Altered allocation to roots and shoots in the endophyte‐infected seedlings of Puccinellia distans (Poaceae)

Endophytes play an important role in ecological and evolutionary processes in plants and have marked economic value. Seed‐transmitted fungal endophytes are conventionally regarded as mutualistic symbionts, but their fitness consequences for the offspring of the host are not clear. Puccinellia distans infected with the fungus Epichloë typhina (E+) produces seeds that are several times smaller than normal (E?). This observation suggests that the E+ seedlings face a developmental disadvantage. Our growth chamber experiments compared the germination rates of the small E+ and large E? seeds of P. distans and examined the biomass allocation of seedlings to roots and shoots. The E+ seedlings germinated more slowly and maintained shorter shoots and a smaller root biomass for 30–50 days after sowing. Despite this disadvantage, the E+ plants more quickly increased their total size, attaining a larger shoot and whole‐plant biomass. The shoot:root biomass ratio increased more rapidly through time in the E+ seedlings, attaining a value nine times higher in the E+ than the E? group 50 days after sowing. Such differences between the E+ and E? seedlings were not explained by the growth allometry between shoots and roots. The seedlings of P. distans infected with the Epichloë endophyte were initially handicapped by their postponed emergence, but this disadvantage was quickly overcome by their superior growth capacity. The decrease in the relative allocation to roots may indicate that endophytes increase the performance of roots as resource‐acquiring organs and/or reduce the role of roots in protection against herbivores.     

Salinomyces polonicus: A moderately halophilic kin of the most extremely halotolerant fungus Hortaea werneckii

A clade where the most halotolerant fungus in the world – Hortaea werneckii, belongs (hereafter referred to as Hortaea werneckii lineage) includes five species: Hortaea werneckii, H. thailandica, Stenella araguata, Eupenidiella venezuelensis, and Magnuscella marina, of which the first species attracts increasing attention of mycologists. The species diversity and phylogenetic relationships within this lineage are weakly known. In this study two moderately halophilic black yeast strains were isolated from brine of graduation tower in Poland. Molecular phylogenetic analyses based on the rDNA ITS1-5.8S-ITS2 (=ITS), rDNA 28S D1–D2 (=LSU), and RNA polymerase II (rpb2) sequences showed that the two strains belong to Hortaea werneckii lineage but cannot be assigned to any described taxa. Accordingly, a new genus and species, Salinomyces and Salinomyces polonicus, are described for this fungus. Furthermore, molecular phylogenetic analyses have revealed that Hortaea thailandica is more closely related to S. polonicus than to H. werneckii. A new combination Salinomyces thailandicus is proposed for this fungus.     

A comparative genomic analysis of plant hormone related genes in different species

Plant hormones are small molecules that play important roles throughout the life span of a plant,known as auxin,gibberellin,cyto-kinin,abscisic acid,ethylene,jasmonic acid,salicylic acid,and brassinosteroid.Genetic and molecular studies in the model organism Arabidopsis thaliana have revealed the individual pathways of various plant hormone responses.In this study,we selected 479 genes that were convincingly associated with various hormone actions based on genetic evidence.By using these 479 genes as querie...     

A comparative genomic analysis of plant hormone related genes in different species

Plant hormones are small molecules that play important roles throughout the life span of a plant,known as auxin,gibberellin,cytokinin,abscisic acid,ethylene,jasmonic acid,salicylic acid,and brassinosteroid.Genetic and molecular studies in the model organism Arabidopsis thaliana have revealed the individual pathways of various plant hormone responses.In this study,we selected 479 genes that were convincingly associated with various hormone actions based on genetic evidence.By using these 479 genes as queries,a genome-wide search for their orthoiogues in several species(microorganisms,plants and animals) was performed.Meanwhile,a comparative analysis was conducted to evaluate their evolutionary relationship.Our analysis revealed that the metabolisms and functions of plant hormones are generally more sophisticated and diversified in higher plant species.In particular,we found that several phytohormone receptors and key signaling components were not present in lower plants or animals.Meanwhile,as the genome complexity increases,the orthologne genes tend to have more copies and probably gain more diverse functions.Our study attempts to introduce the classification and phylogenic analysis of phytohormone related genes,from metabolism enzymes to receptors and signaling components,in different species.     

