Multilocus Molecular Analysis Research Articles

Investigations on Fungi Isolated from Apple Trees with Die-Back Symptoms from Basilicata Region (Southern Italy).

Val d’Agri is an important orchard area located in the Basilicata Region (Southern Italy). A phenomenon affecting cv. “Golden Delicious” apples which lead to tree death has been observed in the past several years in this area. This phenomenon has already been detected in about 20 hectares and is rapidly expanding. The symptoms observed were “scaly bark” and extensive cankers, mainly located in the lower part of the trunk, associated with wood decay. Dead plants ranged from 20% to 80% and, in many cases, trees were removed by farmers. In order to identify the causes of this phenomenon, investigations were started in autumn/winter 2019. In order to determine the possible causal agents, fungal and bacterial isolations, from symptomatic tissues, were performed in laboratory. Bacterial isolations gave negative results, whereas pure fungal cultures (PFCs) were obtained after 3–4 passages on potato dextrose agar (PDA) media. Genetic material was extracted from each PFC and amplified by PCR using three pairs of primers: ITS5/4, Bt2a/Bt2b and ACT-512F/ACT-783R. The amplicons were directly sequenced, and nucleotide sequences were compared with those already present in the NCBI GenBank nucleotide database. All isolated fungi were identified based on morphological features and multilocus molecular analyses. Neofusicoccum parvum, Diaporthe eres and Trametes versicolor were most frequently isolated, while Pestalotiopsis funerea, Phomopsis spp. and Diaporthe foeniculina were less frequently isolated. All nucleotide sequences obtained in this study have been deposited into the EMBL database. Pathogenicity tests showed that N. parvum was the most pathogenic and aggressive fungus, while Phomopsis sp. was demonstrated to be the less virulent one. All the investigated fungi were repeatedly reisolated from artificially inoculated twigs of 2-year-old apple trees, cv. “Golden Delicious”, and subsequently morphologically and molecularly identified. The role played by the above-mentioned fungi in the alterations observed in field is also discussed.

Molecular phylogeny of the genus Chondrina (Gastropoda, Panpulmonata, Chondrinidae) in the Iberian Peninsula

Chondrina Reichenbach, 1828 is a highly diverse genus of terrestrial molluscs currently including 44 species with about 28 subspecific taxa. It is distributed through North Africa, central and southern Europe, from Portugal in the West to the Caucasus and Asia Minor in the East. Approximately 70% of the species are endemic to the Iberian Peninsula constituting its main center of speciation with 34 species. This genus includes many microendemic taxa, some of them not yet described, confined to limestone habitats (being strictly rock-dwelling species). They are distributed on rocky outcrops up to 2000 m.a.s.l. It is a genus of conical-fusiform snails that differ mainly in shell characters and in the number and position of teeth in their aperture. So far, molecular studies on Chondrina have been based exclusively on the mitochondrial Cytochrome Oxidase subunit I region (COI). These studies gave a first view of the phylogeny of the genus but many inner nodes were not statistically supported.The main objective of the study is to obtain a better understanding of the phylogeny and systematics of the genus Chondrina on the Iberian Peninsula, using multilocus molecular analysis. Partial sequences of the COI and 16S rRNA genes, as well as of the nuclear Internal Transcribed Spacer 1 (ITS1-5.8S) and Internal Transcribed Spacer 2 (5.8S-ITS2-28S) were obtained from individuals of all the extant Chondrina species known from the Iberian Peninsula. In addition to this, the newly obtained COI sequences were combined with those previously published in the GenBank. Phylogenetic relationships were inferred using maximum likelihood and Bayesian methods. The reconstructed phylogenies showed high values of support for more recent branches and basal nodes. Moreover, molecular species delimitation allowed to better definethe studied species and check the presence of new taxa.

