The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution
Abstract Background The Ferula genus encompasses 180–185 species and is one of the largest genera in Apiaceae, with many of Ferula species possessing important medical value. The previous studies provided more information for Ferula, but its infrageneric relationships are still confusing. In additio...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2023-01-01
|
| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-022-04027-4 |
| _version_ | 1797958701888307200 |
|---|---|
| author | Huan-Huan Qin Jing Cai Chang-Kun Liu Ren-Xiu Zhou Megan Price Song-Dong Zhou Xing-Jin He |
| author_facet | Huan-Huan Qin Jing Cai Chang-Kun Liu Ren-Xiu Zhou Megan Price Song-Dong Zhou Xing-Jin He |
| author_sort | Huan-Huan Qin |
| collection | DOAJ |
| description | Abstract Background The Ferula genus encompasses 180–185 species and is one of the largest genera in Apiaceae, with many of Ferula species possessing important medical value. The previous studies provided more information for Ferula, but its infrageneric relationships are still confusing. In addition, its genetic basis of its adaptive evolution remains poorly understood. Plastid genomes with more variable sites have the potential to reconstruct robust phylogeny in plants and investigate the adaptive evolution of plants. Although chloroplast genomes have been reported within the Ferula genus, few studies have been conducted using chloroplast genomes, especially for endemic species in China. Results Comprehensively comparative analyses of 22 newly sequenced and assembled plastomes indicated that these plastomes had highly conserved genome structure, gene number, codon usage, and repeats type and distribution, but varied in plastomes size, GC content, and the SC/IR boundaries. Thirteen mutation hotspot regions were detected and they would serve as the promising DNA barcodes candidates for species identification in Ferula and related genera. Phylogenomic analyses with high supports and resolutions showed that Talassia transiliensis and Soranthus meyeri were nested in the Ferula genus, and thus they should be transferred into the Ferula genus. Our phylogenies also indicated the monophyly of subgenera Sinoferula and subgenera Narthex in Ferula genus. Twelve genes with significant posterior probabilities for codon sites were identified in the positively selective analysis, and their function may relate to the photosystem II, ATP subunit, and NADH dehydrogenase. Most of them might play an important role to help Ferula species adapt to high-temperatures, strong-light, and drought habitats. Conclusion Plastome data is powerful and efficient to improve the support and resolution of the complicated Ferula phylogeny. Twelve genes with significant posterior probabilities for codon sites were helpful for Ferula to adapt to the harsh environment. Overall, our study supplies a new perspective for comprehending the phylogeny and evolution of Ferula. |
| first_indexed | 2024-04-11T00:23:52Z |
| format | Article |
| id | doaj.art-407b3b25c56940e887999c583933ea7f |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-11T00:23:52Z |
| publishDate | 2023-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-407b3b25c56940e887999c583933ea7f2023-01-08T12:08:19ZengBMCBMC Plant Biology1471-22292023-01-0123111810.1186/s12870-022-04027-4The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolutionHuan-Huan Qin0Jing Cai1Chang-Kun Liu2Ren-Xiu Zhou3Megan Price4Song-Dong Zhou5Xing-Jin He6Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan UniversityKey Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan UniversityKey Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan UniversityKey Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan UniversityKey Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan UniversityKey Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan UniversityKey Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan UniversityAbstract Background The Ferula genus encompasses 180–185 species and is one of the largest genera in Apiaceae, with many of Ferula species possessing important medical value. The previous studies provided more information for Ferula, but its infrageneric relationships are still confusing. In addition, its genetic basis of its adaptive evolution remains poorly understood. Plastid genomes with more variable sites have the potential to reconstruct robust phylogeny in plants and investigate the adaptive evolution of plants. Although chloroplast genomes have been reported within the Ferula genus, few studies have been conducted using chloroplast