A molecular phylogeny of the grass subfamily Panicoideae (Poaceae) shows multiple origins of C4 photosynthesis

A Machine Learning Framework Identifies Plastid-Encoded Proteins Harboring C3 and C4 Distinguishing Sequence Information

C4 photosynthesis is known to have at least 61 independent origins across plant lineages making it one of the most notable examples of convergent evolution. Of the >60 independent origins, a predicted 22-24 origins, encompassing greater than 50% of all known C4 species, exist within the Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae (PACMAD) clade of the Poaceae family. This clade is therefore primed with species ideal for the study of genomic changes associated with the acquisition of the C4 photosynthetic trait. In this study, we take advantage of the growing availability of sequenced plastid genomes and employ a machine learning (ML) approach to screen for plastid genes harboring C3 and C4 distinguishing information in PACMAD species. We demonstrate that certain plastid-encoded protein sequences possess distinguishing and informative sequence information that allows them to train accurate ML C3/C4 classification models. Our RbcL-trained model, for example, informs a C3/C4 classifier with greater than 99% accuracy. Accurate prediction of photosynthetic type from individual sequences suggests biologically relevant, and potentially differing roles of these sequence products in C3 versus C4 metabolism. With this ML framework, we have identified several key sequences and sites that are most predictive of C3/C4 status, including RbcL, subunits of the NAD(P)H dehydrogenase complex, and specific residues within, further highlighting their potential significance in the evolution and/or maintenance of C4 photosynthetic machinery. This general approach can be applied to uncover intricate associations between other similar genotype-phenotype relationships.

An Update of the Cenchrinae (Poaceae, Panicoideae, Paniceae) and a New Genus for the Subtribe to Clarify the Dubious Position of a Species of Panicum L

Subtribe Cenchrinae, so-called as the "bristle clade", is a monophyletic group of panicoid grasses characterized by having sterile branches or bristles on the inflorescences in most of its species. Within this subtribe is also placed Panicum antidotale Retz., an "incertae sedis" species of Panicum L. which lacks bristles along the inflorescence. In this study, we present an update of the subtribe Cenchrinae based on molecular, morphological, and anatomical evidence to clarify the systematic position of P. antidotale in the Cenchrinae, excluding it from Panicum and establishing it in a new genus (i.e., Janochloa Zuloaga & Delfini); the morphological features distinguishing the new genus from other closely related taxa are properly discussed and an identification key to the 24 genera recognized within Cenchrinae is presented. We also add American Setaria species, not tested before, of subgenera Paurochaetium and Reverchoniae, discussing the position of these taxa in actual phylogeny of the genus as well as defining placements in the tree of Setaria species that were imprecisely located in previous analyses. A comparison with the results from other studies, comments on Stenotaphrum Trin. and a brief discussion on conflicting placements in Cenchrus and related taxa, and of Acritochaete Pilg. are also included.

De novo transcriptome assemblies of C3 and C4 non-model grass species reveal key differences in leaf development

BACKGROUND

C₄ photosynthesis is a mechanism that plants have evolved to reduce the rate of photorespiration during the carbon fixation process. The C₄ pathway allows plants to adapt to high temperatures and light while more efficiently using resources, such as water and nitrogen. Despite decades of studies, the evolution of the C₄ pathway from a C₃ ancestor remains a biological enigma. Interestingly, species with C₃-C₄ intermediates photosynthesis are usually found closely related to the C₄ lineages. Indeed, current models indicate that the assembly of C₄ photosynthesis was a gradual process that included the relocalization of photorespiratory enzymes, and the establishment of intermediate photosynthesis subtypes. More than a third of the C₄ origins occurred within the grass family (Poaceae). In particular, the Otachyriinae subtribe (Paspaleae tribe) includes 35 American species from C₃, C₄, and intermediates taxa making it an interesting lineage to answer questions about the evolution of photosynthesis.

RESULTS

To explore the molecular mechanisms that underpin the evolution of C₄ photosynthesis, the transcriptomic dynamics along four different leaf segments, that capture different stages of development, were compared among Otachyriinae non-model species. For this, leaf transcriptomes were sequenced, de novo assembled, and annotated. Gene expression patterns of key pathways along the leaf segments showed distinct differences between photosynthetic subtypes. In addition, genes associated with photorespiration and the C₄ cycle were differentially expressed between C₄ and C₃ species, but their expression patterns were well preserved throughout leaf development.

CONCLUSIONS

New, high-confidence, protein-coding leaf transcriptomes were generated using high-throughput short-read sequencing. These transcriptomes expand what is currently known about gene expression in leaves of non-model grass species. We found conserved expression patterns of C₄ cycle and photorespiratory genes among C₃, intermediate, and C₄ species, suggesting a prerequisite for the evolution of C₄ photosynthesis. This dataset represents a valuable contribution to the existing genomic resources and provides new tools for future investigation of photosynthesis evolution.

Systematics and Phylogenetic Placement of Panicum L. Species within the Melinidinae Based on Morphological, Anatomical, and Molecular Data (Poaceae, Panicoideae, Paniceae)

Generic boundaries of the African species Panicum deustum Thunb., Panicum trichocladum Hack. ex K. Schum., and Panicum vollesenii Renvoize are analyzed and compared with related genera of the tribe Paniceae and the subtribe Melinidinae. Based on morphological (vegetative and reproductive characters including habit, ligules, inflorescence, spikelets, and ornamentation of the upper anthecium), anatomical (transverse section of leaves), and molecular data (three chloroplast markers), a new genus is proposed for P. deustum, while P. trichocladum and P. vollesenii are transferred to the genus Megathyrsus (Pilg.) B.K. Simon & S.W.L. Jacobs. The phylogenetic position of both taxa within the Melinidinae and their morphological affinities with other genera of the subtribe are also discussed. Additional studies on the Melinidinae will clarify the systematic position of the genera that are still in a doubtful position within the subtribe, such as Eriochloa and Urochloa.

An Overview of the Genetics and Genomics of the Urochloa Species Most Commonly Used in Pastures

Pastures based on perennial monocotyledonous plants are the principal source of nutrition for ruminant livestock in tropical and subtropical areas across the globe. The Urochloa genus comprises important species used in pastures, and these mainly include Urochloa brizantha, Urochloa decumbens, Urochloa humidicola, and Urochloa ruziziensis. Despite their economic relevance, there is an absence of genomic-level information for these species, and this lack is mainly due to genomic complexity, including polyploidy, high heterozygosity, and genomes with a high repeat content, which hinders advances in molecular approaches to genetic improvement. Next-generation sequencing techniques have enabled the recent release of reference genomes, genetic linkage maps, and transcriptome sequences, and this information helps improve our understanding of the genetic architecture and molecular mechanisms involved in relevant traits, such as the apomictic reproductive mode. However, more concerted research efforts are still needed to characterize germplasm resources and identify molecular markers and genes associated with target traits. In addition, the implementation of genomic selection and gene editing is needed to reduce the breeding time and expenditure. In this review, we highlight the importance and characteristics of the four main species of Urochloa used in pastures and discuss the current findings from genetic and genomic studies and research gaps that should be addressed in future research.