Integrative Descriptions of Two New Tardigrade Species along with the New Record of Mesobiotus skorackii Kaczmarek et al., 2018 from Canada

Two new tardigrade species from a moss sample collected in Canada, one representing Macrobiotus hufelandi complex and the second one belonging to the genus Bryodelphax, are described. Integrative analysis was undertaken based on morphological and morphometric data (using both light and scanning electron microscopy (SEM)) combined with multilocus molecular analysis (nuclear sequences, i.e., 18S rRNA, 28S rRNA and ITS-2 as well as mitochondrial COI barcode sequences). Based on COI sequences, Macrobiotus birendrai sp. nov. is most similar to Mac. canaricus (p-distance 17%), whereas Bryodelphax mareki sp. nov. is most similar to Bry. parvulus (p-distance 16%). Both species differ also from their congeners in some morphological and morphometric characters of adults and/or details of egg chorion. Additionally, a large population of Mesobiotus skorackii was found in the sample and this is the first report of this species outside its terra typica in Kirghizia. The original description of this species was prepared based solely on the morphology and morphometry, therefore, here we provide updated data for this species enclosing morphometric and molecular data for the Canadian population.

Cast netting new species: Integrative taxonomy of emDistichodus/em emnotospilus/em (Characiformes: Distichodontidae) discovers new species and overlooked areas of endemism in Central Africa.

Distichodus notospilus was described from the Ogooué River and is considered to occur throughout the Lower Guinea ichthyofaunal province and the western tributaries of the middle and lower Congo River. Recent expeditions in Equatorial Guinea collected D. notospilus specimens in the Mbini River drainage and the Mbia River; a small coastal river that is located between the Ntem and Mbini river drainages. Detailed morphological analyses and multilocus molecular analyses confirm that these two populations are distinct from one another. Topotypic populations of D. notospilus were included in the analyses and demonstrated that populations in the Mbini and Mbia rivers are distinct and these two new species are described herein. Distichodus microps sp. nov. is endemic to the Mbia River drainage and is distinguished from D. notospilus in having more scales along the lateral line (41, rarely 40 versus 37-39, rarely 40), a nearly inferior mouth versus subterminal in D. notospilus, a curved posterolateral margin of the opercle versus straight in D. notospilus, a smaller eye (56.7-80.4 versus 70.1-104.3 % of snout length), and a less prominent elongated spot at the base of the caudal fin. Distichodus mbiniensis sp. nov. is endemic to the upper Mbini River drainage and distinguished from D. notospilus in having more scales along the lateral line (41-42, rarely 40 versus 37-39, rarely 40), a much less prominent elongated dark spot at the base of the caudal fin, and a shorter dorsal fin (21.4-27.2 versus 22.7-34.2% standard length). Distichodus microps is distinguished from D. mbiniensis in having a shallower body (usually six scales from lateral line to the pelvic fin versus seven), fewer anal-fin rays (usually 12 total rays versus 13 or 14), a more inferior mouth, a deeper and longer caudal peduncle, a smaller eye, and differences in several features associated with the head. In addition to the two new species described this study also revealed potential undescribed diversity in the D. notospilus species complex in the Ntem River and Dja River (Congo R. basin) in Cameroon. The biogeography of these fishes in the rivers of Lower Guinea suggests that the Mbini River and smaller coastal rivers are overlooked areas of endemism. Studies of other reported widespread species will likely reveal additional diversity and further elucidate the processes promoting and maintaining freshwater diversity in Central Africa.

Persimmon anthracnose: a comparative study of aggressiveness on shoot and fruit among Colletotrichum horii isolates in southern Brazil

ABSTRACT: The persimmon tree is known for its rusticity and productivity and was first introduced to Brazil in the late 19th century. However, anthracnose disease is causing immature fruit drop and severe disease symptoms in persimmon fruit, shoots, flowers, and twigs. The causal agent was first described as the fungal species, Colletotrichum horii, which was first confirmed using only the ITS region. In this study, we compared the aggressiveness of 13 isolates of Colletotrichum spp. obtained from fruit and shoots of persimmon grown in the Metropolitan Region of Curitiba, Paraná State, Brazil. A multilocus molecular analysis was carried out based on ITS, GPDH, and EF genes, and we confirmed that the isolates were confirmed as C. horii. All isolates were pathogenic for unwounded and wounded persimmon fruit but differed in aggressiveness. Only one isolate was non-pathogenic when inoculated into unwounded persimmon shoots. Most isolates caused cankers and shoot death whether shoots were wounded or unwounded. In this study, we emphasized the importance of shoots as a source of primary inoculum. In future studies, it will be critical to further elucidate the epidemiological basis of anthracnose disease by conducting field studies to establish a more effective strategy for disease control.

