Molecular evolution and phylogenetic relationships of Ligusticum (Apiaceae) inferred from the whole plastome sequences

Abstract

Background The genus Ligusticum belongs to Apiaceae, and its taxonomy has long been a major difficulty. A robust phylogenetic tree is the basis of accurate taxonomic classification of Ligusticum. We herein used 26 (including 14 newly sequenced) plastome-scale data to generate reliable phylogenetic trees to explore the phylogenetic relationships of Chinese Ligusticum. Results We found that these plastid genomes exhibited diverse plastome characteristics across all four currently identified clades in China, while the plastid protein-coding genes were conserved. The phylogenetic analyses by the concatenation and coalescent methods obtained a more robust molecular phylogeny than prior studies and showed the non-monophyly of Chinese Ligusticum. In the concatenation-based phylogeny analyses, the two datasets yielded slightly different topologies that may be primarily due to the discrepancy in the number of variable sites. Conclusions Our plastid phylogenomics analyses emphasized that the current circumscription of the Chinese Ligusticum should be reduced, and the taxonomy of Ligusticum urgently needs revision. Wider taxon sampling including the related species of Ligusticum will be necessary to explore the phylogenetic relationships of this genus. Overall, our study provided new insights into the taxonomic classification of Ligusticum and would serve as a framework for future studies on taxonomy and delimitation of Ligusticum from the perspective of the plastid genome.

Backbone phylogeny and adaptive evolution of Pleurospermum s. l.: New insights from phylogenomic analyses of complete plastome data

“…This is a group of alpine herbs that are morphologically diverse, differing in plant size, leaf shape, bracts, bracteoles, etc. The close relationships of these species have been indicated since their attribution to Hymenidium (Pimenov and Kljuykov, 2000b) and verified later by several molecular studies (Zhou et al, 2008;Zhou et al, 2009;Пименов et al, 2011;Valiejo-Roman et al, 2012;Bai et al, 2015;Ren et al, 2022). While it is clear that the proper placement of group D is neither Hymenidium nor Pleurospermum, the estimated phylogeny based on ITS indicated its close relationship to Rupiphila tachiroei (Franch.…”

“…All of these sites were C-to-U conversions, and over half of the sites (960 of 1,720, 32 of each plastome) are shared by all plastomes. Most RNA editing sites are situated in the second codon position ( Regel and Tiling, 1838 ; Klotzsch et al., 1862 ; Handel-Mazzetti, 1933 ; Pimenov and Kljuykov, 1999 ; Пименов et al., 2011 ; Murrell et al., 2012 ; Huipeng et al., 2014; Bai et al., 2015 ; Murrell et al., 2015 ; Smith et al., 2015 ; Zhou et al., 2020b ; Ren et al., 2022 ), followed by the first codon position ( Zhou et al., 2008 ; Zhou et al., 2009 ; Downie et al., 2010 ; Zhou et al., 2020a ; Zhou et al., 2021 ), while no sites are situated in the third codon position. Seventeen genes ( accD , atpA , atpB , matK , ndhA , ndhB , ndhD , ndhF , ndhG , petB , psaI , psbE , psbF , rpoB , rpoC1 , rpoC2 , rps14 ) were found to have at least one editing site in all plastomes, and five ( accD , ndhG , ndhB , matK , rpoC ) possess editing sites of both kinds of codon position.…”

“…Species selected as representatives of each lineage with inflorescence and fruit shown in boxes on the right are as follows: group A, P. uralense and P. davidii; group B, P. angelicoides; group C, P. amabile; group D, P. hookeri; group E, P. apiolens; group F, P. bicolor. Kljuykov, 1999;Пименов et al, 2011;Murrell et al, 2012;Huipeng et al, 2014;Bai et al, 2015;Murrell et al, 2015;Smith et al, 2015;Zhou et al, 2020b;Ren et al, 2022), followed by the first codon position (Zhou et al, 2008;Zhou et al, 2009;Downie et al, 2010;Zhou et al, 2020a;Zhou et al, 2021), while no sites are situated in the third codon position. Seventeen genes (accD, atpA, atpB, matK, ndhA, ndhB, ndhD, ndhF, ndhG, petB, psaI, psbE, psbF, rpoB, rpoC1, rpoC2, rps14) were found to have at least one editing site in all plastomes, and five (accD, ndhG, ndhB, matK, rpoC) possess editing sites of both kinds of codon position.…”

Evidence from Phylogenomics and Morphology Provide Insights into the Phylogeny, Plastome Evolution, and Taxonomy of Kitagawia

“…In particular, the plastome-based phylogeny performed by Liu et al [ 47 ] constructed a robust phylogenetic framework for Peucedanum sensu lato and provided a valuable reference to our investigation of Kitagawia . In addition, comparative analyses of plastomes can also provide useful information for eliciting evolutionary and interspecific relationships [ 48 , 49 , 50 ], which should further improve our understanding of the taxonomic classification of Kitagawia .…”

Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization

“…Currently, plastid genomes have been widely used to reveal the phylogeny of complicated genera or closely related species and developed as field known as phylogenomics [ 24 , 26 , 50 ]. Gentiana is an extremely complicated genus in Gentianaceae with approximately 362 species worldwide, including a series of confusing species such as G. rigescens and G. cephalantha [ 2 ].…”