Commelinid Monocots Research Articles

Modification of plant cell walls with hydroxycinnamic acids by BAHD acyltransferases.

In the last decade it has become clear that enzymes in the "BAHD" family of acyl-CoA transferases play important roles in the addition of phenolic acids to form ester-linked moieties on cell wall polymers. We focus here on the addition of two such phenolics-the hydroxycinnamates, ferulate and p-coumarate-to two cell wall polymers, glucuronoarabinoxylan and to lignin. The resulting ester-linked feruloyl and p-coumaroyl moities are key features of the cell walls of grasses and other commelinid monocots. The capacity of ferulate to participate in radical oxidative coupling means that its addition to glucuronoarabinoxylan or to lignin has profound implications for the properties of the cell wall - allowing respectively oxidative crosslinking to glucuronoarabinoxylan chains or introducing ester bonds into lignin polymers. A subclade of ~10 BAHD genes in grasses is now known to (1) contain genes strongly implicated in addition of p-coumarate or ferulate to glucuronoarabinoxylan (2) encode enzymes that add p-coumarate or ferulate to lignin precursors. Here, we review the evidence for functions of these genes and the biotechnological applications of manipulating them, discuss our understanding of mechanisms involved, and highlight outstanding questions for future research.

"Exclusive" update: p-coumaroylation of lignin not restricted to commelinid monocots.

"Exclusive" update: p-coumaroylation of lignin not restricted to commelinid monocots.

Evolution of p-coumaroylated lignin in eudicots provides new tools for cell wall engineering.

Ester-linked p-coumarate (pCA) is a hallmark feature of the secondary cell walls in commelinid monocot plants. It has been shown that pCA groups arise during lignin polymerisation from the participation of monolignol conjugates assembled by p-coumaroyl-CoA:monolignol transferase (PMT) enzymes, members of the BAHD superfamily of acyltransferases. Herein, we report that a eudicot species, kenaf (Hibiscus cannabinus), naturally contains p-coumaroylated lignin in the core tissues of the stems but not in the bast fibres. Moreover, we identified a novel acyltransferase, HcPMT, that shares <30% amino acid identity with known monocot PMT sequences. Recombinant HcPMT showed a preference in enzyme assays for p-coumaroyl-CoA and benzoyl-CoA as acyl donor substrates and sinapyl alcohol as an acyl acceptor. Heterologous expression of HcPMT in hybrid poplar trees led to the incorporation of pCA in lignin, but no improvement in the saccharification potential of the wood. This work illustrates the value in mining diverse plant taxa for new monolignol acyltransferases. Furthermore, the occurrence of pCA outside monocot lineages may represent another example of convergent evolution in lignin structure. This discovery expands textbook views on cell wall biochemistry and provides a new molecular tool for engineering the lignin of biomass feedstock plants.

P-Coumaroylation of lignin occurs outside of commelinid monocots in the eudicot genus Morus (mulberry).

The presence of p-coumarate (pCA) in plant cell walls is generally considered to be a trait present only in commelinid monocots. Here, we show that this long-held overgeneralizing assumption is incorrect and that mulberry trees (Morus) are eudicot plants that have lignins derived in part from monolignol pCA esters. As in commelinid monocots, the lignin-bound pCA acylates the sidechain γ-hydroxyl of both coniferyl and syringyl units. This discovery expands mulberry's potential applications to include being a source of p-coumaric acid, a supplier of nutritious berries, a forage crop, a decorative plant, and the main food source for silkworms.

2D-HSQC-NMR-Based Screening of Feruloylated Side-Chains of Cereal Grain Arabinoxylans.

