Geographic and temporal distributions of four genotypes found in Erysiphe gracilis var. gracilis,a powdery mildew of evergreen oaks (Erysiphales)

A survey of 402 samples of Erysiphe gracilis var. gracilis on evergreen oaks collected from a wide area of western Japan showed that they were divided into four distinct genotypes each forming a separate clade with high bootstrap support, which were referred to as E. hiratae (genotype I), E. uncinuloides (genotype II), E. gracilis s. str. (genotype III), and E. pseudogracilis (genotype IV) in a separate taxonomic treatment. However, there are no clear differences in geographic distributions among these four genotypes. Quercus myrsinifolia was only infected by genotype II and Q. salicina only by genotype IV, whereas Q. glauca was infected by all four. These results strongly suggest an association between host species and speciation of these genotypes. A further 312 samples of Q. glauca with E. gracilis s. lat. colonies were collected from four locations in the Mie University campus to investigate frequency of genotypes I and II every month from May 2015 to January 2016. No temporal isolation was found in genotype frequencies. These genotypes frequently co-existed on a single leaf surface, especially at the locations disturbed by human activities. Two oak powdery mildews, E. gracilis s. lat. and Cystotheca wrightii, produced conidia only one month a year and their life cycle differed from most other powdery mildew species. This suggests that these oak mildews developed their unique life cycles to synchronize with the life cycle of evergreen oaks.     

First record of Erysiphe quercicola (Ascomycota: Erysiphales) on species of Quercus subgenus Cyclobalanopsis (evergreen oaks,Fagaceae)

During the DNA sequence analyses of specimens on Quercus subgenus Cyclobalanopsis deposited as Erysiphe gracilis or Cystotheca wrightii, some specimens exhibited DNA sequences that are different from the sequences of the two species. Based on BLAST search and morphological observations, the true causal agent was identified as E. quercicola. This is the first record of E. quercicola on species of subgenus Cyclobalanopsis. Previous studies revealed that E. quercicola is plurivorous infecting a wide range of tropical fruit trees and woody plants. Further studies are needed to address the question as to why only E. quercicola infect species of subgenus Cyclobalanopsis.     

Flow cytometry distinction between species and between landraces within Lathyrus species and assessment of true-to-typeness of in vitro regenerants

The genus Lathyrus includes a number of neglected wild relatives of pea with potential as genetic resources for acquisition of stress resistance traits, but, due to little breeding, genotypes under culture are mainly landraces and seldom true varieties. Development of in vitro approaches for Lathyrus is also limited, and assessments of nuclear DNA content, for taxonomical or breeding purposes, are sparse. Genome size and AT/GC ratio were determined by flow cytometry, allowing for distinction between protein and forage L. sativus, L. cicera, L. ochrus and L. clymenum and the ornamental sweet pea (L. odoratus), and also between landraces within L. sativus L. and L. cicera L. In addition, explants from in vitro seedlings of eight genotypes from the five Lathyrus species above were cultivated in vitro, plant regeneration was achieved for all landraces and species, and the nuclear DNA content of the regenerants was compared with that of their mother plants, whereby the true-to-typeness of such regenerants was confirmed.     

Bacterial communities associated with the pitcher fluids of three Nepenthes (Nepenthaceae) pitcher plant species growing in the wild

Nepenthes pitcher plants produce modified jug-shaped leaves to attract, trap and digest insect prey. We used 16S rDNA cloning and sequencing to compare bacterial communities in pitcher fluids of each of three species, namely Nepenthes ampullaria, Nepenthes gracilis and Nepenthes mirabilis, growing in the wild. In contrast to previous greenhouse-based studies, we found that both opened and unopened pitchers harbored bacterial DNA. Pitchers of N. mirabilis had higher bacterial diversity as compared to other Nepenthes species. The composition of the bacterial communities could be different between pitcher types for N. mirabilis (ANOSIM: R = 0.340, p < 0.05). Other Nepenthes species had similar bacterial composition between pitcher types. SIMPER showed that more than 50 % of the bacterial taxa identified from the open pitchers of N. mirabilis were not found in other groups. Our study suggests that bacteria in N. mirabilis are divided into native and nonnative groups.     

