Poaceae Species Research Articles

Assembly of the Arctic flora: Highly parallel and recurrent patterns in sedges (Carex).

Understanding the origin of ecosystems and their changes through time is important. Two mutually contrasting types of grasslands existed in the Arctic: dry- and cold-adapted grasslands of the Pleistocene dominated by Poaceae species, and presently dominating graminoid grasslands composed of sedges and rushes. We studied the taxon recruitment of the Arctic flora for Carex, the most species-rich and widespread genus of the Arctic. In this study we explore the possible geographical and altitudinal origins of the species, their ecological provenance in terms of soil moisture and light requirements, and salt tolerance. We addressed these questions in a phylogenetic context using the latest megaphylogeny of Carex comprising almost all Arctic species and about half of the genus' total species diversity. Ecological data were extracted from the literature and analyzed for each clade comprising Arctic species. Arctic Carex species were observed in 48 independent lineages. Almost all areas north of the meridional zone of the Northern Hemisphere may have served as sources of Arctic lineages. Source areas are unrelated to the distribution within the Arctic. Arctic species evolved in lowland and high mountain clades; mostly in wet, rarely in dry adapted clades that occur principally in open conditions. Salt tolerant Arctic species occur in five clades. Many independent lineages of different geographical areas and ecological backgrounds provided species for the northernmost ecosystem; clear main sources were not discernible. Carex shows the whole dynamic of ecosystem assembly from a seemingly simple immigration of preadapted species, evolution in geographical distant areas, to species radiations in the North.

Genomic Constitution and Relationship in Urochloa (Poaceae) Species and Hybrids

Urochloa P. Beauv. [syn. Brachiaria (Trin.) Griseb.] belongs to the family Poaceae and comprises species presenting different ploidy levels and modes of reproduction. Specific studies on genomic constitution and relationship within the genus Urochloa are limited, despite the great economic and agronomic importance of forage species and the high frequency of polyploids. Therefore, molecular cytogenetic analyses can enhance the knowledge about genomes and their differentiation, which allows making inferences about phylogenetic and genomic relationships. The current study aimed to investigate the genomic relationships between Urochloa ruziziensis (R. Germ. & Evrard) Crins (syn. Brachiaria ruziziensis Germain & Evrard.) cultivar ‘Kennedy’, Urochloa decumbens (Stapf) R. D. Webster [syn. Brachiaria decumbens (Stapf)] cultivar ‘Basilisk’, Urochloa brizantha (Hochst. ex. A. Rich.) R. D. Webster [syn. Brachiaria brizantha (A. Rich.) Stapf] cultivar ‘Marandu’, and their interspecific hybrids by means of genomic in situ hybridization, fluorescent in situ hybridization, and nuclear genome quantification by flow cytometry. We proposed the genomic constitution of U. ruziziensis, U. decumbens, and U. brizantha, such as B2B2, B1B1B2B2, and BBB1B1, respectively. Genomes B, B1, and B2 were considered to be homoeologous, but there was less affinity between genomes B and B2.

A database for orphan genes in Poaceae.

Orphan genes refer to a group of protein-coding genes lacking recognizable homologs in the other organisms. Extensive studies have demonstrated that numerous newly sequenced genomes contain a significant number of orphan genes, which have important roles in plant's responses to the environment. Due to a lack of phylogenetic conservation, the origin of orphan genes and their functions are currently not well defined. In the present study, a Poaceae orphan genes database (POGD; http://bioinfo.ahau.edu.cn/pogd) was established to serve as a user-friendly web interface for entry browsing, searching and downloading orphan genes from various plants. Four Poaceae species, including Brachypodium distachyon, Oryza sativa, Sorghum bicolor and Zea mays, are included in the current version of POGD. The database provides gene descriptions (chromosome strands, physical location), gene product records (protein length, isoelectric point, molecular weight as well as gene and protein sequences) and functional annotations (cellular role, gene ontology category, subcellular localization prediction). Basic Local Alignment Search Tool and comparative analyses were also provided on the website. POGD will serve as a comprehensive and reliable repository, which will help uncover regulatory mechanisms of orphan genes and may assist in the development of comparative genomics in plant biology.