Rubisco catalytic adaptation is mostly driven by photosynthetic conditions - Not by phylogenetic constraints

The prevalence of phylogenetic constraints in Rubisco evolution has been emphasised recently by (Bouvier et al., 2021), who argued that phylogenetic inheritance limits Rubisco adaptation much more than the biochemical trade-off between specificity, CO₂ affinity and turn-over. In this Opinion, we have critically examined how a phylogenetic signal can be computed with Rubisco kinetic properties and phylogenetic trees, and we arrive at a different conclusion. In particular, Rubisco's adaptation is partly driven by C₄ vs. C₃ photosynthetic conditions in Angiosperms, apparent phylogenetic signals being mostly due to either homoplasy, computation artefacts or the use of nearly identical sister species. While phylogenetic inheritance of an ancestral enzyme form probably has some role in Rubisco's adaptation landscape, it is a minor player, at least compared to microenvironmental conditions such as CO₂ and O₂ concentrations.

Paper Spray Mass Spectrometry on the Analysis of Phenolic Compounds in Rhynchelytrum repens: A Tropical Grass with Hypoglycemic Activity

The characterization of plant compounds with pharmacological activity is a field of great relevance in research and development. As such, identification techniques with the goal of developing new drugs or even validating the bioactive properties of extracts must be explored in order to further expand the knowledge of plant extract composition. Most works in this field employ HPLC, when exploring non-structural and cell wall carbohydrates from Rhynchelytrum repens. Phenolic compounds were studied by classical chromatography techniques and UV-vis spectrophotometry, with C-glycosylated flavonoids being detected but with no further details regarding the chemical structure of these compounds. In this work we employ paper spray ionization mass spectrometry (PS-MS) for the evaluation of the chemical profile of R. repens methanol extract. Positive ionization mode identified 15 compounds, belonging to flavonoids, fatty acids, and other classes of compounds; negative mode ionization was able to identify 20 compounds comprising the classes of quinic acids, stilbenes and flavonoids. PS-MS proved effective for the evaluation of R. repens extracts, making it possible to identify a total of thirty-five compounds. The bioactive properties attributed to R. repens were confirmed by the identification and characterization of compounds identified by PS-MS.

Coleataenia prionitis, a C4-like species in the Poaceae

C₄-like plants represent the penultimate stage of evolution from C₃ to C₄ plants. Although Coleataenia prionitis (formerly Panicum prionitis) has been described as a C₄ plant, its leaf anatomy and gas exchange traits suggest that it may be a C₄-like plant. Here, we reexamined the leaf structure and biochemical and physiological traits of photosynthesis in this grass. The large vascular bundles were surrounded by two layers of bundle sheath (BS): a colorless outer BS and a chloroplast-rich inner BS. Small vascular bundles, which generally had a single BS layer with various vascular structures, also occurred throughout the mesophyll together with BS cells not associated with vascular tissue. The mesophyll cells did not show a radial arrangement typical of Kranz anatomy. These features suggest that the leaf anatomy of C. prionitis is on the evolutionary pathway to a complete C₄ Kranz type. Phosphoenolpyruvate carboxylase (PEPC) and pyruvate, Pi dikinase occurred in the mesophyll and outer BS. Glycine decarboxylase was confined to the inner BS. Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) accumulated in the mesophyll and both BSs. C. prionitis had biochemical traits of NADP-malic enzyme type, whereas its gas exchange traits were close to those of C₄-like intermediate plants rather than C₄ plants. A gas exchange study with a PEPC inhibitor suggested that Rubisco in the mesophyll could fix atmospheric CO₂. These data demonstrate that C. prionitis is not a true C₄ plant but should be considered as a C₄-like plant.

Emission factors of some common grass species in West Africa

Frequent burnings occurring in the grasslands of the West African region during the dry seasons largely contribute to emissions of trace gases and particulates being released into the ambient environment, which has significantly impacted both regional and global climate patterns. Burning potentials of forty different grassland biomes were examined by determining their Net Heating Value (NHV) and Total Organic Carbon (TOC). Simulations of the field operations which involve open burning were performed in the laboratory using a fabricated combustion chamber for the determination of emission factors. Particulates were collected using Whatman quartz fibre filters and analyzed gravimetrically. Emissions of gaseous pollutants from open burning of these common grass species were measured with portable devices. The values of the NHV and TOC of the grass species ranged from 15,022.19 to 18,181.84 kJ/kg and 21.14 to 55.62%, respectively. The average Emission Factors (EFs) obtained for carbon dioxide (CO₂), carbon monoxide (CO), sulphur dioxide (SO₂), nitrogen dioxide (NO₂), volatile organic compounds (VOC), and PM_2.5 are 1465.55 g/kg, 40.99 g/kg, 0.39 g/kg, 0.02 g/kg, 7.78 g/kg, and 6.00 g/kg, respectively. The study has shown that Digitaria nuda, Digitaria eriantha, Panicum subalbidum, Paspalum polystratchyum, and Perotis indica have the highest emission factors for CO₂, CO, SO₂, NO₂, VOC, and PM_2.5, respectively. The result obtained would help in the quantification of the global warming forcing on the climate in the West African region from grassland burnings. The results will potentially serve as additional information for emission inventories and basis for the formulation of mitigation strategies.

Checklist of the grasses of India

A checklist of the grasses of India is presented, as compiled from survey of all available literature. Of the twelve subfamilies of grasses, ten are represented in India. Most subfamilies have been examined by taxonomic experts for up-to-date nomenclature. The list includes 1506 species plus infraspecific taxa and presents information on types, synonyms, distribution within India, and habit. Twelve new combinations are made, viz. Arctopoa tibetica (Munro ex Stapf) Prob. var. aristulata (Stapf) E.A. Kellogg, comb. nov.; Chimonocalamus nagalandianus (H.B. Naithani) L.G. Clark, comb. nov.; Chionachne digitata (L.f.) E.A. Kellogg, comb. nov.; Chionachne wallichiana (Nees) E.A. Kellogg, comb. nov.; Dinebra polystachyos (R. Br.) E.A. Kellogg, comb. nov.; Moorochloa eruciformis (Sm.) Veldkamp var. divaricata (Basappa & Muniv.) E.A. Kellogg, comb. nov.; Phyllostachys nigra (Lodd. ex Lindl.) Munro var. puberula (Miq.) Kailash, comb. & stat. nov.; Tzveleviochloa schmidii (Hook. f.) E.A. Kellogg, comb. nov.; Urochloa lata (Schumach.) C.E. Hubb. var. pubescens (C.E. Hubb.) E.A. Kellogg, comb. nov.; Urochloa ramosa (L.) T.Q. Nguyen var. pubescens (Basappa & Muniy.) E.A. Kellogg, comb. nov.; Urochloa semiundulata (Hochst. ex A. Rich.) Ashalatha & V.J. Nair var. intermedia (Basappa & Muniy.) E.A. Kellogg, comb. nov.

