Epichloe canadensis, a new interspecific epichloid hybrid symbiotic with Canada wildrye (Elymus canadensis)

Many Epichlo? endophytes found in cool-season grasses are interspecific hybrids possessing much or all of the genomes of two or three progenitors. Here we characterize Epichlo? canadensis sp. nov., a hybrid species inhabiting the grass species Elymus canadensis native to North America. Three distinct morphotypes were identified that were separated into two groups by molecular phylogenetic analysis. Sequence analysis of the translation elongation factor 1-α (tefA) and β-tubulin (tubB) genes revealed two copies in all isolates examined. Phylogenetic analyses indicated that allele 1 of each gene was derived from Epichlo? amarillans and allele 2 from Epichlo? elymi. This is the first documentation of an interspecific hybrid endophyte derived from parents of strictly North American origins. Alkaloid gene profiling using primers specific to genes in the peramine, loline, indole-diterpene and ergot alkaloid pathways may indicate chemotypic variation in the ergot alkaloid and loline pathways between the assigned morphotypes. All isolates have the gene enabling the production of peramine but lack genes in the indole-diterpene biosynthesis pathway. Morphology and phylogenetic evidence support the designation of isolates from El. canadensis as a new interspecific hybrid species.     

中国禾本科植物内生真菌研究4. Epichloё yangzii的人工杂交

作者首先研究Epichloё yangzii在植株上的人工杂交,明确了供试菌株的交配型。然后将分离自无子座鹅观草属植物的23株"Neotyphodium属"真菌孢子分别与E.yangzii的子座杂交,其中发现有21株与E.yangzii(mat-1,mat-2)杂交不亲和,有2株与E.yangzii(mat-1)杂交亲和。利用tubB基因片段对8株"Neotyphodium属"真菌菌株进行系统发育分析,结果表明与E.yangzii杂交亲和的2个菌株和E.yangzii聚为一枝,而其它6个菌株形成独立的分枝,进一步证实了这2个菌株是有时在宿主植物上不形成子座的E.yangzii。这说明了在宿主植物上的人工杂交是区别有时不产子座的E.yangzii和Neotyphodium属真菌的有效手段。     

A new species of Epichloë symbiotic with Chinese grasses

Epichlo? species are fungal symbionts (endophytes) of grasses, six European and four North American biological species in genus Epichlo? have been described in previous researches. In this study we describe a new Epichlo? species, Epichlo? yangzii Li et Wang, found in natural symbioses with Roegneria kamoji native to China. We investigated the host specificity, morphology, interfertility tests and molecular phylogenetic evidences of this new species. The results indicated that E. yangzii is host specific and seedborne. Most morphological characteristics of this new species are typical in the genus. However differences are evident in several features including size of perithecia, asci and ascospores. In mating tests E. yangzii was not interfertile with E. elymi isolates from related hosts in genera Elymus. Phylogenetic relationships based on sequences of beta-tubulin gene (tub2) introns and translation elongation factor 1-alpha gene (tef1) introns showed that members of the new species grouped into exclusive clades with high bootstrap value.     

The evolutionary origins of three new Neotyphodium endophyte species from grasses indigenous to the Southern Hemisphere

