Phylogenetic reappraisal of Allium subgenus Cyathophora (Amaryllidaceae) and related taxa, with a proposal of two new sections

Abstract

The phylogeny of subgenus Cyathophora and representatives of its closely related taxa within Allium were reconstructed based on nrDNA ITS and two plastid fragments (trnL-F and rpl32-trnL). The constructed phylogenies indicated that subgenus Cyathophora was not monophyletic and to be split in three parts positioned in different clusters. Allium kingdonii was unequivocally placed within subgenus Amerallium and formed an immediate sister relationship with New World Amerallium clade, suggesting an unexpected intercontinental disjunct distribution. For another, Allium trifurcatum was firmly nested within subgenus Butomissa next to A. tuberosum and A. ramosum, but it is distinctly different morphologically from the latter by thinly leathery bulb tunics, uniovulate locule and obviously 3-cleft stigma. Based on the geographic features, morphological and molecular evidences, two new sections, Kingdonia X.J.He et D.Q.Huang for A. kingdonii and Trifurcatum X.J.He et D.Q.Huang for A. trifurcatum, were proposed. The remaining three species of subgenus Cyathophora formed a well-defined clade, and the phylogenetic relationships among them recovered were consistent with previous findings. In addition, A. weschniakowii and A. subtilissimum were proven to be a member of subgenera Rhizirideum sensu stricto (s. str.) and Cepa, respectively, rather than subgenera Cepa and Polyprason previously proposed. Section Rhizomatosa represented by A. caespitosum should be subsumed within section Caespitosoprason of subgenus Rhizirideum s. str.

Spatio-temporal evolution of Allium L. in the Qinghai–Tibet-Plateau region: Immigration and in situ radiation

“…(2006) . Yet, consistent with the results of Huang et al. (2014) , A. kingdonii is nested within subgenus Amerallium Traub., as sister to the clade of American Amerallium .…”

Characterization of the complete chloroplast genome of Allium kingdonii

“…Phylogenetic analysis suggested that A. kingdonii is closely clustered with A. paradoxum (Figure 1), which was consistent with a previous study (Huang et al 2014). This complete cp genome can provide a genomic resource and can be further…”

“…He et D.Q. Huang for A. kingdonii was proposed, and A. kingdonii was unequivocally placed into the subgenus Amerallium (Huang et al 2014). In this study, we reported the complete chloroplast genome sequence of A. kingdonii, which will provide a genomic resource and can be used to investigate the phylogenetic relationships in the Allium L. with other previously reported species.…”

Comparative Analysis of the Complete Chloroplast Genomes in Allium Subgenus Cyathophora (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution

“…In previous study, A. spicatum was classified at different taxonomic levels because of its idiographic spicate inflorescence based on morphological and molecular evidences [3]. Five species have been proposed by Huang et al about subgenus Cyathophora [4]: A. mairei, A. rhynchogynum, A. cyathophorum, A. cyathophorum var. farreri, and A. spicatum, while A. kingdonii and A. trifurcatum did not belong to this group.…”

“…Li et al [6] performed phylogenetic and biogeographic analyses for A. cyathophorum and A. spicatum based on chloroplast and nuclear ribosomal DNA and detected distinct different topologies between these two molecular methods, in which A. cyathophorum showed close relationship with A. spicatum in nuclear DNA tree but was sister to A. cyathophorum var. farreri in cpDNA tree [4,6]. Other than this, the relationship between these species is not exactly determined, and phylogenetic analysis using single or several combined chloroplast fragments does not solve the problem effectively, and the complete cp genome can well resolve the relationship of subgenus Cyathophora.…”