Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes.

Dustin R Mayfield,Jeffery M Saarela,J Chris Pires,Robert J Soreng,Lynn G Clark,Craig F Barrett,William P Wysocki,Patrick P Edger,Jerrold I Davis,Scot A Kelchner,Melvin R Duvall

doi:10.1093/aobpla/plv046

Abstract

Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some 'early-diverging' tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae-Meliceae and Ampelodesmeae-Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae-Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae-Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae-Loliinae clade.

Highlights

Advances in next-generation sequencing technologies (Moore et al 2006; Cronn et al 2008; Parks et al 2009; Wysocki et al 2014) have resulted in a rapid increase in completed plastid genomes (Jansen and Ruhlman 2012) sampled widely across the green plant tree of life
Plastome sequencing Complete plastomes were newly sequenced for 25 pooid grass species
Strategies to overcome long-branch attraction (LBA) include using inference methods that are less prone to long branch effects and, may be more accurate; excluding third codon positions, which may be saturated or randomized; representing clades in analyses with only short-branched taxa by excluding taxa with long branches; adding taxa to break up large branches and adding data (Bergsten 2005)

Summary

Introduction

Advances in next-generation sequencing technologies (Moore et al 2006; Cronn et al 2008; Parks et al 2009; Wysocki et al 2014) have resulted in a rapid increase in completed plastid genomes (Jansen and Ruhlman 2012) sampled widely across the green plant tree of life. Plastomes have been used to address diverse phylogenetic questions at deep (Ruhfel et al 2014) to shallow (Parks et al 2009) hierarchical levels, and to characterize plastid genome evolution (e.g. patterns of gene loss and organization, GC content, microstructural events, evolutionary rates) Numerous phylogenetic studies have been conducted and the deep phylogenetic framework for Poaceae is well established. The family contains three small, deeply diverging subfamilies (Anomochlooideae, Pharoideae, Puelioideae) that are the successive sister groups of a large clade comprising two major lineages, the Bambusoideae, Ehrhartoideae, Pooideae (BEP) and the Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, Danthonioideae (PACMAD) clades (Grass Phylogeny Working Group 2001; Duvall et al 2007; Sanchez-Ken and Clark 2007; Bouchenak-Khelladi et al 2008; Saarela and Graham 2010; Grass Phylogeny Working Group II 2012)

Methods

Results

Discussion

Conclusion