Spatial associations among major tree species in a cool-temperate forest community under heterogeneous topography and canopy conditions

Analysis of the spatial pattern of plants may provide insight into the processes and mechanisms that promote species coexistence and community organization. Using torus-translation tests and point-pattern analyses for a heterogeneous Poisson process, we investigated habitat association and intra- and inter-specific spatial relationships of six major tree species in a cool-temperate forest community. All stems ≥5 cm in diameter at breast height were mapped on a 1.4-ha (100 × 140 m) plot and the topographic conditions (convexity and slope degree) and canopy state were assessed. Our results showed that all six species exhibited habitat associations with topographic and/or canopy conditions except for Magnolia salicifolia. Intra-specific aggregation was found for Acer japonicum, M. salicifolia, and Hamamelis japonica var. obtusata. Community-wide analysis of the inter-specific spatial patterns showed mainly mixed or partially overlapped patterns at a scale of up to 30 m, whereas individual pairwise analyses of inter-specific patterns revealed that Fagus crenata was positively associated with two Acer species and M. salicifolia at a spatial scale of up to 5 m. These results highlight that scale-dependant ecologically important processes, such as species-specific habitat preference, regeneration mode, seed dispersal, facilitation and niche complementarity, may operate simultaneously to shape tree distributional patterns, although their presence/absence as well as relative importance vary among species. Given the complexity of the process and mechanisms promoting species coexistence and community organization, more attention should be given to the effect of spatial scale in analyzing the spatial patterns of tree species in forest communities.     

Erysiphe azerbaijanica and E. linderae: Two new powdery mildew species (Erysiphales) belonging to the Microsphaera lineage of Erysiphe

Two new species, Erysiphe azerbaijanica on Castanea sativa and E. linderae on Lindera praecox, both belonging to the Microsphaera lineage of the genus Erysiphe are described based on morphological and molecular data. Erysiphe azerbaijanica is distinguished from other Erysiphe species occurring on Castanea spp. by its cylindrical conidia with a length/width ratio of 2–3.6, longer conidiophore, and foot-cells. Molecular analyses indicated that this species forms a clade of its own, supporting the morphological observations. Molecular phylogenetic analyses showed that E. blasti s. lat. is divided into two genetically differentiated groups associated with different host species. Based on the sequence differences in the 28S rRNA gene and ITS region, connected with differences in the number and length of appendages, the fungus on L. praecox is described as a new species, E. linderae.     

Production of a thermal stress resistant mutant Euglena gracilis strain using Fe-ion beam irradiation

Euglena gracilis is a common phytoplankton species, which also has motile flagellate characteristics. Recent research and development has enabled the industrial use of E. gracilis and selective breeding of this species is expected to further expand its application. However, the production of E. gracilis nuclear mutants is difficult because of the robustness of its genome. To establish an efficient mutation induction procedure for E. gracilis, we employed Fe-ion beam irradiation in the RIKEN RI beam factory. A decrease in the survival rate was observed with the increase in irradiation dose, and the upper limit used for E. gracilis selective breeding was around 50 Gy. For a practical trial of Fe-ion irradiation, we conducted a screening to isolate high-temperature-tolerant mutants. The screening yielded mutants that proliferated faster than the wild-type strain at 32?°C. Our results demonstrate the effectiveness of heavy-ion irradiation on E. gracilis selective breeding.     

Taxonomic study on the genus Eremopyrum (Ledeb.) Jaub. et Spach (Poaceae) in Turkey

In this study, we examined whether a satisfactory infrageneric grouping in Eremopyrum (Ledeb.) Jaub. & Spach can be achieved with the help of cluster analysis based on external vegetative and floral morphological characters of specimens either gathered from the field or borrowed from various herbaria. Twenty morphological characters were chosen and scored for 36 populations representing the genus. The data were subjected to numerical taxonomic analyses, and a phenogram was obtained by applying Gower general similarity index. The results of this study suggest that there are basically five species in Turkey, namely E. triticeum (Gaertner) Nevski, E. orientale (L.) Jaub. & Spach, E. distans (K. Koch) Nevski, E. bonaepartis (Sprengel) Nevski, and E. confusum Melderis. For the first time a new variety, E. bonaepartis (Sprengel) Nevski. var. aristatum Cabi & Do?an, is proposed along with two new combinations: E. bonaepartis (Sprengel) Nevski. var. sinaicum (Steudel) Cabi & Do?an and E. confusum Melderis var. sublanuginosum (Drob.) Cabi & Dogan. An account of Eremopyrum in Turkey is given, including a key to the species and varieties, and a general indication of their distribution.     