Members of the genus Neotyphodium are asexual, seedborne, protective fungal endophytes of cool season grasses that have likely evolved either directly from sexual Epichlo?; species, or by the interspecific hybridization of distinct lineages of Epichlo?; and Neotyphodium. We investigated the evolutionary origins of Neotyphodium endophytes from several grasses that are indigenous to the Southern Hemisphere using a multiple-gene phylogenetic approach. Intron regions of the genes encoding β-tubulin (tub2), translation elongation factor 1-α (tef1) and actin (act1) were amplified by polymerase chain reaction and sequenced. Phylogenetic analyses of these sequences, aligned with homologous sequences from Epichlo?; spp., revealed the evolutionary origins of the Southern Hemisphere endophytes, where one lineage of apparently non-hybrid origin, and three lineages of unique interspecific hybrid origin were identified. On the basis of morphology, host range and evolutionary history, we propose three new species of Neotyphodium. Neotyphodium aotearoae was isolated from Echinopogon ovatus populations from New Zealand and Australia, and comprised a unique, apparently non-hybrid lineage within the Epichlo?; species phylogeny. In contrast, an interspecific hybrid lineage was identified from two Australian Ec. ovatus populations, whose ancestry apparently involved lineages closely related to extant E. festucae and an E. typhina genotype similar to that of isolates from Poa pratensis. Endophytes infecting South African Melica racemosa and M. decumbens (dronkgras) appeared to be hybrids of E. festucae and N. aotearoae or close relatives. The names N. australiense and N. melicicola are proposed for these two hybrid lineages, respectively. The origin of N. tembladerae, an established endophyte species from South American Poa and Festuca spp., was also investigated. Neotyphodium tembladerae appeared to be of hybrid origin, involving E. festucae and an E. typhina genotype similar to that of isolates from Poa nemoralis. The results of this study highlight the widespread occurrence of interspecific hybrid Neotyphodium lineages on a global scale, and the extent of endophyte gene-flow between the Northern and Southern Hemispheres.     

New choke diseases and their molecular phylogenetic analysis in Agropyron ciliare var. minus and Agropyron tsukushiense var. transiens

Choke diseases were surveyed in two closely related grass species, Agropyron ciliare var. minus and Agropyron tsukushiense var. transiens, in Shiga Prefecture, Japan. Perithecia and ascospores were not observed in either case. Stromata on A. ciliare var. minus enclosed and sterilized young inflorescences, as in the typical choke symptoms by Epichlo? typhina. On the other hand stromata on A. tsukusiense var. transiens thinly covered mature spikes with white epiphyllous hyphae, as in stromata of Ephelis spp. The fungal isolates produced typical Neotyphodium-type conidia. Molecular phylogenetic analyses using the beta-tubulin gene (tubB) indicated that the two Agropyron species are infected with the species grouping into a novel single clade among Epichlo? species and they are closely related to a haploid of hybrid Neotyphodium species. The host plant features may be the cause of the differences between stromata of A. ciliare var. minus and A. tsukushiense var.     

Origin, divergence, and phylogeny of epichloe endophytes of native Argentine grasses

The epichlo? endophytes are systemic, constitutive, and often vertically transmitted fungal symbionts of grass species in subfamily Po?ideae. Prior studies indicate that several asexual epichlo? endophytes (Neotyphodium species) have evolved directly from sexual (Epichlo?) species, whereas others evolved by hybridization between two or more endophyte species. In this paper, we investigate the phylogenies of 27 Neotyphodium spp. isolates from 10 native grass species (in 4 tribes) in 22 populations throughout Argentina. Relationships among these fungi and a worldwide collection of epichlo? endophytes were estimated by phylogenetic analysis of sequences from variable portions (mainly introns) of genes for beta-tubulin (tub2) and translation elongation factor 1-alpha (tef1). Most of the Argentine endophyte isolates were interspecific hybrids of Epichlo? festucae and E. typhina. Only one isolate was a hybrid of a different ancestry, and three isolates were apparently non-hybrid endophytes. These results indicate that interspecific hybridization, which promotes genetic variation, was common during the evolution of the endophytes of Argentine grasses.     

Periglandula, a new fungal genus within the Clavicipitaceae and its association with Convolvulaceae