Demographic bottlenecks in tropical plant regeneration: A comparative analysis of causal influences

Mortality factors that act sequentially through the demographic transitions from seed to sapling may have critical effects on recruitment success. Understanding how habitat heterogeneity influences the causal factors that limit propagule establishment in natural populations is central to assess these demographic bottlenecks and their consequences. Bamboos often influence forest structure and dynamics and are a major factor in generating landscape complexity and habitat heterogeneity in tropical forests. To understand how patch heterogeneity influences plant recruitment we studied critical establishment stages during early recruitment of Euterpe edulis, Sloanea guianensis and Virola bicuhyba in bamboo and non-bamboo stands in the Brazilian Atlantic forest. We combined observational studies of seed rain and seedling emergence with seed addition experiments to evaluate the transition probabilities among regeneration stages within bamboo and non-bamboo stands. The relative importance of each mortality factor was evaluated by determining how the loss of propagules affected stage-specific recruitment success. Our results revealed that the seed addition treatment significantly increased seedling survivorship for all three species. E. edulis seedling survival probability increased in the addition treatment in the two stand types. However, for S. guianensis and V. bicuhyba this effect depended strongly on artificially protecting the seeds, as both species experienced increased seed and seedling losses due to post-dispersal seed predators and herbivores. Propagules of all three species had a greater probability of reaching subsequent recruitment stages when protected. The recruitment of large-seeded V. bicuhyba and E. edulis appears to be much more limited by post-dispersal factors than by dispersal limitation, whereas the small-seeded S. guianensis showed an even stronger effect of post-dispersal factors causing recruitment collapse in some situations. We demonstrated that E. edulis, S. guianensis and V. bicuhyba are especially susceptible to predation during early compared with later establishment stages and this early stage mortality can be more crucial than stand differences as determinants of successful regeneration. Among-species differences in the relative importance of dispersal vs. establishment limitation are mediated by variability in species responses to patch heterogeneity. Thus, bamboo effects on the early recruitment of non-bamboo species are patchy and species-specific, with successional bamboo patches exerting a far-reaching influence on the heterogeneity of plant species composition and abundance.     

Techniques for boron determination and their application to the analysis of plant and soil samples

This paper reviews techniques for determining B concentration and isotopic ratio and their application to soil and plant samples. Boron concentration has been determined utilising spectrophotometry, potentiometry, chromatography, flame atomic emission and absorption spectrometry, inductively coupled plasma (ICP) optical emission (OES) and mass spectrometry (MS), and neutron activation analysis using neutron radiography and prompt- activation analysis. Isotopic ratios of B have been measured by ICP–MS, thermal ionisation mass spectrometry (TIMS) and secondary ion mass spectrometry (SIMS). For isotopic measurements, TIMS and SIMS are more sensitive and provide higher degrees of accuracy and resolution than ICP–MS, however, extensive sample preparation and purification, and time-consuming measurements limit their usefulness for routine analyses.While the spectrophotometric technique using a colorimetric reaction of B with azomethine-H has been the most extensively applied B determination method for soil and plant samples, colorimetric methods, in general, suffer from numerous interferences and have poor sensitivity and precision. The prompt- method can determine B concentration in intact samples which enables this method to be especially useful for some applications in agriculture. Research involving B behaviour in plant and soil environments would benefit from this technology. In recent years, the use of ICP–OES and ICP–MS for B determination in plant and soil samples has grown tremendously. The application of ICP–OES brought a significant improvement in B analysis because of its simplicity, sensitivity and multielement detection capability. However, besides matrix interferences, the two most sensitive emission lines for B suffer strong spectral interference from Fe. The ICP–OES is not adequately sensitive for some nutritional work involving low B concentrations and B translocation studies using the isotope tracer technique.Plasma is one of the most effective analyte ionisers and MS is the most sensitive ion detector. Coupling of plasma with MS resulted in the development of plasma source MS technology (ICP–MS) which has outperformed all previous analytical methods for trace element determination. Boron determination by ICP–MS suffers no spectroscopic interferences, and is considered the most practical and convenient technique for B isotope determination. The ability of ICP–MS to measure isotopic ratios as well as B concentration enables: (1) B concentration determination by the isotope dilution method, (2) verification of B concentration by isotope fingerprinting in routine analysis and (3) determination of total B concentration as well as B isotope ratio in the same run for biological tracer studies. Therefore, ICP–MS is the method of choice among the present-day technologies for determining B concentration and a convenient method for B isotope determination. In recent years, new generations of plasma-source MS instruments have been developed using alternative plasma generation methods and high-resolution mass spectrometers. These instruments are expected to bring further improvements in accuracy, sensitivity and precision of B determination.     

Effects of manganese on the microstructures of Chenopodium ambrosioides L., A manganese tolerant plant

Chenopodium ambrosioides L. can tolerate high concentrations of manganese and has potential for its use in the revegetation of manganese mine tailings. Following a hydroponic investigation, transmission electron microscopy (TEM)-energy disperse spectroscopy (EDS) was used to study microstructure changes and the possible accumulation of Mn in leaf cells of C. ambrosioides in different Mn treatments (200, 1000, 10000 μmol·L^?1). At 200 μmol·L^?1, the ultrastructure of C. ambrosioides was clearly visible without any obvious damage. At 1000 μmol·L^?1, the root, stem and leaf cells remained intact, and the organelles were clearly visible without any obvious damage. However, when the Mn concentration exceeded 1000 μmol·L^?1 the number of mitochondria in root cells decreased and the chloroplasts in stem cells showed a decrease in grana lamellae and osmiophilic granules. Compared to controls, treatment with 1000 μmol·L^?1 or 10000 μmol·L^?1 Mn over 30 days, gave rise to black agglomerations in the cells. At 10000 μmol·L^?1, Mn was observed to form acicular structures in leaf cells and intercellular spaces, which may be a form of tolerance and accumulation of Mn in C. ambrosioides. This study has furthered the understanding of Mn tolerance mechanisms in plants, and is potential for the revegetation of Mn-polluted soils.     