Transferability of simple sequence repeat (SSR) markers developed in guava (Psidium guajava L.) to four Myrtaceae species

Present study demonstrated the cross-genera transferability of 23 simple sequence repeat (SSR) primer pairs developed for guava (Psidium guajava L.) to four new targets, two species of eucalypts (Eucalyptus citriodora, Eucalyptus camaldulensis), bottlebrush (Callistemon lanceolatus) and clove (Syzygium aromaticum), belonging to the family Myrtaceae and subfamily Myrtoideae. Off the 23 SSR loci assayed, 18 (78.2 %) gave cross-amplification in E. citriodora, 14 (60.8 %) in E. camaldulensis and 17-17 (73.9 %) in C. lanceolatus and S. aromaticum. Eight primer pairs were found to be transferable to all four species. The number of alleles detected at each locus ranged from one to nine, with an average of 4.8, 2.6, 4.5 and 4.6 alleles in E. citriodora, E. camaldulensis, C. lanceolatus and S. aromaticum, respectively. The high levels of cross-genera transferability of guava SSRs may be applicable for the analysis of intra- and inter specific genetic diversity of target species, especially in E. citriodora, C. lanceolatus and S. aromaticum, for which till date no information about EST-derived as well as genomic SSR is available.     

Equisetum (Equisetaceae) species or hybrids? ISSR fingerprinting profiles help improve diagnoses based on morphology and anatomy

The applicability of “inter-simple sequence repeats” (ISSR)-PCR as a molecular character complex for differentiation of Equisetum taxa is described with a special focus on the detection of hybrids. All Central European Equisetum species and the four most frequent hybrids are considered: E. arvense, E. fluviatile, E. telmateia, E. palustre, E. sylvaticum, E. pratense, E. × litorale, E. ramosissimum, E. hyemale, E. variegatum, E. × moorei, E. × trachyodon and E. × meridionale. The ISSR banding patterns are highly typical for each species. The positions of the clusters of hybrid taxa prove their hybrid origin and enable identification of the parental species. Genetic similarities of populations suggest that in some species vegetative reproduction predominates (e.g. E. arvense), whereas for others (e.g. E. telmateia) sexual reproduction seems to be more frequent. In addition to the molecular analyses, the characteristics of stem cross sections of the four hybrids and their parental species are shown and discussed.     

Molecular phylogeny reveals the presence of cryptic speciation within Erysiphe japonica (≡ Typhulochaeta japonica), a powdery mildew on Quercus spp.

Molecular phylogenetic analyses based on 28S, ITS and IGS rDNA sequences indicate that Erysiphe japonica (≡ Typhulochaeta japonica) consists of two different genetic groups, one group on Quercus aliena, Q. robur and Q. serrata, and another group on Q. crispula var. crispula and Q. crispula var. horikawae. As morphological difference between the two groups are not yet marked distinctly, we suppose that the process of speciation has not yet been finished and propose a new variety, E. japonica var. crispulae, for the latter group based on the difference in host range and the distinct genetic segregation. Quercus robur (pedunculate oak) is a new host of E. japonica.     

Reticulate evolution in the apogamous Dryopteris varia complex (Dryopteridaceae,subg. Erythrovariae,sect. Variae) and its related sexual species in Japan

Apogamous fern species are often difficult to distinguish from related species because of their continuous morphological variations. To clarify the genetic relationships among the members of the Dryopteris varia complex, we analyzed the nucleotide sequences of the plastid gene rbcL and the nuclear gene PgiC. We also analyzed the diploid sexual species D. caudipinna and D. chinensis, which have not been included in the complex, but were recently shown to be closely related to the complex in a molecular phylogenetic study. The PgiC sequences of the diploid sexual species, D. varia, D. saxifraga, D. sp. ‘protobissetiana’ (undescribed diploid sexual species), D. caudipinna, and D. chinensis, were well differentiated and hence designated A, B, C, D, and E, respectively. Thus, the PgiC constitution of apogamous species in the complex was as follows: D. bissetiana, B + C; D. kobayashii, B + C + E); D. pacifica, A + C, A + B + C, or A + C + D; D. sacrosancta, A + C + E; and D. saxifragivaria, B + C. These results suggest that these apogamous species are formed by hybridizations of species including not only the three diploid sexual species of the D. varia complex (A, B, and C) but also the two diploid sexual species D. caudipinna (D) and D. chinensis (E), which do not belong to the complex.     