genomes, especially for endemic species in China. Results Comprehensively comparative analyses of 22 newly sequenced and assembled plastomes indicated that these plastomes had highly conserved genome structure, gene number, codon usage, and repeats type and distribution, but varied in plastomes size, GC content, and the SC/IR boundaries. Thirteen mutation hotspot regions were detected and they would serve as the promising DNA barcodes candidates for species identification in Ferula and related genera. Phylogenomic analyses with high supports and resolutions showed that Talassia transiliensis and Soranthus meyeri were nested in the Ferula genus, and thus they should be transferred into the Ferula genus. Our phylogenies also indicated the monophyly of subgenera Sinoferula and subgenera Narthex in Ferula genus. Twelve genes with significant posterior probabilities for codon sites were identified in the positively selective analysis, and their function may relate to the photosystem II, ATP subunit, and NADH dehydrogenase. Most of them might play an important role to help Ferula species adapt to high-temperatures, strong-light, and drought habitats. Conclusion Plastome data is powerful and efficient to improve the support and resolution of the complicated Ferula phylogeny. Twelve genes with significant posterior probabilities for codon sites were helpful for Ferula to adapt to the harsh environment. Overall, our study supplies a new perspective for comprehending the phylogeny and evolution of Ferula.https://doi.org/10.1186/s12870-022-04027-4ApiaceaeFerulaTalassia and SoranthusPlastome evolutionDNA barcodingPhylogenetic relationships |
| spellingShingle | Huan-Huan Qin Jing Cai Chang-Kun Liu Ren-Xiu Zhou Megan Price Song-Dong Zhou Xing-Jin He The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution BMC Plant Biology Apiaceae Ferula Talassia and Soranthus Plastome evolution DNA barcoding Phylogenetic relationships |
| title | The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution |
| title_full | The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution |
| title_fullStr | The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution |
| title_full_unstemmed | The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution |
| title_short | The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution |
| title_sort | plastid genome of twenty two species from ferula talassia and soranthus comparative analysis phylogenetic implications and adaptive evolution |
| topic | Apiaceae Ferula Talassia and Soranthus Plastome evolution DNA barcoding Phylogenetic relationships |
| url | https://doi.org/10.1186/s12870-022-04027-4 |
| work_keys_str_mv | AT huanhuanqin theplastidgenomeoftwentytwospeciesfromferulatalassiaandsoranthuscomparativeanalysisphylogeneticimplicationsandadaptiveevolution AT jingcai theplastidgenomeoftwentytwospeciesfromferulatalassiaandsoranthuscomparativeanalysisphylogeneticimplicationsandadaptiveevolution AT changkunliu theplastidgenomeoftwentytwospeciesfromferulatalassiaandsoranthuscomparativeanalysisphylogeneticimplicationsandadaptiveevolution AT renxiuzhou theplastidgenomeoftwentytwospeciesfromferulatalassiaandsoranthuscomparativeanalysisphylogeneticimplicationsandadaptiveevolution AT meganprice theplastidgenomeoftwentytwospeciesfromferulatalassiaandsoranthuscomparativeanalysisphylogeneticimplicationsandadaptiveevolution AT songdongzhou theplastidgenomeoftwentytwospeciesfromferulatalassiaandsoranthuscomparativeanalysisphylogeneticimplicationsandadaptiveevolution AT xingjinhe theplastidgenomeoftwentytwospeciesfromferulatalassiaandsoranthuscomparativeanalysisphylogeneticimplicationsandadaptiveevolution AT huanhuanqin plastidgenomeoftwentytwospeciesfromferulatalassiaandsoranthuscomparativeanalysisphylogeneticimplicationsandadaptiveevolution AT jingcai plastidgenomeoftwentytwospeciesfromferulatalassiaandsoranthuscomparativeanalysisphylogeneticimplicationsandadaptiveevolution AT changkunliu plastidgenomeoftwentytwospeciesfromferulatalassiaandsoranthuscomparativeanalysisphylogeneticimplicationsandadaptiveevolution AT renxiuzhou plastidgenomeoftwentytwospeciesfromferulatalassiaandsoranthuscomparativeanalysisphylogeneticimplicationsandadaptiveevolution AT meganprice plastidgenomeoftwentytwospeciesfromferulatalassiaandsoranthuscomparativeanalysisphylogeneticimplicationsandadaptiveevolution AT songdongzhou plastidgenomeoftwentytwospeciesfromferulatalassiaandsoranthuscomparativeanalysisphylogeneticimplicationsandadaptiveevolution AT xingjinhe plastidgenomeoftwentytwospeciesfromferulatalassiaandsoranthuscomparativeanalysisphylogeneticimplicationsandadaptiveevolution |