Arabinoxylans of commelinid monocots are characterized by high contents of ferulic acid that is incorporated into arabinose-bearing side-chains of varying complexity. Species-related differences in the feruloylated side-chain profiles of grain arabinoxylans are observed and lead to differences in arabinoxylan functionality. Here, a semi-quantitative assay based on 1H-13C-correlation NMR spectroscopy (HSQC experiment) was developed to profile feruloylated side-chains of cereal grain arabinoxylans. Following acidic liberation of the feruloylated side-chains from the xylan backbone and a clean-up step using C18 solid phase extraction, the feruloylated oligosaccharides FA (5-O-trans-feruloyl-L-arabinofuranose), FAX (β-d-xylopyranosyl-(1 → 2)-5-O-trans-feruloyl-l-arabinofuranose) and FAXG (α-l-galactopyranosyl-(1 → 2)-β-d-xylopyranosyl-(1 → 2)-5-O-trans-feruloyl-l-arabinofuranose) were analyzed by HSQC-NMR. Marker signals were identified for each compound, and experimental conditions such as solvent and internal standard as well as measurement and processing conditions were optimized for a semi-quantitative determination. The approach was validated with respect to accuracy, precision, limit of detection, and limit of quantification. The newly developed approach was applied to several cereal samples including oats, popcorn maize, wheat, and wild rice. Data were compared to an HPLC-DAD/MS approach published earlier by our group, demonstrating that the results of the HSQC approach were comparable to the more time-consuming and technically more challenging HPLC-DAD/MS method.

Evolution of the Cell Wall Gene Families of Grasses.

Grasses and related commelinid monocot species synthesize cell walls distinct in composition from other angiosperm species. With few exceptions, the genomes of all angiosperms contain the genes that encode the enzymes for synthesis of all cell-wall polysaccharide, phenylpropanoid, and protein constituents known in vascular plants. RNA-seq analysis of transcripts expressed during development of the upper and lower internodes of maize (Zea mays) stem captured the expression of cell-wall-related genes associated with primary or secondary wall formation. High levels of transcript abundances were not confined to genes associated with the distinct walls of grasses but also of those associated with xyloglucan and pectin synthesis. Combined with proteomics data to confirm that expressed genes are translated, we propose that the distinctive cell-wall composition of grasses results from sorting downstream from their sites of synthesis in the Golgi apparatus and hydrolysis of the uncharacteristic polysaccharides and not from differential expression of synthases of grass-specific polysaccharides.

In silico characterization and expression profiling of the diacylglycerol acyltransferase gene family (DGAT1, DGAT2, DGAT3 and WS/DGAT) from oil palm, Elaeis guineensis

The diacylglycerol acyltransferases (DGAT) (diacylglycerol:acyl-CoA acyltransferase, EC 2.3.1.20) are a key group of enzymes that catalyse the final and usually the most important rate-limiting step of triacylglycerol biosynthesis in plants and other organisms. Genes encoding four distinct functional families of DGAT enzymes have been characterised in the genome of the African oil palm, Elaeis guineensis. The contrasting features of the various isoforms within the four families of DGAT genes, namely DGAT1, DGAT2, DGAT3 and WS/DGAT are presented both in the oil palm itself and, for comparative purposes, in 12 other oil crop or model/related plants, namely Arabidopsis thaliana, Brachypodium distachyon, Brassica napus, Elaeis oleifera, Glycine max, Gossypium hirsutum, Helianthus annuus, Musa acuminata, Oryza sativa, Phoenix dactylifera, Sorghum bicolor, and Zea mays. The oil palm genome contains respectively three, two, two and two distinctly expressed functional copies of the DGAT1, DGAT2, DGAT3 and WS/DGAT genes. Phylogenetic analyses of the four DGAT families showed that the E. guineensis genes tend to cluster with sequences from P. dactylifera and M. acuminata rather than with other members of the Commelinid monocots group, such as the Poales which include the major cereal crops such as rice and maize. Comparison of the predicted DGAT protein sequences with other animal and plant DGATs was consistent with the E. guineensis DGAT1 being ER located with its active site facing the lumen while DGAT2, although also ER located, had a predicted cytosol-facing active site. In contrast, DGAT3 and some (but not all) WS/DGAT in E. guineensis are predicted to be soluble, cytosolic enzymes. Evaluation of E. guineensis DGAT gene expression in different tissues and developmental stages suggests that the four DGAT groups have distinctive physiological roles and are particularly prominent in developmental processes relating to reproduction, such as flowering, and in fruit/seed formation especially in the mesocarp and endosperm tissues.

A new commelinid monocot seed fossil from the early Eocene previously identified as Solanaceae.

