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Simple Summary: The small subunit (SSU) of the nuclear ribosomal DNA that codes 18S rRNA is one of the most frequently sequenced genes in phylogenetic analyses of true bugs (Hemiptera: Heteroptera). However, no studies have been identified that use this method with lace bugs (Tingidae). Furthermore, the secondary and tertiary structures of the 18S rRNA have not been described nor used to interpret relationships among lace bug taxa. The number of nucleotides and shapes of the 18S rRNA length-variable regions (LVRs) have been confirmed to be phylogenetically informative; therefore, we verified their usefulness in resolving the validity issues within the Acalyptaini tribe. The lace bug tribe Acalyptaini (Tingidae: Tinginae) includes five genera, Acalypta, Derephysia, Dictyonota, Kalama, and Recaredus, and it was recently resurrected based on morphological and karyological characters. We aimed to validate the distinctiveness of this tribe using 18S rDNA sequences, which have not been used in previous Tingidae phylogenomic studies. Our results confirmed the monophyly of the tribe. Moreover, the monophyly of the subfamily Cantacaderinae and its basal position within the family Tingidae were indicated, as well as the position of the tribe Litadeini as sister to all other Tinginae. In addition, we attempted to determine the apomorphic morpho-molecular characters in the secondary and tertiary structures of length-variable regions of the 18S rRNA sequences of the analysed species. The results showed that two LVRs (LVR X and LVR L) of the hypervariable region V4 exhibited significant variability in the number of nucleotides and could be considered for apomorphic recognition. [ABSTRACT FROM AUTHOR]

Viet Nam has a coastline of 3200 km with thousands of islands providing diverse habitats for benthic harmful algal species including species of Gambierdiscus. Some of these species produce ciguatera toxins, which may accumulate in large carnivore fish potentially posing major threats to public health. This study reports five species of Gambierdiscus from Vietnamese waters, notably G. australes, G. caribaeus, G. carpenteri, G. pacificus, and G. vietnamensis sp. nov. All species are identified morphologically by LM and SEM, and identifications are supported by molecular analyses of nuclear rDNA (D1–D3 and D8–D10 domains of LSU, SSU, and ITS1‐5.8S‐ITS2 region) based on cultured material collected during 2010–2021. Statistical analyses of morphometric measurements may be used to differentiate some species if a sufficiently large number of cells are examined. Gambierdiscus vietnamensis sp. nov. is morphologically similar to other strongly reticulated species, such as G. belizeanus and possibly G. pacificus; the latter species is morphologically indistinguishable from G. vietnamensis sp. nov., but they are genetically distinct, and molecular analysis is deemed necessary for proper identification of the new species. This study also revealed that strains denoted G. pacificus from Hainan Island (China) should be included in G. vietnamensis sp. nov. [ABSTRACT FROM AUTHOR]

The lace bug tribe Acalyptaini (Tingidae: Tinginae) includes five genera, Acalypta, Derephysia, Dictyonota, Kalama, and Recaredus, and it was recently resurrected based on morphological and karyological characters. We aimed to validate the distinctiveness of this tribe using 18S rDNA sequences, which have not been used in previous Tingidae phylogenomic studies. Our results confirmed the monophyly of the tribe. Moreover, the monophyly of the subfamily Cantacaderinae and its basal position within the family Tingidae were indicated, as well as the position of the tribe Litadeini as sister to all other Tinginae. In addition, we attempted to determine the apomorphic morpho-molecular characters in the secondary and tertiary structures of length-variable regions of the 18S rRNA sequences of the analysed species. The results showed that two LVRs (LVR X and LVR L) of the hypervariable region V4 exhibited significant variability in the number of nucleotides and could be considered for apomorphic recognition.