Genome and Transcriptome sequence of Finger millet (Eleusine coracana (L.) Gaertn.) provides insights into drought tolerance and nutraceutical properties

BackgroundFinger millet (Eleusine coracana (L.) Gaertn.) is an important staple food crop widely grown in Africa and South Asia. Among the millets, finger millet has high amount of calcium, methionine, tryptophan, fiber, and sulphur containing amino acids. In addition, it has C4 photosynthetic carbon assimilation mechanism, which helps to utilize water and nitrogen efficiently under hot and arid conditions without severely affecting yield. Therefore, development and utilization of genomic resources for genetic improvement of this crop is immensely useful.ResultsExperimental results from whole genome sequencing and assembling process of ML-365 finger millet cultivar yielded 1196 Mb covering approximately 82% of total estimated genome size. Genome analysis showed the presence of 85,243 genes and one half of the genome is repetitive in nature. The finger millet genome was found to have higher colinearity with foxtail millet and rice as compared to other Poaceae species. Mining of simple sequence repeats (SSRs) yielded abundance of SSRs within the finger millet genome. Functional annotation and mining of transcription factors revealed finger millet genome harbors large number of drought tolerance related genes. Transcriptome analysis of low moisture stress and non-stress samples revealed the identification of several drought-induced candidate genes, which could be used in drought tolerance breeding.ConclusionsThis genome sequencing effort will strengthen plant breeders for allele discovery, genetic mapping, and identification of candidate genes for agronomically important traits. Availability of genomic resources of finger millet will enhance the novel breeding possibilities to address potential challenges of finger millet improvement.

Induced accumulation of tyramine, serotonin, and related amines in response to Bipolaris sorokiniana infection in barley.

The inducible metabolites were analyzed in barley leaves inoculated with Bipolaris sorokiniana, the causal agent of spot blotch of barley. HPLC analysis revealed that B. sorokiniana-infected leaves accumulated 4 hydrophilic compounds. They were purified by ODS column chromatography and preparative HPLC. Spectroscopic analyses revealed that they were tyramine (1), 3-(2-aminoethyl)-3-hydroxyindolin-2-one (2), serotonin (3), and 5,5'-dihydroxy-2,4'-bitryptamine (4). Among these, 2 and 4 have not been reported as natural products. They showed antifungal activity in an assay of inhibition of B. sorokiniana conidia germination, suggesting that they play a role in the chemical defense of barley as phytoalexins. The accumulation of 1-4 was examined also in the leaves of rice and foxtail millet. Rice leaves accumulated 2, 3, and 4, whereas foxtail millet leaves accumulated 3 and 4 in response to pathogen attack, suggesting the generality of accumulation of 3 and 4 in the Poaceae species.

Effects of soil fertility on early development of wetland vegetation from soil seed bank: Focusing on biomass production and plant species diversity

To examine the effects of soil fertility on biomass production, plant species diversity, and early vegetation development, we performed a mesocosm experiment using soil seed bank under three soil fertility levels (ombrotrophic, mesotrophic, and eutrophic). Biomass production linearly increased (P < 0.01), whereas plant species diversity significantly decreased (P < 0.001) as soil fertility increased. Soil fertility seemed to play a role as an environmental sieve in early vegetation development, in turn, lead the patterns of biomass production and plant species diversity. Several Poaceae species which are forming tall and dense canopy, such as Phalaris arundinacea, Miscanthus sacchariflorus, and Zizania latifolia, showed higher importance values under fertilized condition, whereas relatively small macrophytes of Eleocharis acicularis, Carex dickinsii, and Isachne globosa mainly survived under ombrotrophic condition. Although plant species richness decreased as soil fertility increased, the percentages of perennials and exotics increased rather than annuals and natives. Predominance of perennials and exotics under eutrophic condition in early vegetation development seemed to lead a continuous decrease in plant species diversity as a result of competitive effect. A significant negative relationship between plant species diversity and biomass production (P < 0.0001) was obtained when all experimental plots are included in correlation analysis.