LEAF ANATOMY CHARACTERIZATION OF FOUR Apochloa SPECIES: A C3 GENUS RELATED TO EVOLUTION OF C4 PATHWAY IN GRASSES

Leaf anatomy characteristics provide important evidences about the transition between C3 and C4 pathways. The C4 photosynthesis pathway allowed to reduce the C3 photorespiratory rate, concentrating CO2 around the Rubisco site and using structures and machinery already presented in C3 plants. In monocots, it is observed a high number of C4 lineages, most of them phylogenetically related to C3 groups. The genus Apochloa (C3), subtribe Arthropogoninae, is related to two C4 genera Coleataenia and Cyphonanthus. The aim of this study was to evaluate four Apochloa species in order to establish anatomical characteristics related to the evolution of C4 pathway in this group. By means of transverse sections fully expanded leaves of A. euprepes, A. lorea, A. molinioides, and A. poliophylla were collected and the characteristics of the mesophyll (M) and bundle sheath (BS) cells were determined. These species showed a rustic Kranz anatomy with enlarged and radial arranged BS cells, which have few organelles organized in a centrifugal position. Although the modifications of BS cells are probably related to the maintenance of plant water status, we also discuss the evolution for the establishment of C4 photosynthesis in the related C4 genera.

IsoSeq transcriptome assembly of C3 panicoid grasses provides tools to study evolutionary change in the Panicoideae

The number of plant species with genomic and transcriptomic data has been increasing rapidly. The grasses-Poaceae-have been well represented among species with published reference genomes. However, as a result the genomes of wild grasses are less frequently targeted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses can aid the study of domestication, gene discovery for breeding and crop improvement, and improve our understanding of the evolution of C4 photosynthesis. Here, we used long-read sequencing technology to characterize the transcriptomes of three C3 panicoid grass species: Dichanthelium oligosanthes, Chasmanthium laxum, and Hymenachne amplexicaulis. Based on alignments to the sorghum genome, we estimate that assembled consensus transcripts from each species capture between 54.2% and 65.7% of the conserved syntenic gene space in grasses. Genes co-opted into C4 were also well represented in this dataset, despite concerns that because these genes might play roles unrelated to photosynthesis in the target species, they would be expressed at low levels and missed by transcript-based sequencing. A combined analysis using syntenic orthologous genes from grasses with published reference genomes and consensus long-read sequences from these wild species was consistent with previously published phylogenies. It is hoped that these data, targeting underrepresented classes of species within the PACMAD grasses-wild species and species utilizing C3 photosynthesis-will aid in future studies of domestication and C4 evolution by decreasing the evolutionary distance between C4 and C3 species within this clade, enabling more accurate comparisons associated with evolution of the C4 pathway.

High [CO2] and Temperature Increase Resistance to Cyhalofop-Butyl in Multiple-Resistant Echinochloa colona

Changes in the environment, specifically rising temperature and increasing atmospheric carbon dioxide concentration [CO₂], can alter the growth and physiology of weedy plants. These changes could alter herbicide efficacy, crop-weed interaction, and weed management. The objectives of this research were to quantify the effects of increased atmospheric [CO₂] and temperature on absorption, translocation and efficacy of cyhalofop-butyl on multiple-resistant (MR) and susceptible (S) Echinochloa colona genotypes. E. colona, or junglerice, is a troublesome weed in rice and in agronomic and horticultural crops worldwide. Cyhalofop-butyl is a grass herbicide that selectively controls Echinochloa spp. in rice. Maximum ¹⁴C-cyhalofop-butyl absorption occurred at 120 h after herbicide treatment (HAT) with >97% of cyhalofop-butyl retained in the treated leaf regardless of [CO₂], temperature, or genotype. Neither temperature nor [CO₂] affected herbicide absorption into the leaf. The translocation of herbicide was slightly reduced in the MR plants vs. S plants either under elevated [CO₂] or high temperature. Although plants grown under high [CO₂] or high temperature were taller than those in ambient conditions, neither high [CO₂] nor high temperature reduced the herbicide efficacy on susceptible plants. However, herbicide efficacy was reduced on MR plants grown under high [CO₂] or high temperature about 50% compared to MR plants at ambient conditions. High [CO₂] and high temperature increased the resistance level of MR E. colona to cyhalofop-butyl. To mitigate rapid resistance evolution under a changing climate, weed management practitioners must implement measures to reduce the herbicide selection pressure. These measures include reduction of weed population size through reduction of the soil seedbank, ensuring complete control of current infestations with multiple herbicide modes of action in mixture and in sequence, augmenting herbicides with mechanical control where possible, rotation with weed-competitive crops, use of weed-competitive cultivars, use of weed-suppressive cover crops, and other practices recommended for integrated weed management.

High density genetic maps of St. Augustinegrass and applications to comparative genomic analysis and QTL mapping for turf quality traits

BACKGROUND

St. Augustinegrass [Stenotaphrum secundatum (Walt.) Kuntze] is a warm-season, perennial turfgrass species well adapted for home lawns and commercial landscapes with economic and ecological value. However, a lack of genomic resources in St. Augustinegrass has hindered the full utilization of genetic variance for maximizing genetic gain and limited our understanding of the species' evolution.

RESULTS

In this study, we constructed the first high-density linkage map for St. Augustinegrass using a genotyping by sequencing (GBS) approach. The integrated linkage map consists of 2871 single nucleotide polymorphism (SNP) and 81 simple sequence repeat (SSR) markers, spanning 1241.7 cM, with an average distance of 0.4 cM between markers, and thus represents the densest genetic map for St. Augustinegrass to date. Comparative genomic analysis revealed inter-chromosome arrangements and independent nested chromosome fusion events that occurred after St. Augustinegrass, foxtail millet, sorghum, and rice diverged from a common ancestor. Forty-eight candidate quantitative trait loci (QTL) were detected for turf quality-related traits, including overall turf quality, leaf texture, genetic color, and turf density. Three hot spot regions were identified on linkage groups LG3 and LG8, where multi-QTL for different traits overlapped. Several leaf development related genes were contained within these identified QTL regions.

CONCLUSIONS

This study developed the first high-density genetic map and identified putative QTL related to turf quality, which provide valuable genetic resources for marker-assisted selection (MAS) in St. Augustinegrass.

Complete Chloroplast Genome Sequence of Broomcorn Millet (Panicum miliaceum L.) and Comparative Analysis with Other Panicoideae Species

Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated cereals worldwide, holding significant agricultural, historical, and evolutionary importance. However, our genomic knowledge of it is rather limited at present, hampering further genetic and evolutionary studies. Here, we sequenced and assembled the chloroplast genome (cp) of broomcorn millet and compared it with five other Panicoideae species. Results showed that the cp genome of broomcorn millet was 139,826 bp in size, with a typical quadripartite structure. In total, 108 genes were annotated and 18 genes were duplicated in the IR (inverted region) region, which was similar to other Panicoideae species. Comparative analysis showed a rather conserved genome structure between them, with three common regions. Furthermore, RNA editing, codon usage, and expansion of the IR, as well as simple sequence repeat (SSR) elements, were systematically investigated and 13 potential DNA markers were developed for Panicoideae species identification. Finally, phylogenetic analysis implied that broomcorn millet was a sister species to Panicum virgatum within the tribe Paniceae, and supported a monophyly of the Panicoideae. This study has reported for the first time the genome organization, gene content, and structural features of the chloroplast genome of broomcorn millet, which provides valuable information for genetic and evolutionary studies in the genus Panicum and beyond.

