The phylogenetic placement of Ostropales within Lecanoromycetes (Ascomycota) revisited

Results of molecular studies regarding the phylogenetic placement of the order Ostropales and related taxa within Lecanoromycetes were thus far inconclusive. Some analyses placed the order as sister to the rest of Lecanoromycetes, while others inferred a position nested within Lecanoromycetes. We assembled a data set of 101 species including sequences from nuLSU rDNA, mtSSU rDNA, and the nuclear protein-coding RPB1 for each species to examine the cause of incongruencies in previously published phylogenies. MP, minimum evolution, and Bayesian analyses were performed using the combined three-region data set and the single-gene data sets. The position of Ostropales nested in Lecanoromycetes is confirmed in all single-gene and concatenated analyses, and a placement as sister to the rest of Lecanoromycetes is significantly rejected using two independent methods of alternative topology testing. Acarosporales and related taxa (Acarosporaceae group) are basal in Lecanoromycetes. However, if the these basal taxa are excluded from the analyses, Ostropales appear to be sister to the rest of Lecanoromycetes, suggesting different ingroup rooting as the cause for deviating topologies in previously published phylogenies.     

Evolutionary relationships among aquatic anamorphs and teleomorphs: Lemonniera, Margaritispora, and Goniopila

The hypothesis that similar conidial morphologies in aquatic hyphomycetes are a result of convergent evolution was tested using molecular sequence data. Cladistic analyses were performed on partial sequences of 28S rDNA of seven species of Lemonniera, one species of Margaritispora and one species of Goniopila. Lemonniera has tetraradiate conidia with long arms, whereas Margaritispora and Goniopila have typically globose (isodiametric) conidia, with short conical protuberances in a stellate or quadrangular arrangement. Lemonniera and Margaritispora have phialidic conidiogenesis and both produce dark, minute sclerotia in culture whereas Goniopila has holoblastic conidiogenesis and does not produce sclerotia in culture. Goniopila produces a microconidial phialidic synanamorph in culture. All three genera have schizolytic conidial secession. Molecular analyses demonstrate that Lemonniera species are placed in two distinct clades: one within Leotiomycetes; the other within Pleosporales, Dothideomycetes. Margaritispora is placed with Lemonniera species within Leotiomycetes. Goniopila and Lemonniera pseudofloscula are placed within Dothideomycetes. No morphological character was entirely congruent with the molecular derived phylogeny. This suggests that for the group of species studied, conidial shape is not a reliable indicator of phylogeny but more likely the result of convergent evolution in response to the aquatic environment.     

Corylomyces: a new genus of Sordariales from plant debris in France

The new genus Corylomyces, isolated from the surface of a hazelnut (Corylus avellana) in the French Pyrenees, is described, illustrated and compared with morphologically similar taxa. It is characterised by tomentose, ostiolate ascomata possessing long necks composed of erect to sinuose hairs, and one- or two-celled, opaque, lunate to reniform ascospores. Analyses of the SSU and LSU fragments rDNA gene sequences support its placement in the Lasiosphaeriaceae (Sordariales).     

Hypocrella panamensis sp. nov. (Clavicipitaceae, Hypocreales): a new species infecting scale insects on Piper carrilloanum in Panama

A new species, Hypocrella panamensis, is described from collections and cultures obtained on Barro Colorado Island, Panama. In order to aid in placement of this fungus, phylogenetic analyses were conducted using LSU (rDNA) sequences. Hypocrella panamensis is characterized by possessing pulvinate stromata with a Lecanicillium-like anamorphic state and superficial perithecia. Hypocrella panamensis consistently grouped in a clade containing Hypocrella nectrioides, H. phyllogena, and H. africana (100 % PP). Most species of Hypocrella possess Aschersonia or Hirsutella anamorphs. Hypocrella panamensis is unique in the genus Hypocrella in possession of a Lecanicillium-like anamorphic state. In its biological habit Hypocrella panamensis is similar to other species in Hypocrella in that it infects and degrades the scale insect, then grows superficially on nutrients that emerge to the plant surface through the stylet wound.     