Effects of climate, habitat and land use on the cover and diversity of the savanna herbaceous layer in Burkina Faso, West Africa

Herbaceous plants account for more than three-fourths of the total biomass in savanna ecosystems. However, which environmental factors mainly drive the biodiversity of herbaceous species is still under debate. In this study, we investigated the influence of climate, habitat and land use on species richness and cover in the West African savanna ecosystems of Burkina Faso. For a broader understanding, we analysed responses of the most important taxonomical groups of the herbaceous layer (Poaceae, Cyperaceae, Fabaceae s.l. and juvenile woody species) to the above mentioned environmental factors. We found light limitation by trees or shrubs and nutrient availability to be the variables that were mainly able to explain the differences in species richness, whereas precipitation and soil water-holding capacity, in general, drive species cover. However, specifically which environmental parameters influenced species richness and cover differed between taxonomical groups. Species richness of Cyperaceae species depended on water availability, while high Cyperaceae cover was found in soils with high water-holding capacity. Cyperaceae species are able to tolerate stagnant water. By contrast, Poaceae species cover was higher in dry habitats, and species richness declined with higher mean annual precipitation. Fabaceae species richness and cover were both higher in communal areas and sandy soils. This study revealed that both species richness and species cover, important aspects to describe the community composition, should be examined, as they are driven by sometimes different environmental conditions. Differentiating between the most important taxonomical groups of the savanna ecosystem increases the understanding in the important ecological processes that effect the herbaceous vegetation composition.

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.

Management of the biological diversity of AM fungi by combination of host plant succession and integrity of extraradical mycelium

As functional diversity influences the benefits conferred on host plants by arbuscular mycorrhizal fungi (AMF) and large scale commercial inoculation is currently impracticable, strategies are required to manage communities of indigenous AMF associated with different hosts within agricultural cropping systems. In a non-sterilized soil, using 454 pyrosequencing of the LSU-D2 rDNA gene, host plant AMF diversity was assessed following successions of different plant species, grown with or without prior soil disturbance. Diversity present in the roots of two species of the Fabaceae (Ornithopus compressus and Trifolium subterraneum) was compared with those of two species of Poaceae (Lolium rigidum and Triticum aestivum). When spores and colonised root fragments formed were the main propagules source (disturbed soil), the communities of AMF present in the two legumes were clearly different from those of the two members of the Poaceae but were similar for plants within each family, consistent with there being preferential symbioses existing within an AMF population for host classes. Significantly, wheat grown in undisturbed soil immediately after the legume O. compressus acquired a mycorrhizal fungal community closely related to that of the previous host plant, and different to that found when the soil was disturbed or not cropped prior to the growth of the wheat. Parallel effects were seen in the succession from L. rigidum to T. subterraneum, indicating that these effects are not unique to the legume-wheat sequence. These results also suggest that, under no-till cropping, selected cover crops or crops in rotation could help build mycorrhizal communities that function throughout a sequence of several main crops.

45S rDNA external transcribed spacer organization reveals new phylogenetic relationships in Avena genus.

The genus Avena comprises four distinct genomes organized in diploid (AA or CC), tetraploid (AABB or AACC) and hexaploid species (AACCDD), constituting an interesting model for phylogenetic analysis. The aim of this work was to characterize 45S rDNA intergenic spacer (IGS) variability in distinct species representative of Avena genome diversity–A. strigosa (AA), A. ventricosa (CvCv), A. eriantha (CpCp), A. barbata (AABB), A. murphyi (AACC), A. sativa (AACCDD) and A. sterilis (AACCDD) through the assessment of the 5’ external transcribed spacer (5’-ETS), a promising IGS region for phylogenetic studies poorly studied in Avena genus. In this work, IGS length polymorphisms were detected mainly due to distinct 5’-ETS sequence types resulting from major differences in the number and organization of repeated motifs. Although species with A genome revealed a 5’-ETS organization (A-organization) similar to the one previously described in A. sativa, a distinct organization was unraveled in C genome diploid species (C-organization). Interestingly, such new organization presents a higher similarity with other Poaceae species than A-genome sequences, supporting the hypothesis of C-genome being the ancestral Avena genome. Additionally, polyploid species with both genomes mainly retain the A-genome 5’-ETS organization, confirming the preferential elimination of C-genome sequences in Avena polyploid species. Moreover, 5’-ETS sequences phylogenetic analysis consistently clustered the species studied according to ploidy and genomic constitution supporting the use of ribosomal genes to highlight Avena species evolutive pathways.

