Insight in to the Epilobium L. genus systematics by using multiple data sets and bioinformatic and phylogenetic approaches

Genetic Resources and Crop Evolution - The genus Epilobium of Family Onagraceae is taxonomically a difficult group due to frequent inter-specific hybridization and species morphological overlaps....     

A review of molecular data for the phylogeny of basal hexapods

Molecular data have been increasingly used to study the phylogenetic relationships among many animal taxa, including arthropods. Sometimes they have provided phylogenetic reconstructions that are in conflict with morphological data leading to a re-evaluation of long-standing evolutionary hypotheses. In this paper, we review the major contributions to the phylogeny of hexapods based on molecular data, with emphasis on the relationships of basal hexapod taxa. The placement and the monophyly of the five basal hexapod lineages (the “apterygotes”: Protura, Collembola, Diplura, Microcoryphia and Zygentoma) are one of the hottest issues in arthropod phylogeny. We discuss methods of data collection and analysis, and we describe the areas of conflict and agreement between molecular phylogenies and the evidence provided by morphological characters.     

Aegilops tauschii Coss. molecular phylogeny: nuclear gene Got2 versus chloroplast DNA data

Genetic Resources and Crop Evolution - Aegilops tauschii Coss. phylogenetic tree based on DNA sequences of nuclear gene Got2, about 3000 b.p., studied in 114 accessions of the species was...     

Nature-inspired soluble iron-rich humic compounds: new look at the structure and properties

Purpose

Humic substances (HS) being natural polyelectrolyte macromolecules with complex and disordered molecular structures are a key component of the terrestrial ecosystem. They have remarkable influence on environmental behavior of iron, the essential nutrient for plants. They might be considered as environmental friendly iron deficiency correctors free of synthetic iron (III) chelates disadvantages. The main goal of this study was to obtain water-soluble iron-rich humic compounds (IRHCs) and to evaluate their efficiency as chlorosis correctors.

Materials and methods

A facile preparation technique of IRHCs based on low-cost and available parent material was developed. The iron-containing precursor (ferrous sulfate) was added dropwisely into alkaline potassium humate solution under vigorous stirring and pH-control. A detailed characterization both of organic and inorganic parts of the compounds was provided, the iron species identification was carried out jointly by EXAFS and Mössbauer spectroscopy. Bioassay experiments were performed using cucumber Cucumis sativus L. as target plants. Plants were grown in modified Hoagland nutrient solution, prepared on deionized water and containing iron in the form of IRHCs. Total iron content in dry plants measured by spectrophotometry after oxidative digestion and the chlorophyll a content determined after acetone extraction from fresh plant were used as parameters illustrating plants functional status under iron deficiency condition.

Results and discussion

The high solubility (up to130 g/l) and iron content (about 11 wt%) of the IRHCs obtained allow considering them to be perspective for practical applications. A set of analytical methods has shown that the main iron species in IRHCs are finely dispersed iron (III) oxide and hydroxide nanoparticles. An application of the precursor solution acidification allows to obtain compounds containing a significant part of total iron (up to 30 %) in the form of partly disordered iron (II–III) hydroxysulphate green rust GR(SO₄ ^2?). Bioavailability of iron from IRHCs was demonstrated using bioassay in cucumber plants grown up on hydroponics under iron deficiency conditions.

Conclusions

The application of iron oxides chemistry for humic substance containing solution was proved to be an effective approach to synthesis of IRHCs. Using bioassay on cucumber plants C. sativus L. under iron deficiency conditions, the efficiency of compounds obtained as chlorosis correctors was demonstrated. Application of water-soluble IRHCs led to significant increase of chlorophyll a content (up to 415 % of the blank) and iron content in plants (up to 364 % of the blank) grown up on hydroponics.     