We describe two newly discovered fungi living on the adaxial leaf surface of plants belonging to the Convolvulaceae, Ipomoea asarifolia and Turbina corymbosa. The fungi apparently are epibionts because hyphae were never observed to penetrate epidermal cells or stomata of their respective host plants, and most remarkably are intimately associated with secretory glands on the leaf surface. Hyphae and structures resembling chlamydospores and synnemata (but lacking conidia), formed by both fungal species are phenotypically nearly indistinguishable after in vitro growth or when examined in vivo on the leaf surface. Phylogenetic trees based on aligned DNA sequences from nuclear genes for β-tubulin (tubB) and RNA Polymerase II subunit 1 (rpbA), and the mitochondrial gene for ATP synthase F0 subunit A (atp6), grouped the fungal species in a clade within the Clavicipitaceae. Clavicipitaceous fungi isolated from the two different plant species could be distinguished by their atp6 and rpbA sequences, and nuclear genes for γ-actin (actG), translation elongation factor 1-α (tefA), and 4-(γ,γ-dimethylallyl)tryptophan synthase (dmaW), the determinant step in ergoline (i.e. ergot) alkaloid biosynthesis. Based on these findings we propose a new fungal genus, Periglandula, gen. nov., and describe two new species, Periglandula ipomoeae sp. nov., from host plant I. asarifolia, and Periglandula turbinae sp. nov., from T. corymbosa.     

中国产禾本科植物内生真菌的遗传多样性及rDNA-ITS系统发育分析

采用RAPD技术对分离自我国的13株Epichlo?spp.和9株Neotyphodiumspp.的禾本科植物内生真菌进行了遗传多样性分析,同时对其中的4株进行了rDNA-ITS序列分析及系统发育研究。RAPD分析结果显示:原产自我国的菌株与原产自欧洲的菌株N.uncinatum之间亲缘关系较远;我国的21个菌株之间也存在一定的遗传多样性。rDNA-ITS序列分析表明:原产自我国的菌株聚为一枝,表明我国的Neotyphodium属真菌很有可能直接由我国的Epichlo?属真菌演化而来的新的类群;我国的Epichlo?属真菌有可能和国外推测的一个未确定的Neotyphodium属真菌的杂交进化起源(LAC)有关。     

Neotyphodium sinicum, from several Roegneria species throughout China, provides insights into the evolution of asexual endophytes

The fungus Neotyphodium sinicum forms an asymptomatic symbiosis with Roegneria grass species which are widely distributed in China. We collected 1,809 asymptomatic specimens of Roegneria, belonging to six species, from around 14 cities in nine provinces. 45.7% of the 1,809 asymptomatic Roegneria plants were endophyte-infected. Of 100 Neotyphodium isolates subsequently obtained, 31 were tested for cultural characteristics. These isolates showed morphological diversity and varying growth rates as well as differences in colony appearance and in conidial lengths. While conidial length of most of the isolates was typical of interspecific hybrid Neotyphodium species, conidial length of some isolates was smaller, similar to that of haploid species. A phylogenetic study was conducted of the tubB and tefA genes in 21 Neotyphodium isolates. The isolates were phylogenetically clustered into three types: 15/21 isolates had two divergent alleles of both tubB and tefA; 3/21 had two alleles of only tubB and 3/21 had two alleles of only tefA. In the tubB NJ tree, alleles-1 formed two distinct sub-clades in the Epichlo? bromicola/E. yangzii clade (EBY); allele-2 was located in three sub-clades widely distributed within the E. typhina clade (ETC). The allele-1 of the tefA gene was also located within the EBY clade and formed two sub-clades; allele-2 was located in 3 sub-clades within the ETC clade. No relationship was observed between phylogenetic relationships and morphology in the N. sinicum isolates. The phylogenetic characteristics had little relationship to the host species or site of origin of the isolates. An explanation consistent with the phylogenetic findings is that N. sinicum is a complex of species that has resulted from multiple independent hybridization events.     

