Gene Losses and Homology of the Chloroplast Genomes of <i>Taxillus</i> and <i>Phacellaria</i> Species
Research on the chloroplast genome of parasitic plants is limited. In particular, the homology between the chloroplast genomes of parasitic and hyperparasitic plants has not been reported yet. In this study, three chloroplast genomes of <i>Taxillus</i> (<i>Taxillus chinensis</i&...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-04-01
|
| Series: | Genes |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4425/14/4/943 |
| _version_ | 1797605305229508608 |
|---|---|
| author | Liwei Wu Panhui Fan Jianguo Zhou Yonghua Li Zhichao Xu Yulin Lin Yu Wang Jingyuan Song Hui Yao |
| author_facet | Liwei Wu Panhui Fan Jianguo Zhou Yonghua Li Zhichao Xu Yulin Lin Yu Wang Jingyuan Song Hui Yao |
| author_sort | Liwei Wu |
| collection | DOAJ |
| description | Research on the chloroplast genome of parasitic plants is limited. In particular, the homology between the chloroplast genomes of parasitic and hyperparasitic plants has not been reported yet. In this study, three chloroplast genomes of <i>Taxillus</i> (<i>Taxillus chinensis</i>, <i>Taxillus delavayi</i>, and <i>Taxillus thibetensis</i>) and one chloroplast genome of <i>Phacellaria</i> (<i>Phacellaria rigidula</i>) were sequenced and analyzed, among which <i>T. chinensis</i> is the host of <i>P. rigidula</i>. The chloroplast genomes of the four species were 119,941–138,492 bp in length. Compared with the chloroplast genome of the autotrophic plant <i>Nicotiana tabacum</i>, all of the <i>ndh</i> genes, three ribosomal protein genes, three tRNA genes and the <i>infA</i> gene were lost in the three <i>Taxillus</i> species. Meanwhile, in <i>P. rigidula</i>, the <i>trnV-UAC</i> gene and the <i>ycf15</i> gene were lost, and only one <i>ndh</i> gene (<i>ndhB</i>) existed. The results of homology analysis showed that the homology between <i>P. rigidula</i> and its host <i>T. chinensis</i> was low, indicating that <i>P. rigidula</i> grows on its host <i>T. chinensis</i> but they do not share the chloroplast genome. In addition, horizontal gene transfer was not found between <i>P. rigidula</i> and its host <i>T. chinensis</i>. Several candidate highly variable regions in the chloroplast genomes of <i>Taxillus</i> and <i>Phacellaria</i> species were selected for species identification study. Phylogenetic analysis revealed that the species of <i>Taxillus</i> and <i>Scurrula</i> were closely related and supported that <i>Scurrula</i> and <i>Taxillus</i> should be treated as congeneric, while species in <i>Phacellaria</i> had a close relationship with that in <i>Viscum</i>. |
| first_indexed | 2024-03-11T04:59:11Z |
| format | Article |
| id | doaj.art-89fba1762eb2486597e4db56a6a94dfc |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T04:59:11Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-89fba1762eb2486597e4db56a6a94dfc2023-11-17T19:24:49ZengMDPI AGGenes2073-44252023-04-0114494310.3390/genes14040943Gene Losses and Homology of the Chloroplast Genomes of <i>Taxillus</i> and <i>Phacellaria</i> SpeciesLiwei Wu0Panhui Fan1Jianguo Zhou2Yonghua Li3Zhichao Xu4Yulin Lin5Yu Wang6Jingyuan Song7Hui Yao8Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaKey Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaKey Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaFaculty of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530004, ChinaCollege of Life Science, Northeast Forestry University, Harbin 150040, ChinaKey Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaKey Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaKey Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaKey Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaResearch on the chloroplast genome of parasitic plants is limited. In particular, the