Biochemical diversity in the genus Coffea L.: chlorogenic acids,caffeine and mozambioside contents

Summary The extent and nature of biochemical diversity in green coffee beans was established by a large sampling of genus Coffea, representing nine species from the Guineo-Congolian region, nine species from east Africa and seven species from Madagascar. HPLC analyses were used to determine the contents of caffeine, chlorogenic acids and mozambioside. Data processed by principal component analyses showed the existence of two metabolic pathways. One leads to the synthesis of small quantities of chlorogenic acids (< 2.5% dmb) and caffeine ( < 0.3 % dmb) while the other leads to large concentrations of chlorogenic acids (> 4.5% dmb) and caffeine (> 0.4% dmb). Their distribution in the genus Coffea is discussed in relation to the biogeographic origin of the plant material.     

Morphological and molecular characterization of arbuscular mycorrhizal fungal communities inhabiting the roots and the soil of saffron (Crocus sativus L.) under different agricultural management practices

Crocus sativus L. cultivation is expanding to areas with low soil fertility, where mycorrhizal fungi are supposed to be essential for plants growth and ecosystems functioning. Agricultural practices applied under these conditions should lead to good saffron productivity and quality. Our objective was to study the density and diversity of mycorrhizal fungi populations associated with saffron grown in Taliouine (Morocco) under different agricultural management practices (fertilization type, age and plantation method). Morpho-anatomical studies identified rhizospheric mycorrhizal spores and assessed root colonization by arbuscular mycorrhizal fungi (AMF). Molecular identification of AMF was realized by sequencing the Large Subunit (LSU) rDNA gene region. Among the eleven species of AMF spores identified, Funneliformis and Rhizoglomus species were the most abundant (> 35%). Modern saffron plantation showed higher roots colonization rates (mycorrhization intensity (100%) and frequency (51.6%)), while in traditional plantations lower mycorrhization frequency values were found (17.4%). LSU sequencing identified five AMF genera and three unknown genomic groups, whereas Shannon diversity index indicated that AMF community composition changed significantly according to plantation age and fertilization type. Our results contribute to a better knowledge of saffron AMF communities and open new perspectives for a rational utilization of the agricultural practices for organic saffron production.     

A new gross morphological variation in the genus <Emphasis Type="Italic">Triticum</Emphasis> L.

The new character state “hairy neck” was found in Triticum dicoccoides from Lebanon differing morphologically from that which can be occasionally found as an introgressed character from rye into wheat. The material is newly described as botanical variety: T. dicoccoides var. johnsonii     

广西龙州蝗属一新种记述(直翅目:斑腿蝗科)

记述龙州蝗属一新种,即斑角龙州蝗Longzhouacris annulicornis,sp.nov..模式标本保存在广西大学农学院昆虫标本室.编制了龙州蝗属已知种分类检索表.     

DNA barcoding of important fruit tree species of agronomic interest in the genus Garcinia L. from the Western Ghats

Genetic Resources and Crop Evolution - Garcinia L. is a pantropically distributed genus with high species richness in South East Asia. It is a tropical evergreen plant with distinct morphological...     

The genus Amygdalus L. (Rosaceae): Species relationships, distribution and evolution under domestication

Summary The paper reviews the taxonomic relationships, morphological distinction, geographical distribution and ecological specificities of the twenty six species recognized (by us) in Amygdalus L. It also surveys the intra-genetic structure in this genus stressing the fact that they fall into five groups of closely related vicarious species: (i) Communis group (9 species), (ii) Orientalis group (6 species), (iii) Sect. Chamaeamygdalus (4 species), (iv) Sect. Spartioides (2 species), and (v) Subgenus Dodecandara (5 species). Within each group, species are separated from one another geographically (in few cases by altitude). The only major exception to such allopatric distribution is found in A. communis L., and this is interpreted as an outcome of domestication. Interspecific sterility barriers are absent, or only weakly developed in Amygdalus, and numerous inter-specific hybrids (particularly between the crop and various wild almond species) have been detected. Therefore most (may be all) wild almond species constitute the primary gene-pool of the cultivated nut crop.The combined botanical and archaeological evidene points to the Levant countries as the place where the almond was taken into cultivation. Wild forms of A. communis are very likely native only to this area. Also the earliest archaeological signs of almond domestication come from this area.     