Structural organization of the nuclear ribosomal RNA genes in Cannabis and Humulus (Cannabaceae)

The structural organization of the nuclear ribosomal DNA (rDNA) of Humulus lupulus, H. japonicus and Cannabis sativa was determined by restriction site mapping. A high degree of DNA sequence similarity was evident in the coding regions of the rDNA repeats of the taxa and supports the placement of Cannabis and Humulus in one family, Cannabaceae. However, the presence of a BstEII site, an additional SacI site, absence of the SpeI site and positional differences of the SspI sites in the 25 S gene distinguished H. japonicus from H. lupulus. Humulus lupulus has an additional EcoRV site in the IGS region. A XhoI site in the 18S region of C. sativa distinguishes it from the two hop species. The diagnostic differences in the IGS of C. sativa include the EcoRI, HindIII and XhoI sites. These sites were not detected in the IGS of the two hop species.     

Truffle trouble: what happened to the Tuberales?

An overview of truffles (now considered to belong in the Pezizales, but formerly treated in the Tuberales) is presented, including a discussion on morphological and biological traits characterizing this form group. Accepted genera are listed and discussed according to a system based on molecular results combined with morphological characters. Phylogenetic analyses of LSU rDNA sequences from 55 hypogeous and 139 epigeous taxa of Pezizales were performed to examine their relationships. Parsimony, ML, and Bayesian analyses of these sequences indicate that the truffles studied represent at least 15 independent lineages within the Pezizales. Sequences from hypogeous representatives referred to the following families and genera were analysed: Discinaceae–Morchellaceae (Fischerula, Hydnotrya, Leucangium), Helvellaceae (Balsamia and Barssia), Pezizaceae (Amylascus, Cazia, Eremiomyces, Hydnotryopsis, Kaliharituber, Mattirolomyces, Pachyphloeus, Peziza, Ruhlandiella, Stephensia, Terfezia, and Tirmania), Pyronemataceae (Genea, Geopora, Paurocotylis, and Stephensia) and Tuberaceae (Choiromyces, Dingleya, Labyrinthomyces, Reddellomyces, and Tuber). The different types of hypogeous ascomata were found within most major evolutionary lines often nesting close to apothecial species. Although the Pezizaceae traditionally have been defined mainly on the presence of amyloid reactions of the ascus wall several truffles appear to have lost this character. The value of the number of nuclei in mature ascospores as a delimiting family character is evaluated and found to be more variable than generally assumed.     

Molecular Systematics of Zopfiella and allied genera: evidence from multi-gene sequence analyses

This study aims to reveal the phylogenetic relationships of Zopfiella and allied genera in the Sordariales. Multiple gene sequences (partial 28 S rDNA, ITS/5.8 S rDNA and partial β-tubulin) were analysed using MP and Bayesian analyses. Analyses of different gene datasets were performed individually and then combined to infer phylogenies. Phylogenetic analyses show that currently recognised Zopfiella species are polyphyletic. Based on sequence analyses and morphology, it appears that Zopfiella should be restricted to species having ascospores with a septum in the dark cell. Our molecular analysis also shows that Zopfiella should be placed in Lasiosphaeriaceae rather than Chaetomiaceae. Cercophora and Podospora are also polyphyletic, which is in agreement with previous studies. Our analyses show that species possessing a Cladorrhinum anamorph are phylogenetically closely related. In addition, there are several strongly supported clades, characterised by species possessing divergent morphological characters. It is difficult to predict which characters are phylogenetically informative for delimiting these clades.     

Development of Molecular Identification Method for Genus Alexandrium (Dinophyceae) Using Whole-Cell FISH

We have developed a method to identify species in the genus Alexandrium using whole-cell fluorescent in situ hybridization with FITC-labeled oligonucleotide probes that target large subunit ribosomal rRNA molecules. The probes were designed based on the sequence of the rDNA D1-D2 region of Alexandrium species. DNA probes specific for toxic A. tamarense and A. catenella and nontoxic A. affine, A. fraterculus, A. insuetum, and A. pseudogonyaulax, respectively, were applied to vegetative cells of all above Alexandrium species to test the sensitivity of the probes. Each DNA probe hybridized specifically with vegetative cells of the corresponding Alexandrium species and showed no cross-reactivity to noncorresponding Alexandrium species. In addition, no cross-reactivity of the probes was observed in experiments using concentrated natural seawater samples. The TAMAD2 probe, which is highly specific to A. tamarense, a common toxic species in Korean coastal waters, provides a simple and reliable molecular tool for identification of toxic Alexandrium species.     