<Emphasis Type="Italic">Leandra altomacaensis</Emphasis> (Melastomataceae), a new species from Brazil

Leandra altomacaensis (sect. Oxymeris), a new endemic species of Melastomataceae from Rio de Janeiro, Brazil, is described and illustrated. Diagnostic characteristics of the species are the leaves sparsely stellulate-lepidote, triplinerved, and calyx lobes small, with apex acute-apiculate. Leandra gracilis var. glazioviana is proposed as a synonym of this new species.     

Diversity of Fusarium species and mycotoxins contaminating pineapple

Pineapple (Ananas comosus var. comosus) is an important perennial crop in tropical and subtropical areas. It may be infected by various Fusarium species, contaminating the plant material with mycotoxins. The aim of this study was to evaluate Fusarium species variability among the genotypes isolated from pineapple fruits displaying fungal infection symptoms and to evaluate their mycotoxigenic abilities. Forty-four isolates of ten Fusarium species were obtained from pineapple fruit samples: F. ananatum, F. concentricum, F. fujikuroi, F. guttiforme, F. incarnatum, F. oxysporum, F. polyphialidicum, F. proliferatum, F. temperatum and F. verticillioides. Fumonisins B₁–B₃, beauvericin (BEA) and moniliformin (MON) contents were quantified by high-performance liquid chromatography (HPLC) in pineapple fruit tissue. Fumonisins are likely the most dangerous metabolites present in fruit samples (the maximum FB₁ content was 250 μg g^?1 in pineapple skin and 20 μg ml^?1 in juice fraction). In both fractions, BEA and MON were of minor significance. FUM1 and FUM8 genes were identified in F. fujikuroi, F. proliferatum, F. temperatum and F. verticillioides. Cyclic peptide synthase gene (esyn1 homologue) from the BEA biosynthetic pathway was identified in 40 isolates of eight species. Based on the gene-specific polymerase chain reaction (PCR) assays, none of the isolates tested were found to be able to produce trichothecenes or zearalenone.     

Seed size and recruitment limitation influence seedling establishment in three tallgrass prairie species

A seed size–seed number tradeoff predicts that large numbers of seeds have an establishment advantage under low levels of competition, while large seed size is advantageous under asymmetric competition. Testing these predictions in the context of tallgrass prairie restoration should increase predictability of outcomes of species composition—restoration technique combinations. I conducted field and greenhouse experiments comparing seedling establishment among three tallgrass prairie species with different seed mass-seed number combinations, but with similar mass of seeds sown. Species were prairie dock [Silphium terebinthinaceum, mass = 33.2 + 2.1 mg ( \(\overline{x}\)  + SE, n = 100)], wild quinine (Parthenium integrifolium, mass = 3.1 + 0.3 mg), and smooth blue aster (Symphyotrichum laeve var. laeve, mass = 0.53 + 0.02 mg). Seeds were sown into mowed or tilled plots with shade and mulch treatments in an old field in northeastern Illinois USA, and seeds were sown into containers with or without vegetative cover in a greenhouse. In mowed plots, species with larger numbers of seeds sown had higher seedling densities. In tilled plots, seedling densities of the large-seeded Silphium were reduced less by shade than the small-seeded Parthenium. Symphyotrichum, however, did not respond to treatments as expected based on its seed size. High relative growth rate possibly increased Symphyotrichum seedling establishment in competitive environments. Results of this study demonstrated recruitment limitation when seedlings established into existing vegetation, and suggest that species composition resulting from specific seeding rates during prairie restoration may be more predictable when species are interseeded into existing vegetation, than when seeds are sown into tilled fields.     