Fossils provide minimum age estimates for extant lineages. Here we critically evaluate Cantisolanum daturoides Reid & Chandler and two other early putative seed fossils of Solanaceae, an economically important plant family in the Asteridae. Three earliest seed fossil taxa of Solanaceae from the London Clay Formation (Cantisolanum daturoides) and the Poole and Branksome Sand Formations (Solanum arnense Chandler and Solanispermum reniforme Chandler) were studied using x-ray microcomputed tomography (MCT) and scanning electron microscopy (SEM). The MCT scans of Cantisolanum daturoides revealed a high level of pyrite preservation at the cellular level. Cantisolanum daturoides can be clearly excluded from Solanaceae and has more affinities to the commelinid monocots based on a straight longitudinal axis, a prominent single layer of relatively thin-walled cells in the testa, and a clearly differentiated micropyle surrounded by radially elongated and inwardly curved testal cells. While the MCT scans show no internal preservation in Solanum arnense and Solanispermum reniforme, SEM images show the presence of several characteristics that allow the placement of these taxa at the stem node of Solanaceae. Cantisolanum daturoides is likely a member of commelinid monocots and not Solanaceae as previously suggested. The earliest fossil record of Solanaceae is revised to consist of fruit fossil with inflated calyces from the early Eocene of Patagonia (52 Ma) and fossilized seeds from the early to mid-Eocene of Europe (48-46 Ma). The new identity for Cantisolanum daturoides does not alter a late Cretaceous minimum age for commelinids.

Extraction and characterization of pectins from primary cell walls of edible açaí (Euterpe oleraceae) berries, fruits of a monocotyledon palm

Açaí berries (Euterpe oleracea) are greatly consumed in Brazil and exported to other countries as a nutritional supplement, due to health benefits attributed to its consumption. However, the complete chemical structure of bioactive polysaccharides was not fully elucidated yet. In this work, we characterize pectic polysaccharides from açaí berries through monosaccharide composition, HPSEC, methylation and 13C and 1H/13C HSQC-DEPT-NMR analyses. A highly methoxylated homogalacturonan with a DM of 88% and Mw of 22kDa together with small amounts of a mannoglucan were found. Moreover, a type II arabinogalactan (Mw=45kDa) containing a backbone with high portions of 6-O-linked and 3,6-O-linked Galp chains rather than 3-O-linked Galp was also isolated and structurally characterized. The type II arabinogalactan was found as a side chain of a type I rhamnogalacturonan. These findings contribute to correlate the fine chemical structure with the previously reported action of açaí polysaccharides on innate immune response. Moreover, from the taxonomic point of view, the results bring new information about polysaccharide composition of primary cell walls of palms (Arecaceae), that despite being commelinid monocots, have a distinct cell wall composition.

Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots.

Despite progress based on multilocus, phylogenetic studies of the palms (order Arecales, family Arecaceae), uncertainty remains in resolution/support among major clades and for the placement of the palms among the commelinid monocots. Palms and related commelinids represent a classic case of substitution rate heterogeneity that has not been investigated in the genomic era. To address questions of relationships, support and rate variation among palms and commelinid relatives, 39 plastomes representing the palms and related family Dasypogonaceae were generated via genome skimming and integrated within a monocot-wide matrix for phylogenetic and molecular evolutionary analyses. Support was strong for 'deep' relationships among the commelinid orders, among the five palm subfamilies, and among tribes of the subfamily Coryphoideae. Additionally, there was extreme heterogeneity in the plastid substitution rates across the commelinid orders indicated by model based analyses, with c. 22 rate shifts, and significant departure from a global clock. To date, this study represents the most comprehensively sampled matrix of plastomes assembled for monocot angiosperms, providing genome-scale support for phylogenetic relationships of monocot angiosperms, and lays the phylogenetic groundwork for comparative analyses of the drivers and correlates of such drastic differences in substitution rates across a diverse and significant clade.

Morphological diversity and evolution of Centrolepidaceae (Poales), a species‐poor clade with diverse body plans and developmental patterns