共球藻纲丝状藻中国新记录属种——洪泛拟寇丽藻

从甘肃省张掖市黑河流域分离了一株不分枝的丝状绿藻,对其进行纯培养并保藏于中国科学院淡水藻种库,编号FACHB 2451。形态观察表明,该藻株具有相对较长的营养细胞 (细胞长为宽的3~8倍)、双叶形的片状叶绿体、末端细胞顶端钝圆或略尖细等特征。结合形态比较和基于18S rDNA 基因序列的系统发育分析,确定该藻株为中国淡水共球藻纲新记录属种——洪泛拟寇丽藻 (Koliellopsis inundata Lokhorst)。分子系统发育研究结果表明,所分离的藻株与分离自比利时与荷兰边境农地的洪泛拟寇丽藻模式藻株序列相似度极高,且拟寇丽藻属与寇丽藻属、针丝藻属和拟针丝藻属等不分枝丝状拟寇丽藻科成员亲缘关系密切,可以较好地聚成一个亚支。     

Cardicola aurata sp. n. (Digenea: Sanguinicolidae) from Mediterranean Sparus aurata L. (Teleostei: Sparidae) and its unexpected phylogenetic relationship with Paradeontacylix McIntosh, 1934

A new sanguinicolid trematode, Cardicola aurata sp. n., is described from gilthead seabream Sparus aurata L., from off the Spanish Mediterranean coast. The morphology of C. aurata sp. n. generally agrees with the diagnosis of the genus, however, in contrast to all other reported Cardicola spp. the male pore is located sub-medially at the posterior end of the body instead of sinistrally before the posterior end of the body. Based on a comparison of the morphology as well as partial 28S and ITS2 rDNA sequence data from the present species with that from closely related species, it was decided to emend the diagnosis of Cardicola rather than create a new genus, as the aberrant position of the male pore is likely to be an autapomorphy. The phylogenetic analyses revealed a close relationship between Cardicola and Paradeontacylix, two genera with considerable morphological differences; C. aurata sp. n. occupies a position intermediate to these genera. Thus, a morphological comparison of Cardicola, Paradeontacylix and Braya, a genus which is morphologically similar to Cardicola but clusters basal to the Cardicola/Paradeontacylix clade, was conducted. The results of this comparison showed that despite large differences with regard to body shape, the organisation of the internal organs is very similar in species of Cardicola and Paradeontacylix. The synopsis of morphological data and molecular phylogeny allows for interpretations regarding the importance of different morphological features for the phylogenetic inference of the Sanguinicolidae.     

Heterobasidiomycetes from Belize

Summary  Twenty-eight species of heterobasidiomycetes (phylum Basidiomycota) belonging to the orders Auriculariales, Dacrymycetales, Exidiales, Platygloeales, Sebacinales, Septobasidiales and Tremellales from Belize are described or reported. Endoperplexa phlebioides, Heterochaete pentadelphai and Sebacina pileata are described as new. The genus Aphelariopsis is considered a possible synonym of Septobasidium and the new combination Septobasidium kupemontis is proposed. The new combination Endoperplexa obscura is also proposed.     

The halotolerant fungus Glomerobolus gelineus is a member of the Ostropales

Glomerobolus gelineus is a halotolerant species with a unique method of ballistic propagation. The absence of both sexual and asexual spores made reliable placement of this species, based on morphology alone, within the current fungal classification problematical. A phylogenetic analysis of the large and small nuclear ribosomal subunit and the second largest subunit of RNA polymerase II placed this fungus within the Ostropales, an order comprising lichenized and saprobic species, with good statistical support. Subsequently, a more detailed analysis that combined the nuc LSU rDNA and the mt SSU rDNA confirmed a close relationship to the Stictidaceae. The phylogenetic placement of G. gelineus is also supported by morphological characters. We postulate that the hyphoma lobes of Glomerobolus correspond to the periphysoidal layer in the apothecium of Stictis, and the propagule to the hymenium. Moreover, the presence of crystals in the outer lobes of G. gelineus is another indication of its relationship with Ostropales, which have characteristic crystalliferous hyphae. The placement of Glomerobolus within the Ostropales further expands the ecological diversity exhibited by this order. It also provides a phylogenetic hypothesis for assessing the homology of the enigmatic hyphomal morphology with apothecia-forming Ascomycota.     