Abstract Background The black soldier fly (Diptera: Stratiomyidae, Hermetia illucens) is renowned for its bioconversion ability of organic matter, and is the worldwide most widely used source of insect protein. Despite varying extensively in morphology, it is widely assumed that all black soldier flies belong to the same species, Hermetia illucens. We here screened about 600 field-collected and cultured flies from 39 countries and six biogeographic regions to test this assumption based on data for three genes (mitochondrial COI, nuclear ITS2 & 28S rDNA) and in order to gain insights into the phylogeography of the species. Results Our study reveals a surprisingly high level of intraspecific genetic diversity for the mitochondrial barcoding gene COI (divergences up to 4.9%). This level of variability is often associated with the presence of multiple species, but tested nuclear markers (ITS2 and 28S rDNA) were invariant and fly strain hybridization experiments under laboratory conditions revealed reproductive compatibility. COI haplotype diversity is not only very high in all biogeographic regions (56 distinct haplotypes in total), but also in breeding facilities and research centers from six continents (10 haplotypes: divergences up to 4.3%). The high genetic diversity in fly-breeding facilities is mostly likely due to many independent acquisitions of cultures via sharing and/or establishing new colonies from field-collected flies. However, explaining some of the observed diversity in several biogeographic regions is difficult given that the origin of the species is considered to be New World (32 distinct haplotypes) and one would expect severely reduced genetic diversity in the putatively non-native populations in the remaining biogeographic regions. However, distinct, private haplotypes are known from the Australasian (N = 1), Oriental (N = 4), and the Eastern Palearctic (N = 4) populations. We reviewed museum specimen records and conclude that the evidence for introductions is strong for the Western Palearctic and Afrotropical regions which lack distinct, private haplotypes. Conclusions Based on the results of this paper, we urge the black soldier fly community to apply molecular characterization (genotyping) of the fly strains used in artificial fly-breeding and share these data in research publications as well as when sharing cultures. In addition, fast-evolving nuclear markers should be used to reconstruct the recent invasion history of the species.

Two new species of lung-dwelling nematodes are described from North American frogs: Rhabdias aurorae n. sp. from Rana aurora and Rhabdias conni n. sp. from Rana clamitans and Rana catesbeiana from Arkansas; the latter species was also found in Oklahoma and Georgia. Rhabdias aurorae n. sp. differs from other Nearctic congeners in the combination of the following characteristics: buccal capsule 22-25 μm wide, elongated tail covered with inflated cuticle, esophagus with prominent dilatation in anterior part and 6 small circumoral lips. Rhabdias conni n. sp. is morphologically closest to Rhabdias ranae Walton, 1929 and Rhabdias joaquinensisIngles, 1936; it differs from them in the shape of lateral pseudolabia, the dimensions of the body, and the egg size. Both new species were found to be significantly different from the Nearctic congeners in the nucleotide sequences of nuclear ribosomal DNA (18S-ITS-28S region), 12S, and CO1 mitochondrial genes. The 2 new species differ from other currently sequenced Nearctic congeners by 1.1-2.7% of nucleotide positions in the nuclear rDNA region, 1.3-3.4% in the 12S gene, and 3.4-9.4% in CO1 gene. Molecular phylogenetic analysis based on nuclear ribosomal DNA sequences placed both new species into the clade consisting of Nearctic and Neotropical Rhabdias spp. The position of Rh. aurorae n. sp. within the clade is uncertain because of a polytomy, but Rh. conni n. sp. is nested within the "Rh. joaquinensis complex" related to Rh. ranae and Rhabdias tarichaeKuzmin, Tkach, and Snyder, 2003. The phylogenetic analysis based on nuclear ribosomal DNA sequences has revealed 3 evolutionary host-switching events from anuran to caudatan hosts among Rhabdias spp. that occurred in the Nearctic and Palearctic. The molecular phylogeny also suggests that Rhabdias may have originally evolved in what is now Africa., (© American Society of Parasitologists 2024.)

Background: The black soldier fly (Diptera: Stratiomyidae, Hermetia illucens) is renowned for its bioconversion ability of organic matter, and is the worldwide most widely used source of insect protein. Despite varying extensively in morphology, it is widely assumed that all black soldier flies belong to the same species, Hermetia illucens. We here screened about 600 field-collected and cultured flies from 39 countries and six biogeographic regions to test this assumption based on data for three genes (mitochondrial COI, nuclear ITS2 & 28S rDNA) and in order to gain insights into the phylogeography of the species. Results: Our study reveals a surprisingly high level of intraspecific genetic diversity for the mitochondrial barcoding gene COI (divergences up to 4.9%). This level of variability is often associated with the presence of multiple species, but tested nuclear markers (ITS2 and 28S rDNA) were invariant and fly strain hybridization experiments under laboratory conditions revealed reproductive compatibility. COI haplotype diversity is not only very high in all biogeographic regions (56 distinct haplotypes in total), but also in breeding facilities and research centers from six continents (10 haplotypes: divergences up to 4.3%). The high genetic diversity in fly-breeding facilities is mostly likely due to many independent acquisitions of cultures via sharing and/or establishing new colonies from field-collected flies. However, explaining some of the observed diversity in several biogeographic regions is difficult given that the origin of the species is considered to be New World (32 distinct haplotypes) and one would expect severely reduced genetic diversity in the putatively non-native populations in the remaining biogeographic regions. However, distinct, private haplotypes are known from the Australasian (N = 1), Oriental (N = 4), and the Eastern Palearctic (N = 4) populations. We reviewed museum specimen records and conclude that the evidence for introductions is strong for the Western Palearctic and Afrotropical regions which lack distinct, private haplotypes. Conclusions: Based on the results of this paper, we urge the black soldier fly community to apply molecular characterization (genotyping) of the fly strains used in artificial fly-breeding and share these data in research publications as well as when sharing cultures. In addition, fast-evolving nuclear markers should be used to reconstruct the recent invasion history of the species. [ABSTRACT FROM AUTHOR]

