Phylogenetic Relationships in Orobanchaceae Inferred From Low-Copy Nuclear Genes: Consolidation of Major Clades and Identification of a Novel Position of the Non-photosynthetic Orobanche Clade Sister to All Other Parasitic Orobanchaceae

Abstract

Molecular phylogenetic analyses have greatly advanced our understanding of phylogenetic relationships in Orobanchaceae, a model system to study parasitism in angiosperms. As members of this group may lack some genes widely used for phylogenetic analysis and exhibit varying degrees of accelerated base substitution in other genes, relationships among major clades identified previously remain contentious. To improve inferences of phylogenetic relationships in Orobanchaceae, we used two pentatricopeptide repeat (PPR) and three low-copy nuclear (LCN) genes, two of which have been developed for this study. Resolving power and level of support strongly differed among markers. Despite considerable incongruence among newly and previously sequenced markers, monophyly of major clades identified in previous studies was confirmed and, especially in analyses of concatenated data, strongly supported after the exclusion of a small group of East Asian genera ( Pterygiella and Phtheirospermum ) from the Euphrasia-Rhinanthus clade. The position of the Orobanche clade sister to all other parasitic Orobanchaceae may indicate that the shift to holoparasitism occurred early in the evolution of the family. Although well supported in analyses of concatenated data comprising ten loci (five newly and five previously sequenced), relationships among major clades, most prominently the Striga-Alectra clade, the Euphrasia-Rhinanthus clade, and the Castilleja-Pedicularis clade, were uncertain because of strongly supported incongruence also among well-resolving loci. Despite the limitations of using a few selected loci, congruence among markers with respect to circumscription of major clades of Orobanchaceae renders those frameworks for detailed, species-level, phylogenetic studies.

Genesis, Evolution, and Genetic Diversity of the Hexaploid, Narrow Endemic Centaurea tentudaica

“…The PgiC region is used here for the first time in section Acrocentron of genus Centaurea and shows great resolution, as found in previous phylogenetic studies on Compositae [15] and Onagraceae [71,72]. The lack of resolution obtained herein with the AGT1 was already observed in other studies, including those of Li et al (2019) [73] in Orobanchaceae, but in opposition to studies carried out in Centaurea of Compositae [37] and in a large number of families within angiosperms [43], where it proved to be particularly useful.…”

Parasitic angiosperms: How often and how many?

“…() used nuclear ribosomal ITS sequences to show that this clade diverged later and was sister to the remaining members of the family. This topology places the holoparasitic Orobancheae as sister to the entire family, a result also obtained using low‐copy nuclear genes (Li & al., ). If this topology is correct, it appears there was a divergence that split the hemiparasites from one clade of holoparasites early in the evolutionary history of the family.…”

“…In that chapter, the phylogenetic relationships of the various clades in the family were discussed, and five disconnected phylogenetic trees were shown that included lists of unplaced taxa based on their assumed affinity. Although there have been numerous phylogenetic studies since 2013 (e.g., Schneider & al., ; Uribe‐Convers & Tank, ; Fu & al., ; Pinto‐Carrasco & al., ; Gaudeul & al., ; Yu & al., ; Li & al., ), most have been focused on a particular group (tribe) within Orobanchaceae. It appears that there does not exist in the literature an attempt to incorporate all the available phylogenetic information to produce a “super tree” of Orobanchaceae.…”

“…Recent work using five‐ and ten‐locus datasets of low‐copy nuclear genes (Li & al., ) showed different topologies for the Pterygiella clade relative to Rhinantheae, Buchnereae, and Pedicularidae. This clade, composed of the Asian genera Pterygiella Oliv., Pseudobartsia D.Y.Hong, and Xizangia D.Y.Hong, is therefore shown as arising from a polytomy involving Buchnereae, Rhinantheae, and Pedicularideae in Fig.…”

Orobanchaceae parasite–host interactions

“…Parasitic plant species are distributed among 18–22 families in 12 taxonomic orders. Orobanchaceae is the family with the largest number of parasitic species in which the genera Striga , Orobanche and Phelipanche belong (Yoshida et al ., 2016; Li et al ., 2019). The phylogeny analysis shows there are six clades in the Orobanchaceae (Fig.…”