• Premise of the study: The small primarily Australian commelinid monocot family Centrolepidaceae displays remarkably high structural diversity that has been hitherto relatively poorly explored. Data on Centrolepidaceae are important for comparison with other Poales, including grasses and sedges.• Methods: We examined vegetative and reproductive morphology in a global survey of Centrolepidaceae based on light and scanning electron microscopy of 18 species, representing all three genera. We used these data to perform a cladistic analysis to assess character evolution.• Key results: Each of the three genera is monophyletic; Centrolepis is sister to Aphelia. Some Centrolepidaceae show a change from spiral to distichous phyllotaxy on inflorescence transition. In Aphelia and most species of Centrolepis, several morphologically distinct leaf types develop along the primary shoot axis and flowers are confined to dorsiventral lateral spikelets. Centrolepis racemosa displays secondary unification of programs of leaf development, absence of the leaf hyperphyll and loss of shoot dimorphism. Presence or absence of a leaf ligule and features of inflorescence and flower morphology are useful as phylogenetic characters in Centrolepidaceae.• Conclusions: Ontogenetic changes in phyllotaxy differ fundamentally between some Centrolepidaceae and many grasses. Inferred evolutionary transformations of phyllotaxy in Centrolepidaceae inflorescences also differ from those in grasses. In contrast with grasses, some Centrolepidaceae possess ligulate leaves where the ligule represents the boundary between the bifacial hypophyll and unifacial hyperphyll. All the highly unusual features of the morphological‐misfit species Centrolepis racemosa could result from the same saltational event. Centrolepidaceae offer good perspectives for studies of evolutionary developmental biology.

Phylogenetic effects on shoot magnesium concentration

Insufficient calcium (Ca) or magnesium (Mg) in the diets of humans and animals has negative effects on health. Knowledge of the concentrations of Ca and Mg in edible crops can help inform the formulation of appropriate diets. There are large differences in shoot concentrations of both Ca ([Ca]shoot) and Mg ([Mg]shoot) between angiosperm orders. For example, relative to other angiosperms, commelinid monocot species generally have lower [Ca]shoot and [Mg]shoot; species from the Cucurbitales, Malvales and Brassicales generally have higher [Ca]shoot and [Mg]shoot; and species from the Oxalidales and Caryophyllales generally have higher [Mg]shoot but similar [Ca]shoot, which results in higher [Mg]shoot/[Ca]shoot quotients. In this paper the evolution of the combined traits of high [Mg]shoot and high [Mg]shoot/[Ca]shoot quotient in the Caryophyllales was resolved at the family level. All Caryophyllales families had high mean [Mg]shoot and [Mg]shoot/[Ca]shoot quotients, suggesting that both of these traits evolved in an ancient ancestor of all Caryophyllales families.

Integrated syntenic and phylogenomic analyses reveal an ancient genome duplication in monocots.

Unraveling widespread polyploidy events throughout plant evolution is a necessity for inferring the impacts of whole-genome duplication (WGD) on speciation, functional innovations, and to guide identification of true orthologs in divergent taxa. Here, we employed an integrated syntenic and phylogenomic analyses to reveal an ancient WGD that shaped the genomes of all commelinid monocots, including grasses, bromeliads, bananas (Musa acuminata), ginger, palms, and other plants of fundamental, agricultural, and/or horticultural interest. First, comprehensive phylogenomic analyses revealed 1421 putative gene families that retained ancient duplication shared by Musa (Zingiberales) and grass (Poales) genomes, indicating an ancient WGD in monocots. Intergenomic synteny blocks of Musa and Oryza were investigated, and 30 blocks were shown to be duplicated before Musa-Oryza divergence an estimated 120 to 150 million years ago. Synteny comparisons of four monocot (rice [Oryza sativa], sorghum [Sorghum bicolor], banana, and oil palm [Elaeis guineensis]) and two eudicot (grape [Vitis vinifera] and sacred lotus [Nelumbo nucifera]) genomes also support this additional WGD in monocots, herein called Tau (τ). Integrating synteny and phylogenomic comparisons achieves better resolution of ancient polyploidy events than either approach individually, a principle that is exemplified in the disambiguation of a WGD series of rho (ρ)-sigma (σ)-tau (τ) in the grass lineages that echoes the alpha (α)-beta (β)-gamma (γ) series previously revealed in the Arabidopsis thaliana lineage.

Plastid genomes and deep relationships among the commelinid monocot angiosperms.

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.

GC-Biased Gene Conversion Impacts Ribosomal DNA Evolution in Vertebrates, Angiosperms, and Other Eukaryotes