Coexpression network revealing the plasticity and robustness of population transcriptome during the initial stage of domesticating energy crop Miscanthus lutarioriparius

Coexpression network revealing genes with Co-variation Expression pattern (CE) and those with Top rank of Expression fold change (TE) played different roles in responding to new environment of Miscanthus lutarioriparius. Variation in gene expression level, the product of genetic and/or environmental perturbation, determines the robustness-to-plasticity spectrum of a phenotype in plants. Understanding how expression variation of plant population response to a new field is crucial to domesticate energy crops. Weighted Gene Coexpression Network Analysis (WGCNA) was used to explore the patterns of expression variation based on 72 Miscanthus lutarioriparius transcriptomes from two contrasting environments, one near the native habitat and the other in one harsh domesticating region. The 932 genes with Co-variation Expression pattern (CE) and other 932 genes with Top rank of Expression fold change (TE) were identified and the former were strongly associated with the water use efficiency (r ≥ 0.55, P ≤ 10^-7). Functional enrichment of CE genes were related to three organelles, which well matched the annotation of twelve motifs identified from their conserved noncoding sequence; while TE genes were mostly related to biotic and/or abiotic stress. The expression robustness of CE genes with high genetic diversity kept relatively stable between environments while the harsh environment reduced the expression robustness of TE genes with low genetic diversity. The expression plasticity of CE genes was increased less than that of TE genes. These results suggested that expression variation of CE genes and TE genes could account for the robustness and plasticity of acclimation ability of Miscanthus, respectively. The patterns of expression variation revealed by transcriptomic network would shed new light on breeding and domestication of energy crops.

CO2 availability influences hydraulic function of C3 and C4 grass leaves

Atmospheric CO2 (ca) has increased since the last glacial period, increasing photosynthetic water use efficiency and improving plant productivity. Evolution of C4 photosynthesis at low ca led to decreased stomatal conductance (gs), which provided an advantage over C3 plants that may be reduced by rising ca. Using controlled environments, we determined how increasing ca affects C4 water use relative to C3 plants. Leaf gas exchange and mass per area (LMA) were measured for four C3 and four C4 annual, crop-related grasses at glacial (200 µmol mol-1), ambient (400 µmol mol-1), and super-ambient (640 µmol mol-1) ca. C4 plants had lower gs, which resulted in a water use efficiency advantage at all ca and was broadly consistent with slower stomatal responses to shade, indicating less pressure on leaf water status. At glacial ca, net CO2 assimilation and LMA were lower for C3 than for C4 leaves, and C3 and C4 grasses decreased leaf hydraulic conductance (Kleaf) similarly, but only C4 leaves decreased osmotic potential at turgor loss. Greater carbon availability in C4 leaves at glacial ca generated a different hydraulic adjustment relative to C3 plants. At current and future ca, C4 grasses have advantages over C3 grasses due to lower gs, lower stomatal sensitivity, and higher absolute water use efficiency.

Molecular phylogeny of Panicum s. str. (Poaceae, Panicoideae, Paniceae) and insights into its biogeography and evolution

Panicum sensu stricto is a genus of grasses (Poaceae) with nearly, according to this study, 163 species distributed worldwide. This genus is included in the subtribe Panicinae together with Louisiella, the latter with 2 species. Panicum and subtribe Panicinae are characterized by including annual or perennial taxa with open and lax panicles, and spikelets with the lower glume reduced; all taxa also share a basic chromosome number of x = 9 and a Kranz leaf blade anatomy typical of the NAD-me subtype photosynthetic pathway. Nevertheless, the phylogenetic placements of many Panicum species, and the circumscription of the genus, remained untested. Therefore, phylogenetic analyses were conducted using sequence data from the ndhF plastid region, in an extensive worldwide sampling of Panicum and related genera, in order to infer evolutionary relationships and to provide a phylogenetic framework to review the classification of the genus. Diversification times, historical biogeography and evolutionary patterns of the life history (annual vs. perennial) in the subtribe and Panicum were also studied. Results obtained provide strong support for a monophyletic Panicum including 71 species and 7 sections, of which sections Arthragrostis and Yakirra are new in the genus; 7 new combinations are made here. Furthermore, 32 species traditionally assigned to Panicum were excluded from the genus, and discussed in other subtribes of Paniceae. Our study suggested that early diversification in subtribe Panicinae and Panicum occurred through the Early-Mid Miocene in the Neotropics, while the subsequent diversification of its sections mainly occurred in the Late Miocene-Pleistocene, involving multiple dispersals to all continents. Our analyses also showed that transition rates and changes between annual and perennial life history in Panicum were quite frequent, suggesting considerable lability of this trait. Changes of the life history, together with C4 photosynthesis, and the multiple dispersal events since the Mid Miocene, seem to have facilitated a widespread distribution of the genus. All these findings contribute to a better understanding of the systematics and evolution of Panicum.

Location of low copy genes in chromosomes of Brachiaria spp

Repetitive DNA sequences have been widely used in cytogenetic analyses. The use of gene sequences with a low-copy-number, however, is little explored especially in plants. To date, the karyotype details in Brachiaria spp. are limited to the location of rDNA sites. The challenge lies in developing new probes based on incomplete sequencing data for the genus or complete sequencing of related species, since there are no model species with a sequenced genome in Brachiaria spp. The present study aimed at the physical location of conserved genes in chromosomes of Brachiaria ruziziensis, Brachiaria brizantha, and Brachiaria decumbens using RNAseq data, as well as sequences of Setaria italica and Sorghum bicolor through the fluorescent in situ hybridization technique. Five out of approximately 90 selected sequences generated clusters in the chromosomes of the species of Brachiaria studied. We identified genes in synteny with 5S and 45S rDNA sites, which contributed to the identification of chromosome pairs carrying these genes. In some cases, the species of Brachiaria evaluated had syntenic segments conserved across the chromosomes. The use of genomic sequencing data is essential for the enhancement of cytogenetic analyses.

Molecular diversity, geographic distribution and host range of monocot-infecting mastreviruses in Africa and surrounding islands

Maize streak virus (MSV), an important pathogen of maize in Africa, is the most extensively studied member of the Mastrevirus genus in the family Geminiviridae. Comparatively little is known about other monocot-infecting African mastreviruses, most of which infect uncultivated grasses. Here we determine the complete sequences of 134 full African mastrevirus genomes from predominantly uncultivated Poaceae species. Based on established taxonomic guidelines for the genus Mastrevirus, these genomes could be classified as belonging to the species Maize streak virus, Eragrostis minor streak virus, Maize streak Reunion virus, Panicum streak virus, Sugarcane streak Reunion virus and Sugarcane streak virus. Together with all other publicly available African monocot-infecting mastreviruses, the 134 new isolates extend the known geographical distributions of many of these species, including MSV which we found infecting Digitaria sp. on the island of Grand Canaria: the first definitive discovery of any African monocot-infecting mastreviruses north-west of the Saharan desert. These new isolates also extend the known host ranges of both African mastrevirus species and the strains within these. Most notable was the discovery of MSV-C isolates infecting maize which suggests that this MSV strain, which had previously only ever been found infecting uncultivated species, may be in the process of becoming adapted to this important staple crop.

