Plastid Phylogenomic Analyses Reveal the Taxonomic Position of Peucedanum franchetii

Abstract

Peucedanum franchetii is a famous folk medicinal plant in China. However, the taxonomy of the P. franchetii has not been sufficiently resolved. Due to similar morphological features between P. franchetii and Ligusticopsis members, the World Flora Online (WFO) Plant List suggested that this species transformed into the genus Ligusticopsis and merged with Ligusticopsis likiangensis. However, both species are obviously diverse in leaf shape, bracts, and bracteoles. To check the taxonomic position of P. franchetii, we newly sequenced and assembled the plastome of P. franchetii and compared it with nine other plastomes of the genus Ligusticopsis. Ten plastomes were highly conserved and similar in gene order, codon bias, RNA editing sites, IR borders, and SSRs. Nevertheless, 10 mutation hotspot regions (infA, rps8, matK, ndhF, rps15, psbA-trnH, rps2-rpoC2, psbA-trnK, ycf2-trnL, and ccsA-ndhD) were still detected. In addition, both phylogenetic analyses based on plastome data and ITS sequences robustly supported that P. franchetii was not clustered with members of Peucedanum but nested in Ligusticopsis. P. franchetii was sister to L. likiangensis in the ITS topology but clustered with L. capillacea in the plastome tree. These findings implied that P. franchetii should be transferred to genus Ligusticopsis and not merged with L. likiangensis, but as an independent species, which was further verified by morphological evidences. Therefore, transferring P. franchetii under the genus Ligusticopsis as an independent species was reasonable, and a new combination was presented.

Plastid phylogenomics contributes to the taxonomic revision of taxa within the genus Sanicula L. and acceptance of two new members of the genus

“…In most angiosperms, plastids are usually considered to be inherited from the maternal parent and have low nucleotide substitution rates ( Wicke et al., 2011 ; Wataru and Tsuneaki, 2023 ). Thus, the plastid genomes (plastomes) have been widely and successfully used for plant phylogenetic analyses ( Duminil et al, 2012 ; Miller et al, 2014 ; Razafimandimbison et al, 2014 ; Zhang et al, 2018 ; Schneider et al, 2021 ; Xu and Hong., 2021 ; Ji et al., 2022 ; Scatigna et al, 2022 ; Xiang et al, 2022 ; Baldwin et al, 2023 ; Fu et al, 2023 ), especially for those taxonomically controversial taxa within the family Apiaceae ( Gou et al., 2020 ; Ren et al., 2020 , 2022 ; Cai et al., 2022 ; Liu et al., 2022 ; Guo et al., 2023 ; Liu et al., 2023a ; Lei et al., 2022 ; Gui et al., 2023 ; Peng et al., 2023 ; Qin et al., 2023 ; Song et al., 2023 ; Tian et al., 2023 ; Song et al., 2024 ). For example, Song et al.…”

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“…Unfortunately, the plastome-based and ITS-based phylogenetic trees yielded incongruent topologies. The phenomenon of conflict was also frequently observed in other genera of Apiaceae (Ren et al, 2020;Cai et al, 2022;Ren et al, 2022;Wen et al, 2021;Gui et al, 2023;Qin et al, 2023;Song et al, 2023;Tian et al, 2023;Song et al, 2024). This conflict was likely attributed to the biparental inheritance, higher mutation rate, and the insufficient sequence length of ITS data, whereas plastid DNA was maternal inheritance and has lower mutation rate (Wolfe et al, 1987;Koch et al, 2001).…”

“…In most angiosperms, plastids are usually considered to be inherited from the maternal parent and have low nucleotide substitution rates (Wicke et al, 2011;Wataru and Tsuneaki, 2023). Thus, the plastid genomes (plastomes) have been widely and successfully used for plant phylogenetic analyses (Duminil et al, 2012;Miller et al, 2014;Razafimandimbison et al, 2014;Zhang et al, 2018;Schneider et al, 2021;Xu and Hong., 2021;Ji et al, 2022;Scatigna et al, 2022;Xiang et al, 2022;Baldwin et al, 2023;Fu et al, 2023), especially for those taxonomically controversial taxa within the family Apiaceae (Gou et al, 2020;Ren et al, 2020Ren et al, , 2022Cai et al, 2022;Liu et al, 2022;Guo et al, 2023;Liu et al, 2023a;Lei et al, 2022;Gui et al, 2023;Peng et al, 2023;Qin et al, 2023;Song et al, 2023;Tian et al, 2023;Song et al, 2024). For example, Song et al (2023) transferred Peucedanum franchetii C.Y.Wu & F.T.Pu under the genus Ligusticopsis Leute based on phylogenetic analysis of ten plastomes.…”

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“…Unfortunately, the plastome-based and ITS-based phylogenetic trees yielded incongruent topologies. The phenomenon of conflict was also frequently observed in other genera of Apiaceae (Ren et al, 2020;Cai et al, 2022;Ren et al, 2022;Wen et al, 2021;Gui et al, 2023;Qin et al, 2023;Song et al, 2023;Tian et al, 2023;Song et al, 2024). This conflict was likely attributed to the biparental inheritance, higher mutation rate, and the insufficient sequence length of ITS data, whereas plastid DNA was maternal inheritance and has lower mutation rate (Wolfe et al, 1987;Koch et al, 2001).…”

“…In most angiosperms, plastids are usually considered to be inherited from the maternal parent and have low nucleotide substitution rates (Wicke et al, 2011;Wataru and Tsuneaki, 2023). Thus, the plastid genomes (plastomes) have been widely and successfully used for plant phylogenetic analyses (Duminil et al, 2012;Miller et al, 2014;Razafimandimbison et al, 2014;Zhang et al, 2018;Schneider et al, 2021;Xu and Hong., 2021;Ji et al, 2022;Scatigna et al, 2022;Xiang et al, 2022;Baldwin et al, 2023;Fu et al, 2023), especially for those taxonomically controversial taxa within the family Apiaceae (Gou et al, 2020;Ren et al, 2020Ren et al, , 2022Cai et al, 2022;Liu et al, 2022;Guo et al, 2023;Liu et al, 2023a;Lei et al, 2022;Gui et al, 2023;Peng et al, 2023;Qin et al, 2023;Song et al, 2023;Tian et al, 2023;Song et al, 2024). For example, Song et al (2023) transferred Peucedanum franchetii C.Y.Wu & F.T.Pu under the genus Ligusticopsis Leute based on phylogenetic analysis of ten plastomes.…”