Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships
Autor: | Xing-Jin He, Jun Wen, Deng-Feng Xie, Zi-Xuan Li, Ling-Jian Gui, Chang Peng, Ting Ren |
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Rok vydání: | 2020 |
Předmět: |
0106 biological sciences
0301 basic medicine Genome evolution Genotype Evolution Characterization Genome Plastid Plant Science Biology Genes Plant 01 natural sciences Coalescent theory Evolution Molecular 03 medical and health sciences Phylogenetics lcsh:Botany Ligusticum Internal transcribed spacer Genome size Phylogeny Phylogenetic tree Genetic Variation Sequence Analysis DNA Plastome biology.organism_classification Relaxed selection lcsh:QK1-989 030104 developmental biology Chloroplast DNA Evolutionary biology Phylogenetic relationships Research Article 010606 plant biology & botany |
Zdroj: | BMC Plant Biology, Vol 20, Iss 1, Pp 1-14 (2020) BMC Plant Biology |
ISSN: | 1471-2229 |
DOI: | 10.1186/s12870-020-02696-7 |
Popis: | Background The genus Ligusticum consists of approximately 60 species distributed in the Northern Hemisphere. It is one of the most taxonomically difficult taxa within Apiaceae, largely due to the varied morphological characteristics. To investigate the plastome evolution and phylogenetic relationships of Ligusticum, we determined the complete plastome sequences of eight Ligusticum species using a de novo assembly approach. Results Through a comprehensive comparative analysis, we found that the eight plastomes were similar in terms of repeat sequence, SSR, codon usage, and RNA editing site. However, compared with the other seven species, L. delavayi exhibited striking differences in genome size, gene number, IR/SC borders, and sequence identity. Most of the genes remained under the purifying selection, whereas four genes showed relaxed selection, namely ccsA, rpoA, ycf1, and ycf2. Non-monophyly of Ligusticum species was inferred from the plastomes and internal transcribed spacer (ITS) sequences phylogenetic analyses. Conclusion The plastome tree and ITS tree produced incongruent tree topologies, which may be attributed to the hybridization and incomplete lineage sorting. Our study highlighted the advantage of plastome with mass informative sites in resolving phylogenetic relationships. Moreover, combined with the previous studies, we considered that the current taxonomy system of Ligusticum needs to be improved and revised. In summary, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of Ligusticum species. |
Databáze: | OpenAIRE |
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