Stomatal cell wall composition: distinctive structural patterns associated with different phylogenetic groups

Background and Aims

Stomatal morphology and function have remained largely conserved throughout ∼400 million years of plant evolution. However, plant cell wall composition has evolved and changed. Here stomatal cell wall composition was investigated in different vascular plant groups in attempt to understand their possible effect on stomatal function.

Methods

A renewed look at stomatal cell walls was attempted utilizing digitalized polar microscopy, confocal microscopy, histology and a numerical finite-elements simulation. The six species of vascular plants chosen for this study cover a broad structural, ecophysiological and evolutionary spectrum: ferns ( Asplenium nidus and Platycerium bifurcatum ) and angiosperms ( Arabidopsis thaliana and Commelina erecta ) with kidney-shaped stomata, and grasses (angiosperms, family Poaceae) with dumbbell-shaped stomata ( Sorghum bicolor and Triticum aestivum ).

Key Results

Three distinct patterns of cellulose crystallinity in stomatal cell walls were observed: Type I (kidney-shaped stomata, ferns), Type II (kidney-shaped stomata, angiosperms) and Type III (dumbbell-shaped stomata, grasses). The different stomatal cell wall attributes investigated (cellulose crystallinity, pectins, lignin, phenolics) exhibited taxon-specific patterns, with reciprocal substitution of structural elements in the end-walls of kidney-shaped stomata. According to a numerical bio-mechanical model, the end walls of kidney-shaped stomata develop the highest stresses during opening.

Conclusions

The data presented demonstrate for the first time the existence of distinct spatial patterns of varying cellulose crystallinity in guard cell walls. It is also highly intriguing that in angiosperms crystalline cellulose appears to have replaced lignin that occurs in the stomatal end-walls of ferns serving a similar wall strengthening function. Such taxon-specific spatial patterns of cell wall components could imply different biomechanical functions, which in turn could be a consequence of differences in environmental selection along the course of plant evolution.

Museomics resolve the systematics of an endangered grass lineage endemic to north-western Madagascar

BACKGROUND AND AIMS

Recent developments in DNA sequencing, so-called next-generation sequencing (NGS) methods, can help the study of rare lineages that are known from museum specimens. Here, the taxonomy and evolution of the Malagasy grass lineage Chasechloa was investigated with the aid of NGS.

METHODS

Full chloroplast genome data and some nuclear sequences were produced by NGS from old herbarium specimens, while some selected markers were generated from recently collected Malagasy grasses. In addition, a scanning electron microscopy analysis of the upper floret and cross-sections of the rachilla appendages followed by staining with Sudan IV were performed on Chasechloa to examine the morphology of the upper floret and the presence of oils in the appendages.

KEY RESULTS

Chasechloa was recovered within tribe Paniceae, sub-tribe Boivinellinae, contrary to its previous placement as a member of the New World genus Echinolaena (tribe Paspaleae). Chasechloa originated in Madagascar between the Upper Miocene and the Pliocene. It comprises two species, one of them collected only once in 1851. The genus is restricted to north-western seasonally dry deciduous forests. The appendages at the base of the upper floret of Chasechloa have been confirmed as elaiosomes, an evolutionary adaptation for myrmecochory.

CONCLUSIONS

Chasechloa is reinstated at the generic level and a taxonomic treatment is presented, including conservation assessments of its species. Our study also highlights the power of NGS technology to analyse relictual or probably extinct groups.

Cross species selection scans identify components of C4 photosynthesis in the grasses

C4 photosynthesis is perhaps one of the best examples of convergent adaptive evolution with over 25 independent origins in the grasses (Poaceae) alone. The availability of high quality grass genome sequences presents new opportunities to explore the mechanisms underlying this complex trait using evolutionary biology-based approaches. In this study, we performed genome-wide cross-species selection scans in C4 lineages to facilitate discovery of C4 genes. The study was enabled by the well conserved collinearity of grass genomes and the recently sequenced genome of a C3 panicoid grass, Dichanthelium oligosanthes This method, in contrast to previous studies, does not rely on any a priori knowledge of the genes that contribute to biochemical or anatomical innovations associated with C4 photosynthesis. We identified a list of 88 candidate genes that include both known and potentially novel components of the C4 pathway. This set includes the carbon shuttle enzymes pyruvate, phosphate dikinase, phosphoenolpyruvate carboxylase and NADP malic enzyme as well as several predicted transporter proteins that likely play an essential role in promoting the flux of metabolites between the bundle sheath and mesophyll cells. Importantly, this approach demonstrates the application of fundamental molecular evolution principles to dissect the genetic basis of a complex photosynthetic adaptation in plants. Furthermore, we demonstrate how the output of the selection scans can be combined with expression data to provide additional power to prioritize candidate gene lists and suggest novel opportunities for pathway engineering.

The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes

BACKGROUND

Comparisons between C3 and C4 grasses often utilize C3 species from the subfamilies Ehrhartoideae or Pooideae and C4 species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C3 panicoid grass Dichanthelium oligosanthes from the independent C4 lineages represented by Setaria viridis and Sorghum bicolor occurred approximately 15 million years ago, which is significantly more recent than members of the Bambusoideae, Ehrhartoideae, and Pooideae subfamilies. D. oligosanthes is ideally placed within the panicoid clade for comparative studies of C3 and C4 grasses.

RESULTS

We report the assembly of the nuclear and chloroplast genomes of D. oligosanthes, from high-throughput short read sequencing data and a comparative transcriptomics analysis of the developing leaf of D. oligosanthes, S. viridis, and S. bicolor. Physiological and anatomical characterizations verified that D. oligosanthes utilizes the C3 pathway for carbon fixation and lacks Kranz anatomy. Expression profiles of transcription factors along developing leaves of D. oligosanthes and S. viridis were compared with previously published data from S. bicolor, Zea mays, and Oryza sativa to identify a small suite of transcription factors that likely acquired functions specifically related to C4 photosynthesis.

CONCLUSIONS

The phylogenetic location of D. oligosanthes makes it an ideal C3 plant for comparative analysis of C4 evolution in the panicoid grasses. This genome will not only provide a better C3 species for comparisons with C4 panicoid grasses, but also highlights the power of using high-throughput sequencing to address questions in evolutionary biology.

Breeding system diversification and evolution in American Poa supersect. Homalopoa (Poaceae: Poeae: Poinae)

BACKGROUND AND AIMS

Poa subgenus Poa supersect. Homalopoa has diversified extensively in the Americas. Over half of the species in the supersection are diclinous; most of these are from the New World, while a few are from South-East Asia. Diclinism in Homalopoa can be divided into three main types: gynomonoecism, gynodioecism and dioecism. Here the sampling of species of New World Homalopoa is expanded to date its origin and diversification in North and South America and examine the evolution and origin of the breeding system diversity.