Molecular and ultrastructural characterization of two ascomycetes found on sunken wood off Vanuatu Islands in the deep Pacific Ocean

A new genus of a deep-sea ascomycete with one new species, Alisea longicolla, is described based on analyses of 18S and 28S rDNA sequences and morphological characters. A. longicolla was found together with Oceanitis scuticella, on small twigs and sugar cane debris trawled from the bottom of the Pacific Ocean off Vanuatu Islands. Molecular and morphological characters indicate that both fungi are members of Halosphaeriaceae. Within this family, O. scuticella is phylogenetically related to Ascosalsum and shares similar ascospore morphology and appendage ontogeny. The genus Ascosalsum is considered congeneric with Oceanitis and Ascosalsum cincinnatulum, Ascosalsum unicaudatum and Ascosalsum viscidulum are transferred to Oceanitis, an earlier generic name.     

Morphological and molecular phylogenetic analysis of <Emphasis Type="Italic">Melampsora</Emphasis> species on poplars in China

Many species of Melampsora on Populus have been reported in China, based on morphological characteristics of both uredial and telial states, and on host species, but their morphology and taxonomy are still poorly defined. In this study, 196 specimens representing Melampsora species on poplars and collected from various areas of China were used for morphological observations. The morphological characteristics of urediniospores and teliospores were examined with light and scanning electron microscopy. The specimens could be classified into five groups based on their morphology. For the sequencing of the nuclear large subunit rDNA (D1/D2), 5.8S rDNA and their internal transcribed spacers, ITS1 and ITS2 region, 54 specimens were selected from the specimens used in morphological observations. These specimens were separated into six clades by phylogenetic analyses of the D1/D2 and ITS regions. Correlations among morphological groups and phylogenetic clades based on these results suggest a revision of these species. In particular, no evidence to discriminate specimens of M. acedioides, M. magnusiana, and M. rostrupii was found from either morphological characteristics or sequence analysis.Contribution no. 185 Laboratory of Plant Parasitic Mycology, Institute of Agriculture and Forestry, University of Tsukuba, Japan     

Molecular and morphological characterization of Leveillula (Ascomycota: Erysiphales) on monocotyledonous plants

Leveillula on monocotyledonous plants have been recorded as L. taurica by several authors, whereas the fungus on Allium has been described as an independent species, namely L. allii, by some authors. We sequenced ca 600 bp of the rDNA ITS region for two Leveillula specimens from Allium and Polianthes (both from monocotyledons) and compared them with several already published sequences from Leveillula isolates from dicotyledons. Pair-wise percentages of sequence divergences were calculated for all Leveillula isolates. The ITS sequence of the Polianthes isolate was identical to L. taurica on Helianthus and Vicia. The sequence of the Allium isolate was 99.5 % identical to L. taurica on Euphorbia, Haplophylum, Peganum, etc. These results suggest close relationships between monocot and dicot pathogenic Leveillula species. The identity between two monocot isolates was 98.4 %. Phylogenetic analysis revealed that the two monocot isolates do not group into a clade together. This result suggests that Leveillula acquired parasitism to monocots at least twice independently.     

A new fungal genus, Teracosphaeria, with a phialophora-like anamorph (Sordariomycetes, Ascomycota)

The new genus and species Teracosphaeria petroica is described for a perithecial ascomycete and its anamorph occurring on decayed wood collected in New Zealand. The fungus produces immersed, non-stromatic ceratosphaeria-like perithecia in nature, with hyaline, septate ascospores produced in unitunicate, non-amyloid asci. The anamorph produced in vitro is phialophora-like with lightly pigmented phialides terminating in flaring, deep collarettes that are often noticeably brown with conspicuous periclinal thickening. Phylogenetic analysis of LSU rDNA sequence data indicates that this fungus is distinct from morphologically similar fungi classified in the Chaetosphaeriales, the Trichosphaeriales or the Magnaporthaceae. It forms a monophyletic group with recently described, chaetosphaeria-like ascomycetes, such as the pyrenomycete genus Mirannulata, and shows affinity with the anamorphic species Dictyochaeta cylindrospora. The usefulness of describing anamorph genera for morphologically reduced anamorphs, when anamorph characteristics are actually part of the holomorph diagnosis, is discussed. An apparently contradictory example of the so-called Cordana and Pseudobotrytis anamorphs of Porosphaerella spp. is also discussed.     