Endangered species management requires a new look at the benefit of fire: The Cape Sable seaside sparrow in the Everglades ecosystem

Although disturbance processes play important roles in maintaining habitat heterogeneity, the potential effects of such processes on rare or endangered species is virtually unknown and difficult to test. We use an unplanned fire, which burned half of a long-term study plot, as a natural experiment to test the effects of fire on the federally endangered Cape Sable seaside sparrow in Everglades National Park. By implementing a before-after-control-impact study design we determine the mechanistic link between fire and demography of this endangered sparrow. Our results show that while the sparrow tolerates fire, neither sparrow density nor nesting success are enhanced by fire, which runs contrary to the current paradigm in which sparrows are expected to benefit and therefore require fire for persistence. Our results caution against the assumption that occupancy of disturbance-prone habitat automatically suggests dependence on disturbance. Land managers must prevent large and frequent fires from burning occupied sparrow habitat to best manage for the species. Moreover, it is imperative that more studies focus on the effects of disturbance processes on rare and endangered species in order to prevent further loss of biodiversity.     

Pteroside A2--a new illudane-type sesquiterpene glucoside from pteridium caudatum L. Maxon,and the spectrometric characterization of caudatodienone

Fractionation of an extract of Pteridium caudatum L. Maxon. (syn P. aquilinum L. Kuhn var. caudatum) which had earlier yielded the illudane-type sesquiterpene glucosides, ptaquiloside (1a), isoptaquiloside (1b), and caudatoside (1c) afforded a mixture containing 1a and two minor components. Preparative HPLC afforded ptaquiloside Z (1d) and a new pteroside glucoside (pteroside A2) (3e), which was identified using a combination of mass spectral and one- and two-dimensional NMR analyses. The (1)H and (13)C NMR and mass spectrometric characterization of caudatodienone (2b), an unstable dienone derived from the degradation of caudatoside (1c) in pyridine solution, and the GC-MS characterization of some pterosin-type degradation products produced by reacting this solution with cosolvents is also reported.     

RAPD and seed coat morphology variation in annual and perennial species of the genus Cicer L.

Molecular and morphological variation of six perennial and five annual species including domesticated chickpea, C. arietinum, were inferred on the basis of RAPD and S.E.M. seed coat features using three outgroup taxa (Lens ervoides, Lathyrus japonica and Pisum sativum). Of the 66 decamer arbitrary primers tested, eight primers revealed 87 informative fragments. Neighbor-joining cluster analysis using Jaccard's coefficient of similarity on the basis of polymorphic fragments indicated a narrow variation in C. arietinum and recognized two major clusters in the genus Cicer. The first one included four species of sect. Monocicer: C. echinospermum, C. arietinum, C. reticulatum and Iranian material of C. bijugum. The second cluster contained annual and perennial species belonging to sections Chamaecicer, Polycicer and Acanthocicer. The character state of morphological and ecological traits on the RAPD phenogram indicated no monophyletic incision. Our results suggested that the high genetic difference between annual and perennial species might be regarded as a rapid speciation of section Monocicer. Reconsideration of traditional classification of sections Polycicer and Acanthocicer is necessary. The Desi and Kabuli types of C. arietinum could not be separately grouped at the DNA level, and the low level of genetic variation of C. arietinum may result from a bottleneck during the domestication process.     

From plant communities to landscapes in conservation inventories: A look at the nature conservancy (USA)