METHODS

A total of 124 specimens were included in the matrix, of which 89 are species of Poa supersect. Homalopoa sections Acutifoliae, Anthochloa, Brizoides, Dasypoa, Dioicopoa, Dissanthelium, Homalopoa sensu lato (s.l.), Madropoa and Tovarochloa, and the informal Punapoa group. Bayesian and parsimony analyses were conducted on the data sets based on four markers: the nuclear ribosomal internal tanscribed spacer (ITS) and external transcribed spacer (ETS), and plastid trnT-L and trnL-F. Dating analyses were performed on a reduced Poa matrix and enlarged Poaceae outgroup to utilize fossils as calibration points. A relaxed Bayesian molecular clock method was used.

KEY RESULTS

Hermaphroditism appears to be pleisiomorphic in the monophyletic Poa supersect. Homalopoa, which is suggested to have originated in Eurasia 8·4-4·2 million years ago (Mya). The ancestor of Poa supersect. Homalopoa radiated throughout the New World in the Late Miocene-Early Pliocene, with major lineages originating during the Pliocene to Pleistocene (5-2 Mya). Breeding systems are linked to geographic areas, showing an evolutionary pattern associated with different habitats. At least three major pathways from hermaphroditism to diclinism are inferred in New World Homalopoa: two leading to dioecism, one via gynodioecism in South America and another directly from hermaphroditism in North America, a result that needs to be checked with a broader sampling of diclinous species in North America. A third pathway leads from hermaphroditism to gynomonoecism in Andean species of South America, with strictly pistillate species evolving in the highest altitudes.

CONCLUSIONS

Divergence dating provides a temporal context to the evolution of breeding systems in New World Poa supersect. Homalopoa The results are consistent with the infrageneric classification in part; monophyletic sections are confirmed, it is proposed to reclassify species of sect. Acutifoliae, Dasypoa and Homalopoa s.l. and it is acknowledged that revision of the infrageneric taxonomy of the gynomonoecious species is needed.

Evolutionary relationships in Panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae)

BACKGROUND

Panicoideae are the second largest subfamily in Poaceae (grass family), with 212 genera and approximately 3316 species. Previous studies have begun to reveal relationships within the subfamily, but largely lack resolution and/or robust support for certain tribal and subtribal groups. This study aims to resolve these relationships, as well as characterize a putative mitochondrial insert in one linage.

RESULTS

35 newly sequenced Panicoideae plastomes were combined in a phylogenomic study with 37 other species: 15 Panicoideae and 22 from outgroups. A robust Panicoideae topology largely congruent with previous studies was obtained, but with some incongruences with previously reported subtribal relationships. A mitochondrial DNA (mtDNA) to plastid DNA (ptDNA) transfer was discovered in the Paspalum lineage.

CONCLUSIONS

The phylogenomic analysis returned a topology that largely supports previous studies. Five previously recognized subtribes appear on the topology to be non-monophyletic. Additionally, evidence for mtDNA to ptDNA transfer was identified in both Paspalum fimbriatum and P. dilatatum, and suggests a single rare event that took place in a common progenitor. Finally, the framework from this study can guide larger whole plastome sampling to discern the relationships in Cyperochloeae, Steyermarkochloeae, Gynerieae, and other incertae sedis taxa that are weakly supported or unresolved.

Gene expression patterns of two dominant tallgrass prairie species differ in response to warming and altered precipitation

To better understand the mechanisms underlying plant species responses to climate change, we compared transcriptional profiles of the co-dominant C4 grasses, Andropogon gerardii Vitman and Sorghastrum nutans (L.) Nash, in response to increased temperatures and more variable precipitation regimes in a long-term field experiment in native tallgrass prairie. We used microarray probing of a closely related model species (Zea mays) to assess correlations in leaf temperature (Tleaf) and leaf water potential (LWP) and abundance changes of ~10,000 transcripts in leaf tissue collected from individuals of both species. A greater number of transcripts were found to significantly change in abundance levels with Tleaf and LWP in S. nutans than in A. gerardii. S. nutans also was more responsive to short-term drought recovery than A. gerardii. Water flow regulating transcripts associated with stress avoidance (e.g., aquaporins), as well as those involved in the prevention and repair of damage (e.g., antioxidant enzymes, HSPs), were uniquely more abundant in response to increasing Tleaf in S. nutans. The differential transcriptomic responses of the co-dominant C4 grasses suggest that these species may cope with and respond to temperature and water stress at the molecular level in distinct ways, with implications for tallgrass prairie ecosystem function.

The Coordination of Gene Expression within Photosynthesis Pathway for Acclimation of C4 Energy Crop Miscanthus lutarioriparius

As a promising candidate for the second-generation C4 energy crop, Miscanthus lutarioriparius has well acclimated to the water-limited and high-light Loess Plateau in China by improving photosynthesis rate and water use efficiency (WUE) compared to its native habitat along Yangtze River. Photosynthetic genes were demonstrated as one major category of the candidate genes underlying the physiological superiority. To further study how photosynthetic genes interact to improve the acclimation potential of M. lutarioriparius, population expression patterns within photosynthesis pathway were explored between one mild environment and one harsh environment. We found that 108 transcripts in assembled transcriptome of M. lutarioriparius were highly similar to genes in three Kyoto Encyclopedia of Genes and Genomes (KEGG) photosynthesis pathways of sorghum and maize. Phylogenetic analyses using sorghum, maize, rice, and Arabidopsis genes of dark reaction identified 23 orthologs and 30 paralogs of M. lutarioriparius photosynthetic genes. These genes were also clustered into two kinds of expression pattern. 87% of transcripts in dark reaction were up-regulated and all 14 chloroplast-encoded transcripts in light reaction increased degradation in the harsh environment compared to the mild environment. Moreover, 80.8% of photosynthetic transcripts were coordinated at transcription level under the two environments. Interestingly, LHCI and PSI were significantly correlated with F-ATPase and C4 cycle. Overall, this study indicates the coordinated expression between cyclic electron transport (consisting of LHCI, PSI, and ATPase) and CO2-concentrating mechanism (C4 cycle) could account for photosynthesis plasticity on M. lutarioriparius acclimation potential.

Molecular understandings on 'the never thirsty' and apomictic Cenchrus grass

The genus Cenchrus comprises around 25 species of 'bristle clade' grasses. Cenchrus ciliaris (buffel grass) is a hardy, perennial range grass that survives in poor sandy soils and limiting soil moisture conditions and, due to the very same reasons, this grass is one of the most prevalent fodder grasses of the arid and semi-arid regions. Most of the germplasms of Cenchrus produce seeds asexually through the process of apomeiosis. Therefore, the lack of sufficient sexual lines has hindered the crop improvement efforts in Cenchrus being confined to simple selection methods. Many attempts have been initiated in buffel grass to investigate the various molecular aspects such as genomic signatures of different species and genotypes, molecular basis of abiotic stress tolerance and reproductive performance. Even though it is an important fodder crop, molecular investigations in Cenchrus lack focus and the molecular information available on this grass is scanty. Cenchrus is a very good gene source for abiotic stress tolerance and apomixis studies. Biotechnological interventions in Cenchrus can help in crop improvement in Cenchrus as well as other crops through transgenic technology or marker assisted selection. To date no consolidated review on biotechnological interventions in Cenchrus grass has been published. Therefore we provide a thorough and in depth review on molecular research in Cenchrus focusing on molecular signatures of evolution, tolerance to abiotic stress and apomictic reproductive mechanism.