Concerted evolution in the ribosomal RNA genes of an Epichloë endophyte hybrid: comparison between tandemly arranged rDNA and dispersed 5S rrn genes

We examined ribosomal RNA concerted evolution in an Epichlo? endophyte interspecific hybrid (Lp1) and its progenitors (Lp5 and E8). We show that the 5S rrn genes are organized as dispersed copies. Cloned 5S gene sequences revealed two subfamilies exhibiting 12% sequence divergence, with substitutions forming coevolving pairs that maintain secondary structure and presumably function. Observed sequence patterns are not fully consistent with either concerted or classical evolution. The 5S rrn genes are syntenic with the tandemly arranged rDNA genes, despite residing outside the rDNA arrays. We also examined rDNA concerted evolution. Lp1 has rDNA sequence from only one progenitor and contains multiple rDNA arrays. Using 5S rrn genes as chromosomal markers, we propose that interlocus homogenization has replaced all Lp5 rDNA sequence with E8 sequence in the hybrid. This interlocus homogenization appears to have been rapid and efficient and is the first demonstration of hybrid interlocus homogenization in the Fungi.     

Epichlo? festucae and related mutualistic symbionts of grasses.

Epichlo? and Neotyphodium species (Ascomycota) are mutualistic symbionts (endophytes) of temperate grasses, to which they impart numerous and profound fitness benefits. Epichlo? festucae, a common symbiont of Festuca, Lolium,and Koeleria spp., is a model for endophyte research that is amenable to Mendelian and molecular genetic analysis. Characteristics of E. festucae include: (i) production of the anti-insect alkaloids peramine and lolines, (ii) production of the anti-vertebrate alkaloids lolitrem B and ergovaline, (iii) efficient vertical transmission via host seeds, (iv) a mildly pathogenic state associated with the E. festucae sexual cycle, and (v) a clear role in enhancing survival of host plants. Genetic analysis of alkaloid production has recently begun. Also, physiological and ultrastructural studies suggest that signals communicated between E. festucae and host plants ensure an exquisitely balanced interaction to the mutual benefit of both partners. Several mutualistic Neotyphodium species are hybrids between E. festucae and other endophyte species.     

Limited phylogeographical structure across Eurasia in two red wood ant species Formica pratensis and F. lugubris (Hymenoptera, Formicidae)

The phylogeography and demographic history of two closely related species of the red wood ant (Formica pratensis and F. lugubris) were examined across Eurasia. The phylogeny based on a 1.5-kilobase mitochondrial DNA fragment, including the cytochrome b gene and part of the ND6 gene, showed one phylogeographical division in F. pratensis. This division (0.7% of nucleotide divergence) suggests postglacial colonization of western Europe and of a wide area ranging from Sweden on the west to Lake Baikal on the east from separate forest refugia. In two localities, mitochondrial DNA has been transferred from F. lugubris to F. pratensis and all the individuals of F. pratensis sampled from the Pyrenees had haplotypes clustering in the lugubris clade. No phylogeographical divisions were detected in F. lugubris. Comparison of species-wide phylogeography between the two sympatrically distributed species of ant demonstrates a difference in phylogeographical structure that implies different vicariant histories. However, over most of the species' distribution ranges, similar signs of demographic expansion predating the last glaciation and the lack of phylogeographical structure were found in both the eastern phylogroup of F. pratensis and F. lugubris. This finding is highly consistent with the results reported for all other boreal forest animal species studied to date in Eurasia. Contraction of the distribution range of each species to a single refugial area at different times during the late Pleistocene and a subsequent population expansion seem to be an explanation for the lack of phylogeographical structure across most of Eurasia in species that are ecologically associated with the boreal forest.     

Host Adaptation and Speciation through Hybridization and Polyploidy in Phytophthora

It is becoming increasingly evident that interspecific hybridization is a common event in phytophthora evolution. Yet, the fundamental processes underlying interspecific hybridization and the consequences for its ecological fitness and distribution are not well understood. We studied hybridization events in phytophthora clade 8b. This is a cold-tolerant group of plant pathogenic oomycetes in which six host-specific species have been described that mostly attack winter-grown vegetables. Hybrid characterization was done by sequencing and cloning of two nuclear (ITS and Ypt1) and two mitochondrial loci (Cox1 and Nadh1) combined with DNA content estimation using flow cytometry. Three different mtDNA haplotypes were recovered among the presumed hybrid isolates, dividing the hybrids into three types, with different parental species involved. In the nuclear genes, additivity, i.e. the presence of two alleles coming from different parents, was detected. Hybrid isolates showed large variations in DNA content, which was positively correlated with the additivity in nuclear loci, indicating allopolyploid hybridization followed by a process of diploidization. Moreover, indications of homeologous recombination were found in the hybrids by cloning ITS products. The hybrid isolates have been isolated from a range of hosts that have not been reported previously for clade 8b species, indicating that they have novel pathogenic potential. Next to this, DNA content measurements of the non-hybrid clade 8b species suggest that polyploidy is a common feature of this clade. We hypothesize that interspecific hybridization and polyploidy are two linked phenomena in phytophthora, and that these processes might play an important and ongoing role in the evolution of this genus.     

