New insights into the phylogeny and infrageneric taxonomy of Saussurea based on hybrid capture phylogenomics (Hyb-Seq)

<i>Saussurea</i> is one of the largest and most rapidly evolving genera within the Asteraceae, comprising approximately 520 species from the Northern Hemisphere. A comprehensive infrageneric classification, supported by robust phylogenetic trees and corroborated by morphological and other data, has not yet been published. For the first time, we recovered a well-resolved nuclear phylogeny of <i>Saussurea</i> consisting of four main clades, which was also supported by morphological data. Our analyses show that ancient hybridization is the most likely source of deep cytoplasmic-nuclear conflict in <i>Saussurea</i>, and a phylogeny based on nuclear data is more suitable than one based on chloroplast data for exploring the infrageneric classification of <i>Saussurea</i>. Based on the nuclear phylogeny obtained and morphological characters, we proposed a revised infrageneric taxonomy of <i>Saussurea</i>, which includes four subgenera and 13 sections. Specifically, 1) <i>S</i>. sect. <i>Cincta</i>, <i>S</i>. sect. <i>Gymnocline, S</i>. sect. <i>Lagurostemon</i>, and <i>S</i>. sect. <i>Strictae</i> were moved from <i>S</i>. subg. <i>Saussurea</i> to <i>S</i>. subg. <i>Amphilaena</i>, 2) <i>S</i>. sect. <i>Pseudoeriocoryne</i> was moved from <i>S</i>. subg. <i>Eriocoryne</i> to <i>S</i>. subg. <i>Amphilaena</i>, and 3) <i>S</i>. sect. <i>Laguranthera</i> was moved from <i>S</i>. subg. <i>Saussurea</i> to <i>S</i>. subg. <i>Theodorea</i>.