Plastid genomes and deep relationships among the commelinid monocot angiosperms

Abstract

The commelinid monocots comprise the orders Arecales (A), Commelinales (C), Poales sensu Angiosperm Phylogeny Group III (APGIII) (P), Zingiberales (Z), plus the unplaced family Dasypogonaceae (D), collectively containing numerous economically and ecologically important species and encompassing enormous morphological diversity. Commelinids are supported as monophyletic based on anatomy and molecular data; however, relationships among major commelinid groupings conflict among previous studies, representing a long-standing problem in monocot systematics, with major implications for interpretations of character evolution. In more recent analyses, with whole-plastome sampling largely focused on Poales, areas of conflict remain, suggesting the need for closer investigation of relationships and support. Here, we increased sampling of plastomes among non-Poalean commelinid orders to investigate deep nodal support. Analysis of 83 plastid genes recovered relationships as ((A, D) (ZC, P)) with robust support, regardless of reconstruction method (parsimony ⁄ likelihood). However, conflict among genes was evident when grouped by genomic region. Cumulative analyses of genes ranked by decreasing numbers of informative characters indicated continued fluctuation in support, even as small genes were added to a nearly complete matrix, contrary to the expected pattern of stabilization in support. Topology tests among major commelinid groups suggested that the data were not powerful enough to reject all alternatives. This study provides clues to the limits of the plastid genome for resolving deep relationships among the commelinid monocots.

Comparative Genomics and Phylogenomics of East Asian Tulips (Amana, Liliaceae)

“…Compared with phylogenetic studies limited to a few cpDNA regions, cp phylogenomic studies involve many more informative sites for potentially greater resolution and support (Burke et al, 2012). With the rapid development of next-generation sequencing, cp genome-scale data have been increasingly employed to infer phylogenetic relationships at almost any taxonomic levels in the past decade (Jansen et al, 2007; Moore et al, 2007, 2010; Parks et al, 2009; Barrett et al, 2013; Ma P. F. et al, 2014; Carbonell-Caballero et al, 2015; Zhang et al, 2016). In addition, based on comparative genomic analyses, cp genomic hotspots can be identified as DNA barcodes in discriminating species, in terms of informative regions for a specific plant genus, tribe or family (Doorduin et al, 2011; Li et al, 2013, 2014).…”

Complete Sequence and Comparative Analysis of the Chloroplast Genome of Coconut Palm (Cocos nucifera)

“…Both are members of the palm family (Arecaceae), which is the third most economically important family of plants after the grasses and legumes [7]. Complete sequence information on cp genomes from three additional palms - Calamus caryotoides , Pseudophoenix vinifera , Bismarkia nobilis – has recently been deposited in GenBank [8]. However, the complete cp genome sequence of coconut palm ( Cocos nucifera L.), which is a universal symbol of the tropics and equally important as oil palm [7], has not yet been reported.…”

Systematic Placement of Dasypogonaceae Among Commelinid Monocots: Evidence from Flowers and Fruits

“…Chase et al 2000) and morphological (e.g., Rudall et al 1999), have rejected these relationship hypotheses, instead linking Hanguana with either Zingiberales or Commelinales. Combined multigene analyses for monocots have placed Dasypogonaceae either as sister to Poales sensu lato (Chase et al 2006;Davis et al 2006), sister to Zingiberales plus Commelinales (Graham et al 2006), or sister to palms (Givnish et al 2010;Barrett et al 2012). The currently unresolved relationship between Dasypogonaceae and these three major groups represents one of the primary remaining questions in monocot phylogenetics, currently being addressed by the ongoing Assembling the Monocot Tree of Life project.…”

“…3). Molecular analyses have variously placed them as sister to all other commelinids (Davis et al 2004), closely related to palms (Chase et al 1995a, b;Givnish et al 2010;Barrett et al 2012), sister to Commelinales/Zingiberales (Graham et al 2006) or sister to Poales sensu lato (Chase et al 2006;Davis et al 2006). This paper reviews existing systematic data on Dasypogonaceae, and presents new data on floral structure and ontogeny.…”