The Nature Conservancy (TNC—USA) has developed an efficient system for inventory and evaluation of ‘elements-of-diversity’. The major components of this system are a ‘fine filter’ for species inventory and a ‘coarse filter’ for community-type inventory. As in traditional vegetation science, community sampling and classification are restricted to relatively homogeneous stands and avoid edges, ecotones, and disturbed areas. TNC employs a habitat-based system of natural communities to complement plant community classification. This system is used to identify stands that cumulatively encompass the full range of variation within each defined natural community type. Ecological relationships among community-types in real landscapes, however, are not accounted for.This paper reviews some important ecological functions of heterogeneous landscapes, which are not necessarily protected by conservation strategies that focus on separate, homogeneous community-types. Recommendations to expand TNC's coarse filter to landscapes include: (1) Disturbance regime and regeneration patterns should be evaluated for each major community-type, and for each site representing a type or group of types; (2) Functional combinations of community-types and developmental stages (landscape mosaics) should be addressed in the TNC system; (3) Landscape context (e.g., surrounding habitat types and connectivity) for a site is as important as the habitat content (e.g., the rarity or quality of community-types present). Attention to landscape-level patterns and processes will be helful for evaluating large sites that are composed of many community-types, and in setting selection and stewardship priorities for sites for any size that are surrounded by dissimilar habitat.     

Reciprocal compatibility within the genus Pisum L. as studied in F1 hybrids: 4. Crosses within P. sativum L. subsp. elatius (Bieb.) Aschers. et Graebn.

Genetic Resources and Crop Evolution - Five accessions representing divergent lineages of wild peas (Pisum sativum subsp. elatius) were crossed with each other in both directions and also...     

Genetic diversity and relationships in Corchorus olitorius (Malvaceae s.l.) inferred from molecular and morphological data

In this study, we investigated the genetic diversity and relationships in C. olitorius by analysing populations representing different distribution areas, and developed a hypothesis on the origin and spread of the species in the pantropics. We employed amplified fragment lengths polymorphism (AFLP) and morphometric analyses in a total of 101 C. olitorius accessions. Results of both data sets are mostly congruent. The molecular analysis indicated generally low genetic diversity within populations and the Nei’s gene diversity (H_e) ranged from 0.0457 to 0.0955 with a mean of 0.0763. Qualitative traits, especially related to leaf morphology, branching habit and stipule color were the taxonomically most informative characters. The highest morphological variability occurred within African accessions, indicating that this species originally evolved in Africa. In both analyses, the Asian materials were nested within African populations, especially with those from North and East Africa. This indicates an African origin of the species and we hypothesise that dispersal occurred via the Mediterranean–Indian trade routes instead of natural migration along the coasts from western Africa to the Indian subcontinent. Both analyses revealed materials from Ethiopia to be quite distinct. The highest number of private bands (N?=?35), percent polymorphism (29.29%), and gene diversity (0.0955) were also detected in wild accessions collected from Ethiopia, suggesting a long-term spatial isolation of C. olitorius populations in the country. Germplasm samples from this region could therefore be a useful source of genetic variation in jute breeding programs.     

Direct comparison of individual substrate utilization from a CLPP study: A new analysis for metabolic diversity data

For over a decade, community level physiological profile (CLPP) assays, which assess a microbial community's capacity to metabolize specific sole carbon sources under defined laboratory conditions, have been popular for study of environmental soil samples. One such assay, BiOLOG™ allows for the colorimetric measurement of metabolism through the reduction of a tetrazolium dye, which yields optical density (OD) data for each substrate. Bacterial communities are extracted from soil and 150 μL of this extract is inoculated directly into each well of the microtitre plate. The combined metabolic data obtained are most often analyzed with multivariate statistical analyses, such as principal component analysis (PCA). The objectives of this study were (1) to develop a simple, visual, statistically valid method of determining community capabilities to utilize specific substrates in CLPP studies and (2) to test the number of samples needed for such discrimination to be reliable. This was done by direct comparison of the OD values obtained for two closely related microbial communities (surface and subsurface soil), plotted against a one-to-one (y=x) line. Due to variability in the portion of the soil microbial community inoculated into the individual test wells, the accuracy of the method was dependent on the number of replicates analyzed. A variety of data set sizes were tested, from n=3 samples/soil depth to n=40 samples/depth. The method was statistically valid for all data sets tested. Those substrates that deviated from the one-to-one line consistently had F values greater than 1. Additionally, data sets of n=30,35 and 40 samples/depth consistently allowed identification of the eight substrates whose metabolism varied significantly between the two test soil communities. In conclusion, this one-to-one comparison has been shown to be a statistically valid analytical method to compare individual substrate usage between soils.