Genetic relations among basil taxa (Ocimum L.) based on molecular markers, nuclear DNA content, and chromosome number

Twenty-eight basil accessions including six Ocimum species and six botanical varieties or cultivars of O. basilicum were studied using molecular markers, nuclear DNA content, and chromosome counting. This is the first study reporting the nuclear DNA content in the genus Ocimum. The results supported the existence of more infrageneric groups within the genus. The section Ocimum was further divided into two separate clades. The first clade contained the accessions belonging to different botanical varieties and cultivars of O. basilicum as well as O. minimum, indicating that the separate species rank of O. minimum was not justified. The second clade, comprising O. americanum, O. africanum, and two O. basilicum var. purpurascens accessions, could represent a set of allopolyploid species sharing some common parental genomes. O. tenuiflorum was the most divergent species according to genetic distance; it had the smallest genome size, organized in small chromosomes, and the lowest chromosome number. Chromosome data obtained in our research could indicate that the basic chromosome number for species belonging to section Ocimum is x = 12. This suggestion implies that species belonging to O. basilicum clade are tetraploids, while species belonging to O. americanum clade are hexaploids. It seems that the basic chromosome number for O. gratissimum could be x = 10 and for O. tenuiflorum x = 9. The differences in genome size and chromosome number among Ocimum species indicate that evolution of their genomes was accompanied by both sequence deletion/amplification and chromosome rearrangements and polyploidization.     

Genetic differentiation in Elaeocarpus photiniifolia (Elaeocarpaceae) associated with geographic distribution and habitat variation in the Bonin (Ogasawara) Islands

Gene flow between populations in different environmental conditions can be limited due to divergent natural selection, thus promoting genetic differentiation. Elaeocarpus photiniifolia, an endemic tree species in the Bonin Islands, is distributed in two types of habitats, dry scrubs and mesic forests. We aim to elucidate the genetic differentiation in E. photiniifolia within and between islands and between the habitat types. We investigated genotypes of 639 individuals from 19 populations of E. photiniifolia and its closely-related E. sylvestris at 24 microsatellite loci derived from expressed sequence tags. The data revealed genetic differentiation (1) between E. photiniifolia and E. sylvestris (0.307 ≤ F _ST ≤ 0.470), (2) between the E. photiniifolia populations of the Chichijima and Hahajima Island Groups in the Bonin Islands (0.033 ≤ F _ST ≤ 0.121) and (3) between E. photiniifolia populations associated with dry scrubs and mesic forests in the Chichijima Island Group (0.005 ≤ F _ST ≤ 0.071). Principal coordinate analysis and Bayesian clustering analysis also showed that genetically distinct groups were associated with the habitat types, and isolation by distance was not responsible for the genetic differentiation. These findings suggest that E. photiniifolia is divided into genetically differentiated groups associated with different environmental conditions in the Bonin Islands.     

The effects of algae species and densities on the population growth of the marine rotifer, Colurella dicentra

Colurella dicentra clones isolated from bay water in the Mississippi Gulf Coast were cultured with artificial seawater. Experiments were conducted to determine the effects of six algae species (Nannochloropsis oculata, Tetraselmis chuii, Chaetoceros gracilis, Rhodomonas salina, Isochrysis galbana, and Prorocentrum micans), six C. gracilis densities, and six N. oculata densities (25,000, 50,000, 100,000, 250,000, 500,000, and 1,000,000 cells ml^− 1) on C. dicentra population growth. Algae type influenced rotifer production (p < 0.0001). C. gracilis treatment (9120 ± 3351SD) produced the highest number of rotifers followed by N. oculata (5760 ±2232SD). P. micans had the lowest number of rotifers, although not significantly different from numbers in T. chuii, R. salina, and I. galbana treatments (p > 0.05).The population growth rate (r) varied with algae species treatment. The highest values were recorded for C. gracilis treatment (0.22 to 0.26 d^− 1), followed by N. oculata (0.21 to 0.24 d^− 1), and the lowest for P. micans (− 0.19 to 0.14 d^− 1). C. gracilis and N. oculata densities had significant effects (p < 0.0001) on C. dicentra population growth. The highest rotifer production was recorded at a C. gracilis density of 100,000 cells ml^− 1, followed by 250,000 cells ml^− 1 and 50,000 cells ml^− 1. Algae densities of 500,000 cells ml^− 1 and above produced the lowest rotifer numbers. Population growth rate (r) varied with C. gracilis densities. The highest values were observed for C. gracilis concentrations of 100,000 cells ml^− 1 (0.17 to 0.19 d^− 1), and the lowest for concentrations of 500,000 cells ml^− 1 and above (− 0.19 to 0.09 d^− 1). The 100,000 cells ml^− 1N. oculata density gave the highest rotifer production followed by 50,000, 250,000, 25,000, and 500,000 cells ml^− 1. Algae densities of 1,000,000 cells ml^− 1 produced the lowest rotifer numbers. Population growth rate (r) varied with N. oculata densities, with the highest values obtained for algae densities of 100,000 cells ml^− 1 (0.35 to 0.40 d^− 1), and the lowest for concentrations of 1,000,000 cells ml^− 1 (0.05 to 0.012 d^− 1). This is the first report of C. dicentra in Mississippi Coastal waters, and perhaps the smallest marine rotifer species (93 by 49 μm) ever cultured successfully.     