Parasitological and molecular survey of scattered parasitism by trichomonads in some avian species in Iran

ABSTRACT Outbreaks of avian trichomonosis are being reported worldwide; meanwhile, the genetic and virulence variations are under investigation. In this study, the occurrence and genetic variability of oral or faecal trichomonads among various avian species were investigated. Samples obtained from either the oropharyngeal cavity, crop/oesophagus, droppings/cloaca, or conjunctival swabs of avian species were inspected for flagellates. Phylogenetic analysis of partial ITS1-5.8s rRNA-ITS2 sequences from selected samples was performed to investigate the genetic diversity of the isolates. Investigation of 737 birds revealed an infection rate of 15.7% in the upper gastrointestinal tract, 7.3% in the faecal samples, and 0.7% involvement of the conjunctiva. Phylogenetic analysis of partial ITS1-5.8s rRNA-ITS2 sequences from selected samples, identified genotypes A and B of Trichomonas gallinae and genogroups A-C and E of Tetratrichomonas gallinarum. A novel ITS genotype of intestinal trichomonads was also detected in hooded crow (Corvus cornix) and common mynah (Acridotheres tristis). In the present study, in addition to Columbiformes and Falconiformes, trichomonads were detected in Passeriformes and Galliformes with the involvement of organs other than the gastrointestinal tract. Genotype A T. gallinae was detected in domestic pigeons (Columba livia domestica), a laughing dove (Spilopelia senegalensis), a common kestrel (Falco tinnunculus), a budgerigar (Melopsittacus undulates), and a canary (Serinus canaria). Distinct genotype B was detected in a common mynah and a budgerigar. Genogroups A-C of T. gallinarum were also demonstrated in Galliformes and Anseriformes. Furthermore, two novel trichomonad ITS genotypes were detected in hooded crows and a common mynah warranting detailed multi-locus molecular analysis. RESEARCH HIGHLIGHTS ITS diversity of trichomonads was shown in various avian species. Diversity of the parasites’ target organ and clinical manifestations was demonstrated. Two novel ITS genotype trichomonads from common mynah and hooded crow were identified.

New Fusarium species from the Kruger National Park, South Africa.

Three new Fusarium species, F. convolutans, F. fredkrugeri, and F. transvaalense (Ascomycota, Hypocreales, Nectriaceae) are described from soils collected in a catena landscape on a research supersite in the Kruger National Park, South Africa. The new taxa, isolated from the rhizosphere of three African herbaceous plants, Kyphocarpa angustifolia, Melhania acuminata, and Sida cordifolia, are described and illustrated by means of morphological and multilocus molecular analyses based on sequences from five DNA loci (CAL, EF-1 α, RPB1, RPB2 and TUB). According to phylogenetic inference based on Maximum-likelihood and Bayesian approaches, the newly discovered species are distributed in the Fusarium buharicum, F. fujikuroi, and F. sambucinum species complexes.

Revealing species diversity of Tomocerus ocreatus complex (Collembola: Tomoceridae): integrative species delimitation and evaluation of taxonomic characters

Tomocerus ocreatus species complex is among the commonest groups of Tomoceridae in East Asia and mainly distributed in the southern areas of China. Previous multi-locus molecular analyses have proved its monophyly and revealed extensive cryptic diversity within the complex. However, members of the complex are highly similar in traditional characters, thus morphological diagnosis have not been sufficiently developed in line with the molecular species delimitation. To update the taxonomy of the ocreatus complex, we carried out a molecular-morphological integrative study based on a wide-range survey of the complex in China. In addition to previous molecular analyses, we applied both distance and evolutionary model based methods on an enriched dataset of mitochondrial cytochrome c oxidase subunit I (COI) sequences. The molecular delimitation detected 20–36 molecular operational taxonomic units (MOTUs). In comparison, preliminary diagnosis based on traditional taxonomic characters distinguished only four morphological forms, while the characters previously thought to represent intraspecific variation distinguished 13 forms. According to a set of species validation criteria, the identities of nine independent species were acknowledged. Five new species: Tomocerus huangi sp.n., Tomocerus pseudocreatus sp.n., Tomocerus virgatus sp.n., Tomocerus yueluensis sp.n., and Tomocerus zhuque sp.n. are described, while Tomocerus changbaishanensis, Tomocerus spinulus and Tomocerus zayuensis are redescribed on the basis of holotype and/or topotypes. A key to the species of ocreatus-type tomocerids is provided. Incongruence across delimitation methods may be caused by incomplete sampling of populations and limitations of each method. The dorsal chaetotaxy, the prominent manubrial chaetae and the detailed morphology of dental spines were reviewed and confirmed to be valuable in the taxonomy of Tomocerus. The extensive diversity of the ocreatus complex in the southern areas of China indicates that tomocerid Collembola have much higher species richness than expected in the oriental realm. This study narrows species boundaries within the ocreatus complex and provides an example of how molecular approaches and detailed morphological examination can jointly benefit the exploration of biodiversity and the taxonomy of morphologically conservative groups of Collembola.