Ribosomal DNA (rDNA) is one of the most conserved genes in eukaryotes. The multiples copies of rDNA in the genome evolve in a concerted manner, through unequal crossing over and/or gene conversion, two mechanisms related to homologous recombination. Recombination increases local GC content in several organisms through a process known as GC-biased gene conversion (gBGC). gBGC has been well characterized in mammals, birds, and grasses, but its phylogenetic distribution across the tree of life is poorly understood. Here, we test the hypothesis that recombination affects the evolution of base composition in 18S rDNA and examine the reliability of this thoroughly studied molecule as a marker of gBGC in eukaryotes. Phylogenetic analyses of 18S rDNA in vertebrates and angiosperms reveal significant heterogeneity in the evolution of base composition across both groups. Mammals, birds, and grasses experience increases in the GC content of the 18S rDNA, consistent with previous genome-wide analyses. In addition, we observe increased GC contents in Ostariophysi ray-finned fishes and commelinid monocots (i.e., the clade including grasses), suggesting that the genomes of these two groups have been affected by gBGC. Polymorphism analyses in rDNA confirm that gBGC, not mutation bias, is the most plausible explanation for these patterns. We also find that helix and loop sites of the secondary structure of ribosomal RNA do not evolve at the same pace: loops evolve faster than helices, whereas helices are GC richer than loops. We extend analyses to major lineages of eukaryotes and suggest that gBGC might have also affected base composition in Giardia (Diplomonadina), nudibranch gastropods (Mollusca), and Asterozoa (Echinodermata).

Changes in expression pattern of the teosinte branched1‐like genes in the Zingiberales provide a mechanism for evolutionary shifts in symmetry across the order

Floral symmetry is a trait of key importance when considering floral diversification because it is thought to play a significant role in plant-pollinator interactions. The CYCLOIDEA/TEOSINTE BRANCHED1 (CYC/TB1)-like genes have been implicated in the development and evolution of floral symmetry in numerous lineages. We thus chose to investigate a possible role for these genes in the evolution of floral symmetry within petaloid monocots, using the order Zingiberales as a model system. In the Zingiberales, evolutionary shifts in symmetry have occurred in all floral whorls, making the order ideal for studying the evolution of this ecologically significant trait. We analyzed TB1-like (TBL) genes from taxa spanning the order in a phylogenetic context. Using RNA in situ hybridization, we examined the expression of two TBL genes in Costus spicatus (Costaceae) and Heliconia stricta (Heliconiaceae), taxa with divergent floral symmetry patterns. We identified Zingiberales-specific gene duplications as well as a duplication in the TBL gene lineage that predates the diversification of commelinid monocots. Shifts in TBL gene expression were associated with evolutionary shifts in floral symmetry and stamen abortion. ZinTBL1a expression was found in the posterior (adaxial) staminode of H. stricta and in the abaxial staminodial labellum of C. spicatus. ZinTBL2 expression was strongest in the anterior (abaxial) sepals of H. stricta and in the adaxial fertile stamen of C. spicatus. This study adds to the growing body of evidence that CYC/TB1-like genes have been repeatedly recruited throughout the course of evolution to generate bilateral floral symmetry (zygomorphy).

Inference of phylogenetic relationships among the subfamilies of grasses (Poaceae: Poales) using meso-scale exemplar-based sampling of the plastid genome

To clarify phylogenetic relationships among grass (Poaceae) subfamilies and to better resolve the placement of Poaceae in Poales, we surveyed 17 plastid genes and associated noncoding regions (∼15.5 kb per taxon, about 1/10 of the plastid genome) for exemplar representatives from 10 grass subfamilies and a broad sample of related monocots. We found general concordance in relationships and support levels among gene regions and data partitions across analyses, with some exceptions in Bayesian analyses. Different phylogenetic criteria generally agreed on backbone relationships, and the support values we inferred were generally as good as or better than those in other studies that employed more taxa for fewer genes to estimate the same backbone. Within grasses, we found robust support for the monophyly of subfamily Anomochlooideae and for the Bambusoideae–Ehrhartoideae–Pooideae (BEP) clade, and moderate support for a sister-group relationship between Bambusoideae and Pooideae. Most relationships in the strongly supported Panicoideae–Aristidoideae–Chloridoideae–Micrairoideae–Arundinoideae–Danthonioideae (PACMAD) clade were not resolved consistently, probably because the current intensive sampling of genes is still insufficient to resolve short internal branches. Our data infer a well-supported clade that includes the grass family and two small families of grass-like plants, Ecdeiocoleaceae and Joinvilleaceae, but we did not satisfactorily resolve the relationships among these three families. A generally accelerated substitution rate in Poaceae plastid genomes is shared with some, but not all, lineages that are closely related to grasses in the larger clade of commelinid monocots, which may complicate inference of the sister group of the grasses in all current studies.