Direct classification of related species of fungal endophytes (Epichlo? spp.) using visible and near-infrared spectroscopy and multivariate analysis.

The aim of this work was to investigate the potential of visible and near-infrared (Vis-NIR) reflectance spectroscopy for the classification of three morphologically similar species of fungal endophytes of grasses. Vis-NIR spectra (400-2498 nm) from 34 isolates of Epichlo? sylvatica, 32 of Epichlo? typhina and 38 of Epichlo? festucae were recorded directly from fresh mycelium growing in potato dextrose agar plates. Multivariate procedures applied to the spectral data were discriminant modified partial least squares regression, soft independent modelling of class analogy and discriminant partial least squares regressions (PLS1, PLS2). Several types of data pretreatments were tested to develop the classification models. The best predictive models were achieved with PLS2 analysis; with this method, 90% of E. typhina and 100% of E. festucae and E. sylvatica external validation samples were successfully classified. These results show the potential of Vis-NIR spectroscopy combined with multivariate analysis as a rapid method for classifying morphologically similar species of filamentous fungi.     

Role of odour compounds in the attraction of gamete vectors in endophytic Epichloë fungi

Grass-infecting Epichlo? endophytes (Ascomycota, Calvicipitaceae) depend on Botanophila flies for gamete transfer, while fly larvae feed and develop on the fertilized fungal fruiting structures. Flies are known to be attracted by volatile signals, but the exact mechanisms of chemical communication and the degree of specialization are unknown. Headspace samples collected from five different Epichlo? species were analysed with respect to physiologically active substances using Botanophila flies. In field bioassays using synthetic compounds, their attractiveness and the specificity of the Epichlo?-Botanophila attraction were investigated. The identification of a new natural product, methyl (Z)-3-methyldodec-2-enoate, attracting Botanophila flies is reported here, and chokol K is confirmed as an attractive compound. Different blends of the two compounds attracted Botanophila flies under field conditions, but the three fly taxa present at the study site showed no preference for specific blends of volatiles. Chemical communication in the Epichlo?-Botanophila system relies on a few specific compounds, known as a communication system with 'private channels'. Although ratios of emitted compounds vary in different Epichlo? species, this seems not to lead to specialized attraction of Botanophila flies. Low selective pressure for specialization may have maintained a more generalist interaction between fungi and flies.     

Natural hybridization in tropical spikerushes of Eleocharis subgenus Limnochloa (Cyperaceae): Evidence from morphology and DNA markers

? Premise of the study: Natural hybridization represents an important force driving plant evolution and affecting community structure and functioning. Hybridization may be overlooked, however, among morphologically highly uniform congeners. An excellent example of such a group is Eleocharis subgenus Limnochloa, which has no reliably proven hybrids. Does this reflect biological barriers to interspecific crosses or difficulties in detecting the hybrids? We tested the hypothesis that hybridization occurs among sympatric Eleocharis cellulosa, E. interstincta, and E. mutata in northern Belize, Central America. ? Methods: Morphometric study (407 plants) was followed by examination of inter-simple sequence repeat (ISSR) polymorphisms (44 plants) and ITS sequence variation (33 plants). ? Key results: Two putatively hybrid morphotypes were discerned-E. cellulosa-resembling and E. interstincta-resembling. DNA markers of E. cellulosa and E. interstincta displayed additive constitution in plants from one E. cellulosa-resembling population only. The other putatively hybrid populations contained ISSR and ITS markers of the species they resembled morphologically, several unique ISSR markers, and ITS sequences of an undescribed South American Limnochloa entity. DNA markers of E. mutata were absent in the putative hybrids. ? Conclusions: Simultaneous use of various types of molecular markers can overcome many pitfalls of investigations concerning hybridization among closely related and morphologically similar species. Northern Belize represents a hybrid zone of E. cellulosa and E. interstincta. A third participant in the hybridization events occurring in this zone is an unknown Limnochloa lineage but is not E. mutata. Interspecific hybridization may play a significant role in the diversification of Eleocharis.     