Species delimitation within the Bothryorrhynchapion weevils: Multiple evidence from genetics, morphology and ecological associations

Curculionidae is a hyperdiverse group of beetles, whose taxonomy and phylogenetics are still poorly understood, especially at the genus level. The latest work on the evolution of Apionini showed a noticeable “mess” in the subtribe Oxystomatina, where most of the morphology-based genera were found to be polyphyletic or paraphyletic. These discrepancies between classical taxonomy and molecular phylogenetics implied the need for further taxonomic revision of these groups. Here, we used sets of morphological, molecular and ecological characters to verify the taxonomic statuses and disentangle the phylogenetic relations among the Bothryorrhynchapion apionids, which are classified as a subgenus of Cyanapion. Morphological data including morphometrics, and multilocus molecular analyses confirmed the monophyly of the Bothryorrhynchapion and species statuses of five species. The morphological analyses showed that Cyanapion (Bothryorrhynchapion) protractum (Sharp, 1891) from the southeast Palaearctic is a synonym of C. (B.) gyllenhalii (Kirby). Moreover, ecological features (host plant use and presence/absence of the endosymbiotic bacteria Wolbachia) helped to unravel the relations among the examined weevils. The speciation of Bothryorrhynchapion apionids was probably affected by allopatric distribution, shifts in the preferred host plants (Vicia sp. or Lathyrus sp.) of sympatric taxa, and infection by different strains of Wolbachia. The paper presents the first comprehensive description of the species’ morphology, biology and ecology, and includes a key to the species.

Patterns of specificity and diversity in species of Paraorygmatobothrium Ruhnke, 1994 (Cestoda: Phyllobothriidae) in Moreton Bay, Queensland, Australia, with the description of four new species.

A survey of tapeworms of galeomorph sharks from Moreton Bay (Queensland, Australia) identified a complex of species of Paraorygmatobothrium Ruhnke, 1994 infecting 11 carcharhiniform and two orectolobiform species. Combined morphological and multi-locus molecular analyses (based on the 28S nuclear ribosomal RNA and partial mitochondrial NADH dehydrogenase subunit 1 genes) revealed the presence of 12 species of Paraorygmatobothrium; four species (Paraorygmatobothrium christopheri n. sp., P. harti n. sp., P. sinclairtaylori n. sp. and P. ullmanni n. sp.) are considered to be new to science and are formally described, four represent known species, and four lack sufficient morphological data to allow definitive identification. In contrast to previous records for the genus, four of the species found in this study exhibited low host specificity [P. orectolobi (Butler, 1987) Ruhnke, 2011, P. sinclairtaylori, P. ullmanni and Paraorygmatobothrium sp. 3], three stenoxenic species were each found in two closely-related sharks (P. orectolobi, P. ullmanni and Paraorygmatobothrium sp. 3) and one euryxenic species was found in five species from two shark families (P. sinclairtaylori). One species was found to exhibit mild morphologically plasticity (P. orectolobi), with size range being associated with different shark species. Conversely, collections of almost morphologically indistinguishable specimens from single shark species were found to represent multiple species of Paraorygmatobothrium. The findings of this study indicate that the description of species of this genus on the basis of morphological data alone is problematic and that the inclusion of multi-locus molecular data is essential for future work on Paraorygmatobothrium. Host specificity, morphology and phylogenetic relatedness of species of Paraorygmatobothrium are explored.