Phylogeny and Growth Strategy as Predictors of Differences in Cobalt Concentrations Between Plant Species

Analyses reported here quantify the contribution of plant phylogeny and plant growth strategy to soil-to-plant transfer of Co. Estimated relative mean (ERM) Co concentrations in shoots of 241 species of flowering plant were derived using a residual maximum likelihood (REML) analysis. There were significant differences in, and a loge-normal frequency distribution of, ERM Co concentrations between species. A significant percentage of interspecies variance could be assigned to taxonomic categories above the species, (Family and above 21.5%; Order and above 12.22%). Time-series analysis of ERM Co concentrations ordered in the species-sequence of the Angiosperm Phylogeny Group (APG II (2003)) revealed significant autocorrelation with an increase from Commelinid Monocot to Asterid Eudicot and a pronounced peak in the Core Eudicots. ERM Co concentrations categorized by plant growth strategy sensu Grime (2001) showed an increase toward stress-tolerant strategies. Plant species are not, therefore, independent units of Co concentration--factors derived from higher levels of biological organization exert significant effects. These effects can provide the basis of new techniques for selecting plant species for biotechnologies and for predicting the exposure of organisms to Co. They show that plant phylogeny and growth strategy might help refine predictions of soil-to-plant transfer of a variety of pollutants, and suggest research that might link molecular and higher level processes in contaminated soil-plant systems.

A new subfamily classification of the palm family (Arecaceae): evidence from plastid DNA phylogeny

Published phylogeny reconstructions of the palm family (Arecaceae) are based on plastid DNA sequences or restriction fragment length polymorphisms (RFLPs), nuclear DNA sequences, morphological characters or a combination thereof, and include between 33 and 90 palm species. The present study represents all previously recognized subfamilies, tribes and subtribes of palms and 161 of the 189 genera. The plastid DNA region matK was sequenced for 178 palm species and ten commelinid monocot outgroup species, and was combined with new and previously published plastid DNA sequences of trnL–trnF, rps16 intron and rbcL. The addition of matK sequences and more taxa resulted in a highly resolved and largely well-supported phylogeny. Most importantly, critical basal nodes are now fully resolved and, in most cases, strongly supported. On the basis of this phylogeny, we have established a new subfamilial classification of the palms, in which five subfamilies are recognized, rather than the six that were included in the previous classification. The circumscriptions of the subfamilies Calamoideae and Nypoideae were corroborated. The phylogeny supported a new circumscription for the subfamily Coryphoideae, including all taxa previously recognized in Coryphoideae with the addition of the tribe Caryoteae, formerly of the subfamily Arecoideae. The phylogenetic analysis also supported a new delimitation for the subfamily Ceroxyloideae that contains the tribes Cyclospatheae and Ceroxyleae, and all genera formerly included in the subfamily Phytelephantoideae, but excludes the tribe Hyophorbeae. Finally, the subfamily Arecoideae was modified to exclude the tribe Caryoteae and to include the tribe Hyophorbeae. © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society, 2006, 151, 15–38.

Robust Inference of Monocot Deep Phylogeny Using an Expanded Multigene Plastid Data Set

We use multiple photosynthetic, chlororespiratory, and plastid translation apparatus loci and their associated noncoding regions (ca. 16 kb per taxon, prior to alignment) to make strongly supported inferences of the deep internal branches of monocot phylogeny. Most monocot relationships are robust (an average of ca. 91 % bootstrap support per branch examined), including those poorly supported or unresolved in other studies. Our data strongly support a sister-group relationship between Asparagales and the commelinid monocots, the inclusion of the orchids in Asparagales, and the status of Petrosaviaceae as the sister group of all monocots except Acorus and Alismatales. The latter finding supports recognition of the order Petrosaviales. Also strongly supported is a placement of Petermannia disjunct from Colchicaceae (Liliales) and a sister-group relationship between Commelinales and Zingiberales. We highlight the remaining weak areas of monocot phylogeny, including the positions of Dioscoreales, Liliales, and Pandanales. Despite substantial variation in the overall rate of molecular evolution among lineages, inferred amounts of change among codon-position data partitions are correlated with each other across the monocot tree, consistent with low incongruence between these partitions. Ceratophyllum and Chloranthaceae appear to have a destabilizing effect on the position of the monocots among other angiosperms; the issue of monocot placement in broader angiosperm phylogeny remains problematic.