Phylogeny and photosynthesis of the grass tribe Paniceae

PREMISE OF THE STUDY

The grass tribe Paniceae includes important food, forage, and bioenergy crops such as switchgrass, napiergrass, various millet species, and economically important weeds. Paniceae are also valuable for answering scientific and evolutionary questions about C4 photosynthetic evolution, drought tolerance, and spikelet variation. However, the phylogeny of the tribe remains incompletely resolved.

METHODS

Forty-five taxa were selected from across the tribe Paniceae and outgroups for genome survey sequencing (GSS). These data were used to build a phylogenetic tree of the Paniceae based on 102 markers (78 chloroplast, 22 mitochondrial, 2 nrDNA). Ancestral state reconstruction analyses were also performed within the Paniceae using both the traditional and two subtype classification systems to test hypotheses of C4 subtype evolution.

KEY RESULTS

The phylogenetic tree resolves many areas of the Paniceae with high support and provides insight into the origin and number of C4 evolution events within the tribe. The recovered phylogeny and ancestral state reconstructions support between four and seven independent origins of C4 photosynthesis within the tribe and indicate which species are potentially the closest C3 sister taxa of each of these events.

CONCLUSIONS

Although the sequence of evolutionary events that produced multiple C4 subtypes within the Paniceae remains undetermined, the results presented here are consistent with only a subset of currently proposed models. The species used in this study constitute a panel of C3 and C4 grasses that are suitable for further studies on C4 photosynthesis, bioenergy, food and forage crops, and various developmental features of the Paniceae.

Phylogenetic relationships of Echinolaena and Ichnanthus within Panicoideae (Poaceae) reveal two new genera of tropical grasses

Echinolaena and Ichnanthus are two tropical grass genera distributed mostly in the Americas, characterized by the presence of rachilla appendages in the shape of convex swellings, scars or wings at the base of the upper anthecium. However, recent studies have shown that rachilla appendages arose several times independently in several groups within Paniceae and Paspaleae (Panicoideae). Thus, this study aimed to assess the monophyly of Echinolaena and Ichnanthus and their relationship to other genera of Paniceae and Paspaleae, especially those including species with rachilla appendages. Parsimony and Bayesian analyses of the cpDNA regions ndhF, rpl16, trnH-(rps19)-psbA, trnL-trnF, trnS-(psbZ)-trnG, and the rDNA ITS region included 29 of the 39 known species of Echinolaena and Ichnanthus, 23 of which were sampled for the first time. The multiple loci analyses indicated that Echinolaena and Ichnanthus are polyphyletic in their current circumscriptions, with species in four distinct lineages within subtribe Paspalinae, each one characterized by a single type of rachilla appendage. Thus, Echinolaena and Ichnanthus are each circumscribed in a narrow sense, and the other two lineages excluded from them are proposed as the new genera Hildaea and Oedochloa, resulting in 15 new combinations and the restablishment of I. oplismenoides Munro ex Döll.

An assessment of the capacity for phosphoenolpyruvate carboxykinase to contribute to C4 photosynthesis

Three C4 acid decarboxylases, phosphoenolpyruvate carboxykinase (PEPCK), NADP-malic enzyme (NADP-ME), and NAD-malic enzyme (NAD-ME) were recruited from C3 plants to support C4 photosynthesis. In Poaceae, there are established lineages having PEPCK type species, and some NADP-ME lineages in which PEPCK contributes to C4. Besides family Poaceae, recently PEPCK has been reported to function in C4 photosynthesis in eudicot species including Cleome gynandra (Cleomaceae), Trianthema portulacastrum and Zaleya pentandra (Aizoaceae). We evaluated PEPCK by enzyme assay and western blots in representatives of Poaceae, Aizoaceae, Cleomaceae, and Chenopodiaceae compared to that in the PEPCK type C4 grass Spartina anglica. Eragrostis nutans was identified as the first NAD-ME type C4 grass having substantial amounts of PEPCK. In the eudicots, including C. gynandra, Cleome angustifolia, T. portulacastrum, Z. pentandra, and nine C4 members of family Chenopodiaceae (which has the most C4 species and diversity in forms among eudicot families), amounts of PEPCK were generally very low (barely detectable up to 4% of that in S. anglica). Based on these results, C4 species can be classified biochemically according to the dominant decarboxylase recruited for C4 function; and, Poaceae remains the only family in which PEPCK is known to have a significant role in C4 photosynthesis.

Análisis de diversidad de la familia Poaceae en la región austral de America del Sur

Resumen Análisis de diversidad de la familia Poaceae en la región austral de América del Sur. La familia Poaceae es una de las mejor representadas en América del Sur austral, con un total de 206 géneros que comprenden 1523 especies distribuidas en 10 subfamilias diferentes. En este trabajo analizamos la distribución de estos grupos en Argentina, sur de Brasil (Paraná, Rio Grande do Sul y Santa Catarina), Chile, Paraguay y Uruguay; discutimos la riqueza de las diferentes subfamilias, tribus y géneros, su distribución, especies endémicas, la relación de especies anuales y perennes, así como el número de especies Kranz y no Kranz, su abundancia según regiones geográficas, en relación con la temperatura y las precipitaciones, géneros disyuntos, y la proporción de taxones en relación con las diferentes.

The evolutionary ecology of C4 plants

C4 photosynthesis is a physiological syndrome resulting from multiple anatomical and biochemical components, which function together to increase the CO2 concentration around Rubisco and reduce photorespiration. It evolved independently multiple times and C4 plants now dominate many biomes, especially in the tropics and subtropics. The C4 syndrome comes in many flavours, with numerous phenotypic realizations of C4 physiology and diverse ecological strategies. In this work, we analyse the events that happened in a C3 context and enabled C4 physiology in the descendants, those that generated the C4 physiology, and those that happened in a C4 background and opened novel ecological niches. Throughout the manuscript, we evaluate the biochemical and physiological evidence in a phylogenetic context, which demonstrates the importance of contingency in evolutionary trajectories and shows how these constrained the realized phenotype. We then discuss the physiological innovations that allowed C4 plants to escape these constraints for two important dimensions of the ecological niche--growth rates and distribution along climatic gradients. This review shows that a comprehensive understanding of C4 plant ecology can be achieved by accounting for evolutionary processes spread over millions of years, including the ancestral condition, functional convergence via independent evolutionary trajectories, and physiological diversification.

Echinochloa chloroplast genomes: insights into the evolution and taxonomic identification of two weedy species

The genus Echinochloa (Poaceae) includes numerous problematic weeds that cause the reduction of crop yield worldwide. To date, DNA sequence information is still limited in the genus Echinochloa. In this study, we completed the entire chloroplast genomes of two Echinochloa species (Echinochloa oryzicola and Echinochloa crus-galli) based on high-throughput sequencing data from their fresh green leaves. The two Echinochloa chloroplast genomes are 139,891 and 139,800 base pairs in length, respectively, and contain 131 protein-coding genes, 79 indels and 466 substitutions helpful for discrimination of the two species. The divergence between the genus Echinochloa and Panicum occurred about 21.6 million years ago, whereas the divergence between E. oryzicola and E. crus-galli chloroplast genes occurred about 3.3 million years ago. The two reported Echinochloa chloroplast genome sequences contribute to better understanding of the diversification of this genus.