Phylogeography of ten native herbaceous species in the temperate region of Japan: implication for the establishment of seed transfer zones for revegetation materials

Revegetation using native species requires the development of seed transfer zones that capture genetic distinctiveness and adaptive potentials while avoiding potential maladaptation and genetic contamination by exotic genotypes. Delineation based on phylogeographic information has recently been used to establish seed transfer zones; however, only a few herbaceous species that are suitable for revegetation have been investigated in the temperate regions of Japan. We investigated the phylogeography of non-coding regions of chloroplast DNA of ten native species in the temperate regions of Japan. Although no species showed clear-cut geographical distributions of the 2–14 haplotypes identified, spatially constrained Bayesian clustering showed two clusters in five species (Calamagrostis epigejos, Eragrostis ferruginea, Imperata cylindrica, Microstegium japonicum, and Microstegium vimineum) but not for others. Posterior modes of clusters for I. cylindrica and M. vimineum showed delineations at Chubu (the middle of Honshu Island), which divide the study region into northeastern and southwestern regions, indicating that these species had recovered from glacial refugia. Posterior mode of cluster for E. ferruginea showed that one consists of a coastal zone along the Pacific Ocean side of western Japan, while the other consists of the remaining area, indicating range expansion from south coast to north. Delineation of C. epigejos and M. japonicum were unclear. The mixed results indicated that establishing seed transfer zones for herbaceous species in Japan will require phylogeographical studies on a wide range of species that may be suitable for revegetation.     

Evaluating species nonmonophyly as a trait affecting genetic diversity: a case study of three endangered species of Antirrhinum L. (Scrophulariaceae)

Molecular markers are routinely used to assess levels of diversity within and among populations, particularly with regard to species of conservation concern. However, when interpreting the level and partitioning of diversity observed, an implicit assumption is often made that the populations of the species in question form a monophyletic group. We tested this assumption in three endemics of Antirrhinum (A. charidemi, A. subbaeticum, and A. valentinum) using 79 nuclear [internal transcribed spacer (ITS)] and 85 plastid (psbA-trnH, trnT-trnL, trnK-matK, trnS-trnG) sequences representing multiple accessions of each of 24 Antirrhinum species (single accession of A. cirrhigerum). These species share six life history traits implicated in levels of genetic diversity, and have been the subject of previous population genetic studies. Populations of all three species formed monophyletic groups on ITS analysis. In contrast, none of the three species formed monophyletic groups on plastid sequence analysis: populations of A. charidemi fall in a monophyletic group including one accession of A. mollissimum, populations of A. subbaeticum form a polyphyletic group with plastid sequences shared with A. pulverulentum, and populations of A. valentinum are unresolved within a clade containing six other species. Lack of monophyly using plastid sequences is interpreted as a combination of shared ancestral polymorphism and hybridization in a reticulate evolutionary history of these species. Monophyly in the ITS tree may reflect a more recent sequence homogenization. We draw attention to the evaluation of species monophyly alongside the contribution of other life history traits in the historical interpretation of the level and partitioning of genetic diversity, and its use in recommendations for species conservation programs.