homology between the chloroplast genomes of parasitic and hyperparasitic plants has not been reported yet. In this study, three chloroplast genomes of <i>Taxillus</i> (<i>Taxillus chinensis</i>, <i>Taxillus delavayi</i>, and <i>Taxillus thibetensis</i>) and one chloroplast genome of <i>Phacellaria</i> (<i>Phacellaria rigidula</i>) were sequenced and analyzed, among which <i>T. chinensis</i> is the host of <i>P. rigidula</i>. The chloroplast genomes of the four species were 119,941–138,492 bp in length. Compared with the chloroplast genome of the autotrophic plant <i>Nicotiana tabacum</i>, all of the <i>ndh</i> genes, three ribosomal protein genes, three tRNA genes and the <i>infA</i> gene were lost in the three <i>Taxillus</i> species. Meanwhile, in <i>P. rigidula</i>, the <i>trnV-UAC</i> gene and the <i>ycf15</i> gene were lost, and only one <i>ndh</i> gene (<i>ndhB</i>) existed. The results of homology analysis showed that the homology between <i>P. rigidula</i> and its host <i>T. chinensis</i> was low, indicating that <i>P. rigidula</i> grows on its host <i>T. chinensis</i> but they do not share the chloroplast genome. In addition, horizontal gene transfer was not found between <i>P. rigidula</i> and its host <i>T. chinensis</i>. Several candidate highly variable regions in the chloroplast genomes of <i>Taxillus</i> and <i>Phacellaria</i> species were selected for species identification study. Phylogenetic analysis revealed that the species of <i>Taxillus</i> and <i>Scurrula</i> were closely related and supported that <i>Scurrula</i> and <i>Taxillus</i> should be treated as congeneric, while species in <i>Phacellaria</i> had a close relationship with that in <i>Viscum</i>.https://www.mdpi.com/2073-4425/14/4/943<i>Taxillus</i><i>Phacellaria</i>chloroplast genomegene losseshomology |
| spellingShingle | Liwei Wu Panhui Fan Jianguo Zhou Yonghua Li Zhichao Xu Yulin Lin Yu Wang Jingyuan Song Hui Yao Gene Losses and Homology of the Chloroplast Genomes of <i>Taxillus</i> and <i>Phacellaria</i> Species Genes <i>Taxillus</i> <i>Phacellaria</i> chloroplast genome gene losses homology |
| title | Gene Losses and Homology of the Chloroplast Genomes of <i>Taxillus</i> and <i>Phacellaria</i> Species |
| title_full | Gene Losses and Homology of the Chloroplast Genomes of <i>Taxillus</i> and <i>Phacellaria</i> Species |
| title_fullStr | Gene Losses and Homology of the Chloroplast Genomes of <i>Taxillus</i> and <i>Phacellaria</i> Species |
| title_full_unstemmed | Gene Losses and Homology of the Chloroplast Genomes of <i>Taxillus</i> and <i>Phacellaria</i> Species |
| title_short | Gene Losses and Homology of the Chloroplast Genomes of <i>Taxillus</i> and <i>Phacellaria</i> Species |
| title_sort | gene losses and homology of the chloroplast genomes of i taxillus i and i phacellaria i species |
| topic | <i>Taxillus</i> <i>Phacellaria</i> chloroplast genome gene losses homology |
| url | https://www.mdpi.com/2073-4425/14/4/943 |
| work_keys_str_mv | AT liweiwu genelossesandhomologyofthechloroplastgenomesofitaxillusiandiphacellariaispecies AT panhuifan genelossesandhomologyofthechloroplastgenomesofitaxillusiandiphacellariaispecies AT jianguozhou genelossesandhomologyofthechloroplastgenomesofitaxillusiandiphacellariaispecies AT yonghuali genelossesandhomologyofthechloroplastgenomesofitaxillusiandiphacellariaispecies AT zhichaoxu genelossesandhomologyofthechloroplastgenomesofitaxillusiandiphacellariaispecies AT yulinlin genelossesandhomologyofthechloroplastgenomesofitaxillusiandiphacellariaispecies AT yuwang genelossesandhomologyofthechloroplastgenomesofitaxillusiandiphacellariaispecies AT jingyuansong genelossesandhomologyofthechloroplastgenomesofitaxillusiandiphacellariaispecies AT huiyao genelossesandhomologyofthechloroplastgenomesofitaxillusiandiphacellariaispecies |