Agroecological and environmental factors influence Barley yellow dwarf viruses in grasslands in the US Pacific Northwest

Plant pathogens can play a role in the competitive interactions between plant species and have been understudied in native prairies, which are declining globally, and in Conservation Reserve Program (CRP) lands in the United States. Barley/Cereal yellow dwarf virus (B/CYDV) are among the most economically important disease-causing agents of small grain cereal crops, such as wheat, and are known to infect over 150 Poaceae species, including many of the grass species present in prairies and CRP lands. Field surveys of Poaceae species were conducted in endangered Palouse Prairie and CRP habitats of southeastern Washington and adjacent northern Idaho, USA from 2010 to 2012 to examine for the presence of B/CYDV among plant hosts and aphid vectors. Viral species were identified via cloning and sequencing. Landscape, soil and climate data were retrieved from USDA-NASS and USDA-NRCS databases. Analyses were conducted to examine effects of diverse agroecological and environmental factors on virus prevalence. A total of 2271 grass samples representing 30 species were collected; 28 of these were infected with BYDV in at least one location. BYDV infection was detected at every CRP and prairie remnant sampled, with an overall infection of 46%. BYDV-SGV and BYDV-PAV were the only two B/CYDV species encountered, with BYDV-SGV being more prevalent. Sampling time (season) and host plant identity were the main variables explaining variation in virus prevalence among sites. BYDV was more prevalent in perennial compared to annual grass species. Aphids were encountered only once suggesting non-colonizing aphids, potentially from neighboring cereal fields, are responsible for disease spread in these habitats. BYDV prevalence increased in sampled habitats as cereal crop cover increased within a 1-km radius of a habitat patch. Results demonstrate moderate to high and persistent prevalence of BYDV in an endangered grassland habitat. Species composition and susceptibility to pathogens should be considered when creating seed mixes for CRP sites, especially in relation to agricultural crops and diseases in a region. Future work exploring host abundance, competence and habitat utilization by vectors is required to fully elucidate BYDV ecology and epidemiology in grassland habitats.

EVALUATING THE DYNAMICS OF ALIEN SPECIES (POACEAE) USED FOR EROSION CONTROL ON SAKURAJIMA VOLCANO

Alien species in the family Poaceae play an important role as cover plants for erosion control on slopes, particularly in Japan. However, concerns have arisen regarding the adverse effects of these species on the local ecosystem and biodiversity. This study therefore examined the succession and seed propagation of alien Poaceae that are used for erosion control on the cut slopes of Sakurajima volcano in southwesternJapan. The results were as follows: Although the alien species used as cover plants were dominant for the first couple of years following their introduction to the slopes, they were displaced entirely by native species after the sixth year, which is considerably faster than ordinary succession. In addition, heading (flowering) of alien species was also rarely observed in this period. It is considered that the observed results were caused by the oligotrophic conditions of the slopes on Sakurajima volcano.

