Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (<i>Castanea</i>)
Chloroplast (cp) DNA genomes are traditional workhorses for studying the evolution of species and reconstructing phylogenetic relationships in plants. Species of the genus <i>Castanea</i> (chestnuts and chinquapins) are valued as a source of nuts and timber wherever they grow, and chestn...
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MDPI AG
2021-06-01
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| Series: | Forests |
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| Online Access: | https://www.mdpi.com/1999-4907/12/7/861 |
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| author | Huijuan Zhou Xiaoxiao Gao Keith Woeste Peng Zhao Shuoxin Zhang |
| author_facet | Huijuan Zhou Xiaoxiao Gao Keith Woeste Peng Zhao Shuoxin Zhang |
| author_sort | Huijuan Zhou |
| collection | DOAJ |
| description | Chloroplast (cp) DNA genomes are traditional workhorses for studying the evolution of species and reconstructing phylogenetic relationships in plants. Species of the genus <i>Castanea</i> (chestnuts and chinquapins) are valued as a source of nuts and timber wherever they grow, and chestnut species hybrids are common. We compared the cp genomes of <i>C. mollissima, C. seguinii, C. henryi</i>, and <i>C. pumila</i>. These cp genomes ranged from 160,805 bp to 161,010 bp in length, comprising a pair of inverted repeat (IR) regions (25,685 to 25,701 bp) separated by a large single-copy (LSC) region (90,440 to 90,560 bp) and a small single-copy (SSC) region (18,970 to 19,049 bp). Each cp genome encoded the same 113 genes; 82–83 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. There were 18 duplicated genes in the IRs. Comparative analysis of cp genomes revealed that <i>rpl22</i> was absent in all analyzed species, and the gene ycf1 has been pseudo-genized in all Chinese chestnuts except <i>C. pumlia</i>. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. The phylogenetic analyses based on plastomes confirmed the monophyly of <i>Castanea</i> species. |
| first_indexed | 2024-03-10T09:57:11Z |
| format | Article |
| id | doaj.art-e75f2c6f975a4eb389f8fde1c7142845 |
| institution | Directory Open Access Journal |
| issn | 1999-4907 |
| language | English |
| last_indexed | 2024-03-10T09:57:11Z |
| publishDate | 2021-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Forests |
| spelling | doaj.art-e75f2c6f975a4eb389f8fde1c71428452023-11-22T02:17:17ZengMDPI AGForests1999-49072021-06-0112786110.3390/f12070861Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (<i>Castanea</i>)Huijuan Zhou0Xiaoxiao Gao1Keith Woeste2Peng Zhao3Shuoxin Zhang4College of Forestry, Northwest A&F University, Yangling 712100, ChinaKey Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, ChinaUSDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, IN 47907, USAKey Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, ChinaCollege of Forestry, Northwest A&F University, Yangling 712100, ChinaChloroplast (cp) DNA genomes are traditional workhorses for studying the evolution of species and reconstructing phylogenetic relationships in plants. Species of the genus <i>Castanea</i> (chestnuts and chinquapins) are valued as a source of nuts and timber wherever they grow, and chestnut species hybrids are common. We compared the cp genomes of <i>C. mollissima, C. seguinii, C. henryi</i>, and <i>C. pumila</i>. These cp genomes ranged from 160,805 bp to 161,010 bp in length, comprising a pair of inverted repeat (IR) regions (25,685 to 25,701 bp) separated by a large single-copy (LSC) region (90,440 to 90,560 bp) and a small single-copy (SSC) region (18,970 to 19,049 bp). Each cp genome encoded the same 113 genes; 82–83 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. There were 18 duplicated genes in the IRs. Comparative analysis of cp genomes revealed that <i>rpl22</i> was absent in all analyzed species, and the gene ycf1 has been pseudo-genized in all Chinese chestnuts except <i>C. pumlia</i>. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. The phylogenetic analyses based on plastomes confirmed the monophyly of <i>Castanea</i> species.https://www.mdpi.com/1999-4907/12/7/861<i>Castanea</i>chloroplast genomephylogenyvariable regionssequence divergence |
| spellingShingle | Huijuan Zhou Xiaoxiao Gao Keith Woeste Peng Zhao Shuoxin Zhang Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (<i>Castanea</i>) Forests <i>Castanea</i> chloroplast genome phylogeny variable regions sequence divergence |
| title | Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (<i>Castanea</i>) |
| title_full | Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (<i>Castanea</i>) |
| title_fullStr | Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (<i>Castanea</i>) |
| title_full_unstemmed | Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (<i>Castanea</i>) |
| title_short | Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (<i>Castanea</i>) |
| title_sort | comparative analysis of the complete chloroplast genomes of four chestnut species i castanea i |
| topic | <i>Castanea</i> chloroplast genome phylogeny variable regions sequence divergence |
| url | https://www.mdpi.com/1999-4907/12/7/861 |
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