Stool antigen immunodetection for diagnosis of Giardia duodenalis infection in human subjects with HIV and cancer

Human infection with the protozoan parasite Giardia duodenalis is one the most common parasitic diseases worldwide. Higher incidence rates of giardiasis have been reported from human subjects with multiple debilitating chronic conditions, including hypogammaglobulinemia and common variable immunodeficiency (CVID). In the current study, stool specimens were collected from 199 individuals diagnosed with HIV or cancer and immunocompetent subjects. The sensitivity of microscopy-based detection on fresh stool preparations, trichrome staining and stool antigen immunodetection for the diagnosis of G. duodenalis were 36%, 45.5% and 100%, respectively when compared with a highly sensitive stool-based PCR method as the gold standard. Further multilocus molecular analyses using glutamate dehydrogenase (gdh) and triose phosphate isomerase (tpi) loci demonstrated that the AI genotype of G. duodenalis was the most prevalent, followed by the AII genotype and mixed (AI+B) infections. We concluded that stool antigen immunodetection-based immunoassays and stool-based PCR amplification had comparable sensitivity and specificity for the diagnosis of G. duodenalis infections in these populations. Stool antigen detection-based diagnostic modalities are rapid and accurate and may offer alternatives to conventional microscopy and PCR-based diagnostic methods for the diagnosis of G. duodenalis in human subjects living with HIV or cancer.

Multilocus molecular identification and phylogenetic analysis of Colletotrichum tamarilloi as the causal agent of Tamarillo (Solanum betaceum) anthracnose in the Ecuadorian highlands

Anthracnose caused by Colletotrichum spp., is one of the most serious diseases affecting tamarillo (Solanum betaceum) production in the Ecuadorian highlands. The objective of this study was to characterise Colletotrichum isolates obtained from tamarillo to clarify its taxonomic and phylogenetic position. Based on phenotypic and morphologic characterisation, the isolates of this study were consistently grouped within the Colletotrichum acutatum complex. Multilocus molecular phylogenetic analysis based on combined sequences of actin (ACT), β-tubulin (TUB2), and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) sequences using Bayesian probabilities, indicated that 16 of 20 isolates from Imbabura, Cotopaxi, Tungurahua, Bolivar, Chimborazo, Azuay and Loja provinces, belonged to C. tamarilloi. This study represents the first reported case of anthracnose of S. betaceum caused by C. tamarilloi in the Ecuadorian highlands. Interestingly, pathogenicity tests and multilocus molecular analysis revealed a new infraspecific and more aggressive species formed by four isolates obtained from the Pichincha province. These findings probably provided interesting information related to mutant isolates and a possible description of a new pathogenic species affecting tamarillo fruits.

Species of the Colletotrichum acutatum complex associated with anthracnose diseases of fruit in Brazil

Although Colletotrichum acutatum was recently investigated and shown to be a species complex comprising about 30 species, the name is still used in its broad sense for anthracnose pathogens of fruits in Brazil. In this study, a multilocus molecular analysis was carried out based on a dataset of ITS, HIS3, GAPDH, CHS-1, TUB2 and ACT sequences of Colletotrichum strains belonging to the C. acutatum species complex from fruits collected in different regions in Brazil combined with sequences of ex-type and other reference strains of species belonging to this complex. The strains were revealed to belong to Colletotrichum nymphaeae, Colletotrichum melonis, Colletotrichum abscissum and one new species, namely Colletotrichum paranaense, from apple and peach. Morphological descriptions of the new species and a strain closely related to but diverging from C. melonis are provided. From the data presently available, the most common species on apple fruits in Brazil is C. nymphaeae. In a pathogenicity test, strains of all four species caused lesions on detached apple, peach and guava fruits, except for strain CBS 134730 that did not infect guava fruits.

Mitogenomics of ‘Old World Acraea’ butterflies reveals a highly divergent ‘Bematistes’

