>Euonymus</i>. |
| first_indexed | 2024-03-09T21:56:28Z |
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| language | English |
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| spelling | doaj.art-31a28798384640dbb3915b191898b7b32023-11-23T19:56:48ZengMDPI AGForests1999-49072022-02-0113226510.3390/f13020265Chloroplast Genomic Variation in <i>Euonymus maackii</i> Rupr. and Its Differentiation Time in <i>Euonymus</i>Yu-Cheng Wang0Hao-Yang Zhou1Xiu-Qun Liu2College of Informatics, Huazhong Agricultural University, Wuhan 430070, ChinaKey Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, ChinaKey Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China<i>Euonymus maackii</i> Rupr. is a small deciduous tree belonging to family Celastraceae. It is an important ornamental tree and a potential medicinal plant resource. Here, we assembled and annotated the chloroplast (cp) genome of <i>E. maackii</i>. By combining this genome with seven available cp genomes from <i>Euonymus</i> species, we performed plastome variation analysis of <i>E. maackii</i> and <i>Euonymus</i>. Furthermore, we reconstructed a phylogenetic tree and estimated the differentiation time of <i>E. maackii</i>. The newly assembled cp genome of <i>E. maackii</i> was 157,551 bp in size and had a typical quadripartite structure, which consisted of one large single-copy (LSC 86,524 bp) region, one small single-copy (SSC 18,337 bp) region, and a pair of inverted repeat regions (26,345 bp). A total of 652 single nucleotide polymorphisms (SNPs) and 65 insertions/deletions (indels) were detected between the two cp genomes of <i>E. maackii</i>, with overall genetic variation of 4.1 SNPs per kb or a π value of 0.00443, reflecting a high level of intraspecific variation. Some coding and noncoding regions with higher variation were identified, including <i>trnV-UAC</i>, <i>petN</i>, <i>ycf1-ndhF</i>, <i>trnM<sup>-CAU</sup>-atpE</i>, <i>rpl2-rpl23</i>, <i>psbZ-trnG<sup>-GCC</sup></i>, <i>trnY<sup>-GUA</sup>-trnE<sup>-UUC</sup></i>, <i>trnW<sup>-CCA</sup>-trnP<sup>-UGG</sup></i>, <i>rps16-trnQ<sup>-UUG</sup></i>, and <i>psbC-trnS<sup>-UGA</sup></i>. The hypervariable coding and noncoding regions in <i>E. maackii</i> were not the same as those in <i>Euonymus</i>. The phylogenetic tree and divergence time based on the whole cp genomes showed that the seven <i>Euonymus</i> species formed a clade, which was sister to that formed with <i>Catha edulis</i> and <i>Maytenus guangxiensis</i>, and they separated 24.74 million years ago. <i>E. maackii</i> and <i>E. hamiltonianus</i> were most closely related, having separated from each other only approximately 2.68 million years ago. Our study provides important genetic information for further studies of <i>E. maackii</i>, such as studies on its phylogeography, population genetics and molecular ecology, and provides new insights into the evolution of the cp genome in <i>Euonymus</i>.https://www.mdpi.com/1999-4907/13/2/265<i>Euonymus maackii</i>intraspecific variationchloroplast genomephylogenetic treedivergence time |
| spellingShingle | Yu-Cheng Wang Hao-Yang Zhou Xiu-Qun Liu Chloroplast Genomic Variation in <i>Euonymus maackii</i> Rupr. and Its Differentiation Time in <i>Euonymus</i> Forests <i>Euonymus maackii</i> intraspecific variation chloroplast genome phylogenetic tree divergence time |
| title | Chloroplast Genomic Variation in <i>Euonymus maackii</i> Rupr. and Its Differentiation Time in <i>Euonymus</i> |
| title_full | Chloroplast Genomic Variation in <i>Euonymus maackii</i> Rupr. and Its Differentiation Time in <i>Euonymus</i> |
| title_fullStr | Chloroplast Genomic Variation in <i>Euonymus maackii</i> Rupr. and Its Differentiation Time in <i>Euonymus</i> |
| title_full_unstemmed | Chloroplast Genomic Variation in <i>Euonymus maackii</i> Rupr. and Its Differentiation Time in <i>Euonymus</i> |
| title_short | Chloroplast Genomic Variation in <i>Euonymus maackii</i> Rupr. and Its Differentiation Time in <i>Euonymus</i> |
| title_sort | chloroplast genomic variation in i euonymus maackii i rupr and its differentiation time in i euonymus i |
| topic | <i>Euonymus maackii</i> intraspecific variation chloroplast genome phylogenetic tree divergence time |
| url | https://www.mdpi.com/1999-4907/13/2/265 |
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