Abstract Black (sooty) head mold of wheat and barley, which is commonly characterized by black discoloration of their heads, is caused by different fungi colonizing the mature and senescent heads. It seems that black head mold develops more on plants when humid conditions occurs as the crop matures, or when harvest is delayed due to wet conditions and/or when portions of plants specially heads are died prematurely. During an investigation on fungal species associated with black head mold of wheat and barley in Golestan, Alborz and Qazvin provinces in the spring and summer of 2014 and 2015, a total of 133 Alternaria isolates with the characteristics of the section Infectoriae were collected. Based on the results obtained from morphological studies and data from nucleotide sequences of the two genomic loci, ITS–nrDNA and part of gelyceraldehyde–3–phosphate dehydrogenase (gpdh), four species Viz. Alternaria arbusti, A. ethzedia, A. incomplexa and A. triticimaculans were identified. All identified species in the case of this study are reported for the first time as Alternaria species associated with black head mold symptoms of wheat and barley in the world. Also, except for A. arbusti, which was previously reported from cabbage plants in Iran, the remaining three species are new records for mycobiota of Iran. The species are fully described here.

Three new species of the genus Micractinium were collected from five localities on the South Shetland Islands in maritime Antarctica, and their morphological and molecular characteristics were investigated. The vegetative cells are spherical to ellipsoidal and a single chloroplast is parietal with a pyrenoid. Because of their simple morphology, no conspicuous morphological characters of new species were recognized under light microscopy. However, molecular phylogenetic relationships were inferred from the concatenated small subunit rDNA, and internal transcribed spacer (ITS) sequence data indicated that the Antarctic microalgal strains are strongly allied to the well-supported genus Micractinium, including M. pusillum, the type species of the genus, and three other species in the genus. The secondary structure of ITS2 and compensatory base changes were used to identify and describe six Antarctic Micractinium strains. Based on their morphological and molecular characteristics, we characterized three new species of Micractinium: M. simplicissimum sp. nov., M. singularis sp. nov., and M. variabile sp. nov. [ABSTRACT FROM AUTHOR]

Cladocerans of the genus Daphnia O.F. Müller (Crustacea: Cladocera) are typical members of different types of water bodies and are used as model organisms in various biological disciplines. Within the genus, a considerable number of closely related and cryptic species are noted, the identification of which by morphological traits often causes difficulties. In the present study, species identification in the Daphnia longispina complex, namely, D. longispina O.F. Müller, D. hyalina Leydig, D. umbra Taylor, Hebert et Colbourne, and D. cf. longispina, was performed using data on the predicted secondary structure of the second internal transcribed spacer (ITS2) of the nuclear rDNA. Phylogenetic analysis carried out using the Profile Neighbor-Joining algorithm and the analysis of compensatory base changes supported the species status of D. hyalina and D. cf. longispina. It was demonstrated that the data on the ITS2 secondary structure can be used to resolve complex taxonomic problems in the study of cladocerans in general and the species complexes in particular. [ABSTRACT FROM AUTHOR]

The grass parasitic fungus Claviceps purpurea sensu lato produces sclerotia with toxic indole alkaloids. It constitutes several genetic groups with divergent habitat preferences that recently were delimited into separate proposed species. We aimed to 1) analyze genetic variation of C. purpurea sensu lato in Norway, 2) characterize the associated indole alkaloid profiles, and 3) explore relationships between genetics, alkaloid chemistry and ecology. Approximately 600 sclerotia from 14 different grass species were subjected to various analyses including DNA sequencing and HPLC-MS. Molecular results, supported by chemical and ecological data, revealed one new genetic group (G4) in addition to two of the three known; G1 (C. purpurea sensu stricto) and G2 (C. humidiphila). G3 (C. spartinae) was not found. G4, which was apparently con-specific with the recently described C. arundinis sp. nov, was predominantly found in very wet habitats on Molinia caerulea and infrequently in saline habitats on Leymus arenarius. Its indole-diterpene profile resembled G2, while its ergot alkaloid profile differed from G2 in high amounts of ergosedmam. In contrast to G1, indole-diterpenes were consistently present in G2 and G4. Our study supports and complements the newly proposed species delimitation of the C. purpurea complex, but challenges some species characteristics including host spectrum, habitat preferences and sclerotial floating ability.