Diversity of nodule-endophytic agrobacteria-like strains associated with different grain legumes in Tunisia

This study represents the first report describing the genetic diversity of nodule-endophytic agrobacteria isolated from diverse legumes and their phylogenetic relationships with the valid species of agrobacteria, as well as the non-recognized genomospecies of the former Agrobacterium tumefaciens (Rhizobium radiobacter). The genetic diversity of a collection of 18 non-nodulating agrobacteria-like strains, previously isolated from root nodules of Vicia faba, Cicer arietinum and Phaseolus vulgaris from different geographical regions of Tunisia, was studied by REP-PCR and PCR-RFLP of the 16S-23S rDNA IGS, as well as by sequence analysis of the 16S rDNA and the housekeeping genes recA and atpD. The aim of the work was to study the genetic diversity of the different isolates and to check for any host-specificity. The results from the different techniques were congruent and suggested a specific interaction for P. vulgaris, whereas no specific endophytic interaction was observed for V. faba and C. arietinum. The phylogenetic analysis clearly indicated that some isolates were affiliated to R. radiobacter or to its non-recognized genomic species (genomovars G2, G4 and G9). However, the other isolates probably constitute new species within Rhizobium (Agrobacterium) and Shinella.     

垂穗披碱草与达乌里披碱草基因组细胞遗传学比较

采用顺序FISH-GISH技术,12个重复序列探针,包括9个三核苷酸简单重复序列、2个卫星DNA重复序列pSc119.2和pAs1以及5S rDNA,通过重复序列的物理定位对达乌里披碱草和垂穗披碱草基因组中部分重复序列的分布特征进行了比较分析,为进一步研究垂穗披碱草和达乌里披碱草的物种形成及演化提供新的分子细胞遗传学证据。结果表明:(1)所有的序列在这2个物种的染色体上都能产生可检测的杂交信号,且在2个物种中(AAC)_(10)、(ACT)_(10)、(CAT)_(10)都表现为共分布,(AAG)_(10)与(AGG)_(10)表现为近似共分布;2个物种的H基因组除5S rDNA序列外,其他序列都产生强烈且丰富的杂交位点,St与Y基因组不同重复序列探针的荧光位点数目有所差别,表现为5S rDNA、pSc119.2、(AAC)_(10)、(CAT)_(10)、(ACT)_(10)、(CAC)_(10)探针的信号位点较少或无信号,其余的探针信号位点稍多。(2)达乌里披碱草的第2对染色体上具有(AAC)_(10)、(CAT)_(10)、(ACT)_(10)的杂交位点、第6对染色体上具有(CAC)_(10)的杂交位点,而在垂穗披碱草的St基因组中未观察到上述序列杂交位点;达乌里披碱草St基因组仅有第4对染色体的端部具有pSc119.2杂交位点,而在垂穗披碱草St基因组中的pSc119.2杂交位点位于第5对染色体长臂的间隔区;相对于达乌里披碱草,垂穗披碱草St和Y基因组染色体含有更多的重复序列杂交位点。(3)达乌里披碱草的H/Y基因组间易位在不同材料间是稳定存在的,达乌里披碱草基因组相对稳定,不同材料间H基因组重复序列杂交信号多态性高于St和Y基因组;垂穗披碱草基因组的变异较大,不同材料间St和Y基因组重复序列杂交信号多态性高于H基因组。研究认为,垂穗披碱草和达乌里披碱草的H基因组均起源于布顿大麦,St基因组可能起源于不同的拟鹅观草属物种;与达乌里披碱草相比垂穗披碱草St与Y基因组可能具有更高的染色体结构变异性,而垂穗披碱草St与Y基因组变异较大的原因可能是与同区域分布的含StY基因组的物种发生了种间渗透杂交。