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.

Xi Li,Tao Feng,Chris Randle,Gerald M Schneeweiss

doi:10.3389/fpls.2019.00902

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.

Highlights

Parasitic plants attach to other plants via a specialized organ, the haustorium, to obtain nutrients and water from their hosts (Kuijt, 1969)
Analyses of two pentatricopeptide repeat (PPR) genes, AT1G09680 and AT2G37230, indicated resolved, though not necessarily well-supported, relationships among major clades of Orobanchaceae and among Odontites species (Supplementary Figures S1, S2). This confirms the high potential of PPR genes for molecular phylogenetic studies from the family to the species level (Yuan et al, 2010; Barkan and Small, 2014; Crowl et al, 2014), notwithstanding issues of incongruence among markers from the level of major clades to the infrageneric level, as in Odontites (Supplementary Figures S1, S2)
We analyzed the potential of five nuclear genes to address phylogenetic relationships within Orobanchaceae focusing on major clades identified previously

Summary

Introduction

Parasitic plants attach to other plants via a specialized organ, the haustorium, to obtain nutrients and water from their hosts (Kuijt, 1969). This renders parasitic plants of interest for plant scientists, who investigate structural, physiological, and molecular adaptations of parasitism (dePamphilis and Palmer, 1990; Cubero and Moreno, 1996; Joel et al, 2013) and for farmers and applied scientists, because some parasitic plants are serious agricultural pests that can cause major yield losses (Parker and Riches, 1993). Whereas parasitism has evolved only once in Orobanchaceae, the transition from hemi- to holoparasitism has occurred multiple times (Schneeweiss, 2013)

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