Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships
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RESEARCH ARTICLE
Open Access
Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships Ting Ren, Zi-Xuan Li, Deng-Feng Xie, Ling-Jian Gui, Chang Peng, Jun Wen and Xing-Jin He*
Abstract 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. Keywords: Ligusticum, Plastome, Characterization, Relaxed selection, Evolution, Phylogenetic relationships
Background The genus Ligusticum, belonging to the family Apiaceae with approximately 60 species, is distributed throughout Asia, Europe, and North America [1]. It has two distribution centers: one in the Himalayas, and the other in North America [2]. There are 40 species (35 endemics) of this genus in China, most of which are restricted to alpine regions [1]. Ligusticum is one of the most taxonomically difficult genera within Apiaceae, largely due to the varied * Correspondence: [email protected] Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
morphological characteristics of flowers, leaves, bracteoles, and mericarps that make it difficult to distinguish from its neighbors [1, 3, 4]. So far, its phylogenetic relationships with nearby genera are not clear, such as Ligusticopsis, Tilingia, Cnidium, Selinum, Hymenidium, Pachypleurum, Rupiphila, and Paraligusticum [1], especially, merging Tilingia and Ligusticopsis into Ligusticum is still debatable [2]. The diagnostic characters of Tilingia are the distinct calyx teeth and the mericarp bearing a
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