Afrotropical Acraeini butterflies provide a fascinating potential model system to contrast with the Neotropical Heliconiini, yet their phylogeny remains largely unexplored by molecular methods and their generic level nomenclature is still contentious. To test the potential of mitogenomes in a simultaneous analysis of the radiation, we sequenced the full mitochondrial genomes of 19 African species. Analyses show the potential of mitogenomic phylogeny reconstruction in this group. Inferred relationships are largely congruent with a previous multilocus study. We confirm a monophyletic Telchinia to include the Asiatic Pareba with a complicated paraphylum, traditional (sub)genus Acraea, toward the base. The results suggest that several proposed subgenera and some species groups within Telchinia are not monophyletic, while two other (sub)genera could possibly be combined. Telchinia was recovered without strong support as sister to the potentially interesting system of distasteful model butterflies known as Bematistes, a name that is suppressed in some treatments. Surprisingly, we find that this taxon has remarkably divergent mitogenomes and unexpected synapomorphic tRNA rearrangements. These gene order changes, combined with evidence for deviating dN/dS ratios and evidence for episodal diversifying selection, suggest that the ancestral Bematistes mitogenome has had a turbulent past. Our study adds genetic support for treating this clade as a distinct genus, while the alternative option, adopted by some authors, of Acraea being equivalent to Acraeini merely promotes redundancy. We pave the way for more detailed mitogenomic and multi-locus molecular analyses which can determine how many genera are needed (possibly at least six) to divide Acraeini into monophyletic groups that also facilitate communication about their biology.

Giardia duodenalis and Cryptosporidium occurrence in Australian sea lions (Neophoca cinerea) exposed to varied levels of human interaction.

Giardia and Cryptosporidium are amongst the most common protozoan parasites identified as causing enteric disease in pinnipeds. A number of Giardia assemblages and Cryptosporidium species and genotypes are common in humans and terrestrial mammals and have also been identified in marine mammals. To investigate the occurrence of these parasites in an endangered marine mammal, the Australian sea lion (Neophoca cinerea), genomic DNA was extracted from faecal samples collected from wild populations (n = 271) in Southern and Western Australia and three Australian captive populations (n = 19). These were screened using PCR targeting the 18S rRNA of Giardia and Cryptosporidium. Giardia duodenalis was detected in 28 wild sea lions and in seven captive individuals. Successful sequencing of the 18S rRNA gene assigned 27 Giardia isolates to assemblage B and one to assemblage A, both assemblages commonly found in humans. Subsequent screening at the gdh and β-giardin loci resulted in amplification of only one of the 35 18S rRNA positive samples at the β-giardin locus. Sequencing at the β-giardin locus assigned the assemblage B 18S rRNA confirmed isolate to assemblage AI. The geographic distribution of sea lion populations sampled in relation to human settlements indicated that Giardia presence in sea lions was highest in populations less than 25 km from humans. Cryptosporidium was not detected by PCR screening in either wild colonies or captive sea lion populations. These data suggest that the presence of G. duodenalis in the endangered Australian sea lion is likely the result of dispersal from human sources. Multilocus molecular analyses are essential for the determination of G. duodenalis assemblages and subsequent inferences on transmission routes to endangered marine mammal populations.

Testing monophyly without well-supported gene trees: Evidence from multi-locus nuclear data conflicts with existing taxonomy in the snake tribe Thamnophiini

Ideally, existing taxonomy would be consistent with phylogenetic estimates derived from rigorously analyzed data using appropriate methods. We present a multi-locus molecular analysis of the relationships among nine genera in the North American snake tribe Thamnophiini in order to test the monophyly of the crayfish snakes (genus Regina) and the earth snakes (genus Virginia). Sequence data from seven genes were analyzed to assess relationships among representatives of the nine genera by performing multi-locus phylogeny and species tree estimations, and we performed constraint-based tests of monophyly of classic taxonomic designations on a gene-by-gene basis. Estimates of concatenated phylogenies demonstrate that neither genera are monophyletic, and this inference is supported by a species tree estimate, though the latter is less robust. These taxonomic findings were supported using gene tree constraint tests and Bayes Factors, where we rejected the monophyly of both the crayfish snakes (genus Regina) and the earth snakes (genus Virginia); this method represents a potentially useful tool for taxonomists and phylogeneticists when available data is less than ideal.

