Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships

Ting Ren,Chang Peng,Xing-Jin He,Jun Wen,Ling-Jian Gui,Zi-Xuan Li,Deng-Feng Xie

doi:10.1186/s12870-020-02696-7

Abstract

BackgroundThe 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.ResultsThrough 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.ConclusionThe 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.

Highlights

The genus Ligusticum consists of approximately 60 species distributed in the Northern Hemisphere
Characteristics of Ligusticum plastomes After quality control, 5.76 Gb (L. scapiforme) to 7.47 Gb (L. delavayi) clean reads were generated for the eight Ligusticum species (Table 1), we obtained eight complete plastome sequences by a de novo assembly
The determined complete plastome sequences of the eight Ligusticum species ranged from 146,443 bp in L. pteridophyllum to 155,623 bp in L. delavayi (Table 1)

Summary

Introduction

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. 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]. Ligusticum is one of the most taxonomically difficult genera within Apiaceae, largely due to the varied. More genomic resources are needed for reconstructing phylogenetic relationships and re-evaluating the generic limits of Ligusticum

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Discussion

Conclusion