Differential responses to phosphorus availability in the halophytes Aeluropus Littoralis, Catapodium rigidum, and Hordeum maritimum

ABSTRACTThe objective of this experiment was to explore the variability of response to phosphorus (P) availability in three fodder Poaceae species native of saline biotopes, Aeluropus littoralis, Catapodium rigidum, and Hordeum maritimum. The behavior of these wild species has been compared to that of a cultivated one, Hordeum vulgare. Plants were grown in plastic pots filled with inert sand. The experiment was carried out in a greenhouse with six P levels: 0, 5, 15, 60, 180, and 360 µM P concentration supplied as KH2PO4. Results showed that the growth of the four species is strongly affected by the low phosphorus availability in the medium. Furthermore, to reach 80% of their maximum yield expressed as shoot dry weight (DW), a soil phosphorus concentration of approximately 40 µM P concentration is sufficient for Hordeum maritimum, whereas approximately 66, 120, and 132 µM P concentration are needed for C. rigidum, A. littoralis, and Hordeum vulgare plants, respectively. Thus, our results showed that spontaneous species are more tolerant to P deficiency than cultivated barley. The relative performance of the three wild Poaceae species is likely related to their capacity to maintain higher P acquisition efficiency (PAE) under low P concentration conditions. These native Poaceae species may therefore represent genetic resources for the improvement of barley.

Stable Isotopic Evidence for the Widespread Presence of Oxygen-Containing Chemical Linkages between α-Cellulose and Lignin in Poaceae (Gramineae) Grass Leaves

The chemical linkage between α-cellulose and lignin in plant cell walls has long been a controversial topic and crucial to devising effective strategies for sustainable biomass and bioenergy utilization. In this new contribution, we surveyed 80 Poaceae (Gramineae) species grown in tropical Hainan Island (China) to test the hypothesis that the presence of oxygen-containing chemical linkage in Poaceae species is widespread. Our innovative natural abundance oxygen isotopic analysis allowed us to infer that more than 1/3 of the species investigated has chemical (ether) linkages between α-cellulose and lignin in their leaf cell walls, with a species-specific 2–89 oxygen-containing bonds for every 1000 glucose units. However, the presence of such linkage appears to be phylogeny-dependent. On average, species of C3 photosynthetic mode are found to have more extensive oxygen-containing linkages than those of C4 photosynthetic mode. Our finding challenges the conventional view that no chemical bonds between α-cell...

Genome-wide characterization and evolution analysis of long terminal repeat retroelements in moso bamboo (Phyllostachys edulis)

The availability of nearly complete moso bamboo genome sequences permits the detailed discovery and cross-species comparison of transposable elements (TEs) between Bambusoideae and other Poaceae species at the whole genome level. Long terminal repeat retroelements (LTR-retroelements) are the single largest components of most plant genomes and can substantially impact the genome in various ways. Through a combination of structure- and homology-based approaches, we initially investigated 982 LTR-retroelement families comprising 2,004,644 LTR-retroelement sequences, which accounted for more than 40% of the moso bamboo genome. Further analysis revealed that the ratio of solo LTRs to intact elements (S/I) in moso bamboo is significantly low (approximately 0.28:1), indicating that bamboo LTR-retroelements might have undergone relatively low frequencies of unequal recombination and illegitimate recombination. Phylogenetic analysis revealed four Ty1-copia and five Ty3-gypsy evolutionary lineages that were present before the divergence of eudicot and monocot species, but the scales and timeframes within which they proliferated significantly varied across families and lineages. Insertion time estimates showed that LTR-retroelements were amplified for approximately 0~3 million years and had longer periods of activity than those of rice and Arabidopsis. These findings suggest that the expansion of LTR-retroelements might be responsible for host large genome size during moso bamboo evolution.

Distribution of the tryptophan pathway-derived defensive secondary metabolites gramine and benzoxazinones in Poaceae.

The Poaceae is a large taxonomic group consisting of approximately 12,000 species and is classified into 12 subfamilies. Gramine and benzoxazinones (Bxs), which are biosynthesized from the tryptophan pathway, are well-known defensive secondary metabolites in the Poaceae. We analyzed the presence or absence of garamine and Bxs in 64 species in the Poaceae by LC-MS/MS. We found that Hordeum brachyantherum and Hakonechloa macra accumulated gramine, but the presence of gramine was limited to small groups of species. We also detected Bxs in four species in the Pooideae and six species in the Panicoideae. In particular, four species in the Paniceae tribe in Panicoideae accumulaed Bxs, indicating that this tribe is a center of the Bx distribution. Bxs were absent in the subfamilies other than Pooideae and Panicoideae. These findings provide an overview of biased distribution of gramine and Bxs in Poaceae species.