Haloleptolyngbya alcalis gen. et sp. nov., a new filamentous cyanobacterium from the soda lake Nakuru, Kenya

The food web of the saline-alkaline Lake Nakuru is dominated by the cyanobacterium Arthrospira fusiformis as the primary producer and a huge population of Lesser Flamingos as direct consumers. However, the dense blooms of Arthrospira are not stable, and collapse irregularly and unpredictably. During such periods they are replaced by other algae or cyanobacteria. The wide fluctuation in the cyanobacterial and algal populations of Lake Nakuru has a great influence on food availability for Lesser Flamingos, and is therefore of high ecological importance. To support the descriptive work on these phenomena, we describe here a new cyanobacterial taxon from this soda lake: Haloleptolyngbya alcalis Dadheech, Mahmoud, Kotut et Krienitz gen. et sp. nov. The study was based on multilocus molecular analyses of 16S rRNA gene, 16S-23S internal transcribed spacer, partial sequences of beta and alpha subunits including intergenic spacer (cpcBA-IGS) of phycocyanin operon, phenotypic features using light microscopy, scanning electron microscopy, transmission electron microscopy, and ecology. The new taxon established a separate lineage within the family of Peudanabaenaceae (Oscillatoriales).

Giardia taxonomy, phylogeny and epidemiology: Facts and open questions

Giardia duodenalis (synonymous Giardia lamblia and Giardia intestinalis) is a flagellated protozoan parasite that reproduces in the small intestine causing giardiasis. It is a cosmopolitan pathogen with a very wide host range, including domestic and wild animal species, as well as human beings. In this paper the current knowledge about the taxonomy and phylogeny of G. duodenalis is summarized from the international literature and data on the detection and epidemiology are also reviewed concentrating on the last 20 years. Authors highlighted the current knowledge and some aspects on G. duodenalis in particular, water transmission and in vitro cultivation. The review sheds light on the difficulties of the strain differentiation and multilocus molecular analysis of Giardia strains especially when applied to water samples containing low numbers of cysts and components complicating the problem of tracking sources of contamination. Genetic elements determining or conferring traits such as infectivity, pathogenicity, virulence, and immune interaction contributing to clearance are currently not well established, if at all. These should be useful and important topics for future research.

Redefinition of Aureobasidium pullulans and its varieties.

Using media with low water activity, a large numbers of aureobasidium-like black yeasts were isolated from glacial and subglacial ice of three polythermal glaciers from the coastal Arctic environment of Kongsfjorden (Svalbard, Spitsbergen), as well as from adjacent sea water, sea ice and glacial meltwaters. To characterise the genetic variability of Aureobasidium pullulans strains originating from the Arctic and strains originating pan-globally, a multilocus molecular analysis was performed, through rDNA (internal transcribed spacers, partial 28 S rDNA), and partial introns and exons of genes encoding β-tubulin (TUB), translation elongation factor (EF1α) and elongase (ELO). Two globally ubiquitous varieties were distinguished: var. pullulans, occurring particularly in slightly osmotic substrates and in the phyllosphere; and var. melanogenum, mainly isolated from watery habitats. Both varieties were commonly isolated from the sampled Arctic habitats. However, some aureobasidium-like strains from subglacial ice from three different glaciers in Kongsfjorden (Svalbard, Spitsbergen), appeared to represent a new variety of A. pullulans. A strain from dolomitic marble in Namibia was found to belong to yet another variety. No molecular support has as yet been found for the previously described var. aubasidani. A partial elongase-encoding gene was successfully used as a phylogenetic marker at the (infra-)specific level.

The use of a self-organizing feature map for the treatment of the results of RAPD and ISSR analyses in studies on the genomic polymorphism in the genus Capsicum L.

The results of studies based on multilocus molecular analyses, including random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), and amplified fragment length polymorphism (AFLP) analyses, are usually presented in the form of images (electrophoregrams, photographs, etc.). The interpretation of this information is complicated, labor-consuming, and subjective. Artificial neural networks (ANNs), which are ideal “image processors,” may be useful when solving such tasks. The possibility of using ANNs for the treatment of the results of RAPD and ISSR analyses has been studied. The RAPD and ISSR fragment spectra of the genus Capsicum L. (peppers) were used in this study. The results of clustering the accessions studied by means of the unweighted pair-group method with arithmetic averages (UPGMA), which is often used for phylogenetic constructions based on RAPD and ISSR data, serve as expert estimates. Fundamentally new methods of genetic polymorphism estimation using ANN technologies, namely, self-organizing feature maps (SOFMs) have been developed. The results show that the clusters obtained with the use of UPGMA and SOFM coincide by more than 90%; taking into account that ANNs can deal with high noise levels and incomplete or contradictory data, the approach proposed may prove to be efficient.