Phylogenetics of the florally diverse Andean clade Iochrominae (Solanaceae)

Recent molecular phylogenetic studies of Solanaceae have identified many well-supported clades within the family and have permitted the creation of a phylogenetic system of classification. Here we estimate the phylogeny for Iochrominae, a clade of Physaleae sensu Olmstead et al. (1999), which contains 34 Andean species encompassing an immense diversity of floral forms and colors. Using three nuclear regions, ITS, the second intron of LEAFY, and exons 2 to 9 of the granule-bound starch synthase gene (waxy), we evaluated the monophyly of the traditional genera comprising Iochrominae and assessed the extent of interspecific hybridization within the clade. Only one of the six traditionally recognized genera of Iochrominae was supported as monophyletic. Further, comparison of the individual nuclear data sets revealed two interspecific hybrid taxa and a third possible case. These hybrid taxa occur in the Amotape-Huancabamba zone, a region between the northern and central Andes that has the greatest diversity of Iochroma species and offers frequent opportunities for hybridization in areas of sympatry. We postulate that periodic hybridization events in this area coupled with pollinator-mediated selection and the potential for microallopatry may have acted together to promote diversification in montane Andean taxa, such as Iochrominae.     

Epichloë endophytes: fungal symbionts of grasses

Recent developments have increased our understanding of the evolution of mutualistic associations between Epichlo? endophytes and their grass hosts. Most of the asexual species appear to be interspecific hybrids. Although endophytes form compatible associations with their natural hosts, transfers to other hosts elicit a range of incompatible reactions. Recently, the genes involved in the synthesis of the secondary metabolites ergot alkaloids and indole-diterpenes, which confer protective benefits on the association, have been cloned.     

Molecular evidence for the hybrid origin of species in the soft coral genus Alcyonium (Cnidaria: Anthozoa: Octocorallia)

Several recent studies have suggested that hybridization may play a previously unrecognized and important role in the evolution of corals. Our observations of polymorphic and recombinant sequences in the multicopy ribosomal internal transcribed spacer (ITS) region suggested the possible hybrid origin of two European soft coral species, Alcyonium hibernicum and Bellonella bocagei. To examine this possibility further we cloned and sequenced ITS-1 from multiple individuals and populations of these two species as well as two sympatric congeners, A. coralloides and A. sp. M2. Phylogenetic analyses separated the observed sequence variants into two distinct clades. All A. coralloides sequences belonged to clade A, while A. sp. M2 had only clade B sequences. A majority of A. hibernicum individuals, however, contained both clade A and B sequences that were identical to the predominant sequence variants found in A. coralloides and A. sp. M2, respectively. This pattern of additivity suggests that A. hibernicum originated from a hybrid cross between A. coralloides and A. sp. M2, a hypothesis that is supported by its unusual mode of reproduction (meiotic parthenogenesis). The predominant sequence variant found in B. bocagei was a unique, derived clade B sequence; in addition, however, most individuals of this species also had copies of a sequence identified as a recombinant between clade A and clade B sequence types. The presence of this recombinant sequence in the B. bocagei genome suggests that this species may also be the product of past hybridization events within the clade. Reticulate evolution may explain the failure of several previous studies to resolve the phylogeny of these four species.