Towards a better understanding of El Salvador flora

AbstractThe main objective of this paper is to approximate the current status of the flora of El Salvador. Described as a mountainous region covered with trees and bushes in the 1700s, now El Salvador is pictured as overpopulated, with almost nothing of its original vegetation left. The earliest complete checklists were published by Standley and Calderon. Even though there were several botanical expeditions to the region, only since the 1950s could botanical specimens be deposited in a local herbarium. There are three herbaria in the country: the Tropical Research Institute, located at the University of El Salvador; the Museum of Natural History of El Salvador; and the herbarium of the Botanical Garden La Laguna. Current national and international collaborations have so far permitted the description of new species in the last 2 years and the reporting of more than 300 species of Poaceae. To increase the knowledge of plant species richness in El Salvador is the first step towards its sustainable use and co...

Physiological, anatomical and antioxidant responses to salinity in the Mediterranean pastoral grass plant Stipa lagascae

Soil and water salinity is a major environmental problem in the dry Mediterranean regions, affecting rangeland production. This study investigated the effects of salinity on the wild perennial grass (Poaceae) species Stipa lagascae R. &amp; Sch., a potential forage plant that could be used to rehabilitate degraded rangelands in dry areas. In a laboratory, 3-month-old S. lagascae seedlings were subjected to increasing salt treatments (0–400 mm NaCl) for 45 days. Physiological and biochemical parameters such as leaf water potential (Ψw), leaf relative water content (RWC), proline, total soluble sugars, Na+, K+ and Ca2+ contents, and catalase, ascorbate peroxidase and glutathione reductase activities were measured. Total soluble sugars and proline concentrations increased and Ψw and RWC decreased with increasing salt concentrations. Lower salt concentrations induced a non-significant degradation of chlorophyll pigments. Shoot Na+ content increased with a salinity level, whereas shoot K+ and Ca2+ concentrations decreased and the K+ : Na+ ratio was lower. The salinity threshold, above which S. lagascae showed signs of damage, occurred at 300 mm. Plants have evolved reactive oxygen species (ROS) scavenging enzymes including catalase, ascorbate peroxidase and glutathione reductase, which provide cells with an efficient mechanism to neutralise ROS. The tolerance strategies of S. lagascae to moderate salinity seem to include osmotic adjustment through total soluble sugars and proline accumulation, and highly inducible antioxidative defence. Further investigations are necessary to study the effect of salt stress on distribution of ions (Na+, K+, Ca2+, Mg2+, Cl–, NO3–, SO42–) and osmotic adjustment. Photosynthesis and water-use efficiency parameters could be also useful tools.

Diporate Pollen Grains of Poaceae Species: High Pollen Resolution for Reconstruction of Grasslands Vegetation

Diporate Pollen Grains of Poaceae Species: High Pollen Resolution for Reconstruction of Grasslands Vegetation

Biodiversity islands in the Savanna : analysis of the phytodiversity on termite mounds in northern Benin

Termite mounds represent abundant microhabitats of high biodiversity in tropical savanna ecosystems and are an important source of landscape heterogeneity in Sub–Saharan West Africa. Floristic composition as well as density, structure and zonation of plant cover on the mounds were investigated in northern Benin and compared to the adjacent savanna vegetation. A total of 57 abandoned and densely vegetated termite mounds of comparable size and similarly affected by erosion located in different types of savannas inside and outside of the W National Park and in cotton fields were studied. This study revealed that termitaria are special habitats differing in density, composition and structure from surrounding savannas. The plant cover of termite mounds showed a distinctive zonation. Succulents, geophytes, and lianas were much more abundant on mounds, the family Capparaceae was found exclusively on mounds. The floristic composition and vegetation on termitaria proved to be rather homogeneous; although those mounds located in cotton fields differed by higher abundance of Poaceae and lower species richness.