Transcriptional responses indicate maintenance of photosynthetic proteins as key to the exceptional chilling tolerance of C4 photosynthesis in Miscanthus × giganteus

Miscanthus × giganteus is exceptional among C4 plants in its ability to acclimate to chilling (≤14 °C) and maintain a high photosynthetic capacity, in sharp contrast to maize, leading to very high productivity even in cool temperate climates. To identify the mechanisms that underlie this acclimation, RNA was isolated from M × giganteus leaves in chilling and nonchilling conditions and hybridized to microarrays developed for its close relative Zea mays. Among 21 000 array probes that yielded robust signals, 723 showed significant expression change under chilling. Approximately half of these were for annotated genes. Thirty genes associated with chloroplast membrane function were all upregulated. Increases in transcripts for the lhcb5 (chlorophyll a/b-binding protein CP26), ndhF (NADH dehydrogenase F, chloroplast), atpA (ATP synthase alpha subunit), psbA (D1), petA (cytochrome f), and lhcb4 (chlorophyll a/b-binding protein CP29), relative to housekeeping genes in M. × giganteus, were confirmed by quantitative reverse-transcription PCR. In contrast, psbo1, lhcb5, psbA, and lhcb4 were all significantly decreased in Z. mays after 14 days of chilling. Western blot analysis of the D1 protein and LHCII type II chlorophyll a/b-binding protein also showed significant increases in M. × giganteus during chilling and significant decreases in Z. mays. Compared to other C4 species, M. × giganteus grown in chilling conditions appears to counteract the loss of photosynthetic proteins and proteins protecting photosystem II typically observed in other species by increasing mRNA levels for their synthesis.

Macroevolution of panicoid inflorescences: a history of contingency and order of trait acquisition

BACKGROUND AND AIMS

Inflorescence forms of panicoid grasses (Panicoideae s.s.) are remarkably diverse and they look very labile to human eyes; however, when performing a close inspection one can identify just a small subset of inflorescence types among a huge morphospace of possibilities. Consequently, some evolutionary constraints have restricted, to some extent, the diversification of their inflorescence. Developmental and genetic mechanisms, the photosynthetic type and plant longevity have been postulated as candidate constraints for angiosperms and panicoids in particular; however, it is not clear how these factors operate and which of these have played a key role during the grass inflorescence evolution. To gain insight into this matter the macroevolutionary aspects of panicoid inflorescences are investigated.

METHODS

The inflorescence aspect (lax versus condensed), homogenization, truncation of the terminal spikelet, plant longevity and photosynthetic type were the traits selected for this study. Maximum likelihood and Bayesian Markov chain Monte Carlo methods were used to test different models of evolution and to evaluate the existence of evolutionary correlation among the traits. Both, models and evolutionary correlation were tested and analysed in a phylogenetic context by plotting the characters on a series of trees. For those cases in which the correlation was confirmed, test of contingency and order of trait acquisition were preformed to explore further the patterns of such co-evolution.

KEY RESULTS

The data reject the independent model of inflorescence trait evolution and confirmed the existence of evolutionary contingency. The results support the general trend of homogenization being a prerequisite for the loss of the terminal spikelet of the main axis. There was no evidence for temporal order in the gain of homogenization and condensation; consequently, the homogenization and condensation could occur simultaneously. The correlation between inflorescence traits with plant longevity and photosynthetic type is not confirmed.

CONCLUSIONS

The findings indicate that the lability of the panicoid inflorescence is apparent, not real. The results indicate that the history of the panicoids inflorescence is a combination of inflorescence trait contingency and order of character acquisition. These indicate that developmental and genetic mechanisms may be important constraints that have limited the diversification of the inflorescence form in panicoid grasses.

The recurrent assembly of C4 photosynthesis, an evolutionary tale

Today, plants using C4 photosynthesis are widespread and important components of major tropical and subtropical biomes, but the events that led to their evolution and success started billions of years ago (bya). A CO2-fixing enzyme evolved in the early Earth atmosphere with a tendency to confuse CO2 and O2 molecules. The descendants of early photosynthetic organisms coped with this property in the geological eras that followed through successive fixes, the latest of which is the addition of complex CO2-concentrating mechanisms such as C4 photosynthesis. This trait was assembled from bricks available in C3 ancestors, which were altered to fulfill their new role in C4 photosynthesis. The existence of C4-suitable bricks probably determined the lineages of plants that could make the transition to C4 photosynthesis, highlighting the power of contingency in evolution. Based on the latest findings in C4 research, we present the evolutionary tale of C4 photosynthesis, with a focus on the general evolutionary phenomena that it so wonderfully exemplifies.

Is it easy to move and easy to evolve? Evolutionary accessibility and adaptation

Recent phylogenetic studies have documented high levels of conservatism in ecological traits that seem at odds with the traditional view that organisms can readily adapt to different environments. We highlight the need for a new level of rigour in interpreting such patterns from both organismal and biogeographical perspectives. A handful of closely studied systems are revealing a greater number of ecological transitions than anticipated, but these are typically phylogenetically clustered, suggesting that the relative ease or difficulty of such adaptations is strongly context-dependent. We believe that this differential evolutionary 'accessibility' to certain adaptations is pervasive across the tree of life and we illustrate this with reference to several important ecological syndromes in plants. Differential accessibility derives in large part from the attributes of the organisms themselves - certain traits may act as 'enablers' that increase the likelihood of particular innovations. So far, we have made minimal progress in identifying precursor traits that underlie the evolution of ecological syndromes, but we are hopeful that improved phylogenetic resolution will allow for a surge of new insight. However, the accessibility of particular adaptations also derives from external factors, such as the relative location and extent of certain habitats and the competitive ability of the lineages that already occupy them. Better understanding of where particular lineages have existed in the past, and of the adjacency or connectivity of different environments through time, will also be necessary to explain how both dispersal and ecological diversification have jointly contributed to the assembly of the world's ecosystems.

Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research

Setaria viridis is an emerging model species for genetic studies of C4 photosynthesis. Many basic molecular resources need to be developed to support for this species. In this paper, we performed a comprehensive transcriptome analysis from multiple developmental stages and tissues of S. viridis using next-generation sequencing technologies. Sequencing of the transcriptome from multiple tissues across three developmental stages (seed germination, vegetative growth, and reproduction) yielded a total of 71 million single end 100 bp long reads. Reference-based assembly using Setaria italica genome as a reference generated 42,754 transcripts. De novo assembly generated 60,751 transcripts. In addition, 9,576 and 7,056 potential simple sequence repeats (SSRs) covering S. viridis genome were identified when using the reference based assembled transcripts and the de novo assembled transcripts, respectively. This identified transcripts and SSR provided by this study can be used for both reverse and forward genetic studies based on S. viridis.