Characterisation of the nuclear proteome of a dehydration‐sensitive cultivar of chickpea and comparative proteomic analysis with a tolerant cultivar

Water deficit or dehydration hampers plant growth and development, and shrinks harvest size of major crop species worldwide. Therefore, a better understanding of dehydration response is the key to decipher the regulatory mechanism of better adaptation. In recent years, nuclear proteomics has become an attractive area of research, particularly to study the role of nucleus in stress response. In this study, a proteome of dehydration‐sensitive chickpea cultivar (ICCV‐2) was generated from nuclei‐enriched fractions. The LC‐MS/MS analysis led to the identification of 75 differentially expressed proteins presumably associated with different metabolic and regulatory pathways. Nuclear localisation of three candidate proteins was validated by transient expression assay. The ICCV‐2 proteome was then compared with that of JG‐62, a tolerant cultivar. The differential proteomics and in silico analysis revealed cultivar‐specific differential expression of many proteins involved in various cellular functions. The differential tolerance could be attributed to altered expression of many structural proteins and the proteins involved in stress adaptation, notably the ROS catabolising enzymes. Further, a comprehensive comparison on the abiotic stress‐responsive nuclear proteome was performed using the datasets published thus far. These findings might expedite the functional determination of the dehydration‐responsive proteins and their prioritisation as potential molecular targets for better adaptation.     

AffyTrees: facilitating comparative analysis of Affymetrix plant microarray chips

Microarrays measure the expression of large numbers of genes simultaneously and can be used to delve into interaction networks involving many genes at a time. However, it is often difficult to decide to what extent knowledge about the expression of genes gleaned in one model organism can be transferred to other species. This can be examined either by measuring the expression of genes of interest under comparable experimental conditions in other species, or by gathering the necessary data from comparable microarray experiments. However, it is essential to know which genes to compare between the organisms. To facilitate comparison of expression data across different species, we have implemented a Web-based software tool that provides information about sequence orthologs across a range of Affymetrix microarray chips. AffyTrees provides a quick and easy way of assigning which probe sets on different Affymetrix chips measure the expression of orthologous genes. Even in cases where gene or genome duplications have complicated the assignment, groups of comparable probe sets can be identified. The phylogenetic trees provide a resource that can be used to improve sequence annotation and detect biases in the sequence complement of Affymetrix chips. Being able to identify sequence orthologs and recognize biases in the sequence complement of chips is necessary for reliable cross-species microarray comparison. As the amount of work required to generate a single phylogeny in a nonautomated manner is considerable, AffyTrees can greatly reduce the workload for scientists interested in large-scale cross-species comparisons.     

A comparative analysis on the distribution of nymphal populations of some leaf- and planthoppers on rice plant

The frequency distribution of the number of nymphs per hill of rice plant were analyzed for three species of rice leaf- and planthoppers, Nilaparvata lugens, Delphacodes striatella and Nephotettix cincticeps, based on the sampling data obtained during their last generations in the paddy field. For every species concerned, individual distributions were proved to be contagious and to fit well to the negative binomial distribution. Further, it was found that the value of negative binomial parameter k is so stable for same species that a single value of k is applicable for a series of counts with different means, whereas that k differs remarkably among different species: if the reciprocal of the weighted estimate of common k which is an adequate index measuring degree of contagiousness of the distribution, is compared among different species, it is higher in the order of Nilaparvata, Delphacodes and Nephotettix. The ecological and practical implication of constancy and heterogeneity within and among species was discussed respectively as to the value of parameter k.     

Dissecting plant genomes with the PLAZA comparative genomics platform

With the arrival of low-cost, next-generation sequencing, a multitude of new plant genomes are being publicly released, providing unseen opportunities and challenges for comparative genomics studies. Here, we present PLAZA 2.5, a user-friendly online research environment to explore genomic information from different plants. This new release features updates to previous genome annotations and a substantial number of newly available plant genomes as well as various new interactive tools and visualizations. Currently, PLAZA hosts 25 organisms covering a broad taxonomic range, including 13 eudicots, five monocots, one lycopod, one moss, and five algae. The available data consist of structural and functional gene annotations, homologous gene families, multiple sequence alignments, phylogenetic trees, and colinear regions within and between species. A new Integrative Orthology Viewer, combining information from different orthology prediction methodologies, was developed to efficiently investigate complex orthology relationships. Cross-species expression analysis revealed that the integration of complementary data types extended the scope of complex orthology relationships, especially between more distantly related species. Finally, based on phylogenetic profiling, we propose a set of core gene families within the green plant lineage that will be instrumental to assess the gene space of draft or newly sequenced plant genomes during the assembly or annotation phase.