Black (sooty) head mold of wheat and barley which is commonly characterized by black discoloration of their heads, is caused by different fungi colonizing the mature and senescent heads. It seems that black head mold develop more on plants when humid conditions occurs as the crop matures, or when harvest is delayed due to wet conditions and/or when portions of plants specially heads are died prematurely. During an investigation on fungal species associated with black head mold of wheat and barley in Golestan, Alborz and Qazvin provinces in the spring and summer of 2014 and 2015, a total of 133 Alternaria isolates with the characteristics of the section Infectoriae were collected. Based on the results obtained from morphological studies and data from nucleotide sequences of the two genomic loci, ITS–nrDNA and part of gelyceraldehyde–3–phosphate dehydrogenase (gpdh), four species Viz. Alternaria arbusti, A. ethzedia, A. incomplexa and A. triticimaculans were identified. All identified species in the case of this study are reported for the first time as Alternaria species associated with black head mold symptoms of wheat and barley in the world. Also, except for A. arbusti, which was previously reported from cabbage plants in Iran, the remaining three species are new records for mycobiota of Iran. The species are fully described here. [ABSTRACT FROM AUTHOR]

Freshwater lymnaeid snails are crucial in defining transmission and epidemiology of fascioliasis. In South America, human endemic areas are related to high altitudes in Andean regions. The species Lymnaea diaphana has, however, been involved in low altitude areas of Chile, Argentina and Peru where human infection also occurs. Complete nuclear ribosomal DNA 18S, internal transcribed spacer (ITS)-2 and ITS-1 and fragments of mitochondrial DNA 16S and cytochrome c oxidase (cox)1 genes of L. diaphana specimens from its type locality offered 1,848, 495, 520, 424 and 672 bp long sequences. Comparisons with New and Old World Galba/Fossaria, Palaearctic stagnicolines, Nearctic stagnicolines, Old World Radix and Pseudosuccinea allowed to conclude that (i) L. diaphana shows sequences very different from all other lymnaeids, (ii) each marker allows its differentiation, except cox1 amino acid sequence, and (iii) L. diaphana is not a fossarine lymnaeid, but rather an archaic relict form derived from the oldest North American stagnicoline ancestors. Phylogeny and large genetic distances support the genus Pectinidens as the first stagnicoline representative in the southern hemisphere, including colonization of extreme world regions, as most southern Patagonia, long time ago. The phylogenetic link of L. diaphana with the stagnicoline group may give light to the aforementioned peculiar low altitude epidemiological scenario of fascioliasis.

Sea anemones of the family Aiptasiidae sensu Grajales and Rodríguez (2014) are conspicuous members of shallow-water environments, including several species widely used as model systems for the study of cni darian-dinoflagellate symbiosis and coral bleaching. Although previously published phylogenetic studies of sea anemones recovered Aiptasiidae as polyphyletic, they only included a sparse sample in terms of its taxonomic diversity and membership of the family had not been yet revised. This study explores the phylogenetic relationships of this family using five molecular markers and including newly collected material from the geographical distribution of most of the currently described genera and species. We find a monophyletic family Aiptasiidae. All the currently proposed genera were recovered as monophyletic units, a finding also supported by diagnostic morphological characters. Our results confirm Bellactis and Laviactis as members of Aiptasiidae, also in agreement with previous morphological studies. The monophyly of the group is congruent with the morphological homogeneity of the members of this family. The obtained results also allow discussing the evolution of morphological characters within the family. Furthermore, we find evidence for and describe a new cryptic species, Exaiptasia brasiliensis sp. nov., based on molecular data, geographical distribution, and the identity of its endosymbiotic dinoflagellate. [ABSTRACT FROM AUTHOR]

The evolutionary history and times of divergence of triatomine bug lineages are estimated from molecular clocks inferred from nucleotide sequences of the small subunit SSU (18S) and the second internal transcribed spacer (ITS-2) of the nuclear ribosomal DNA of these reduviids. The 18S rDNA molecular clock rate in Triatominae, and Prosorrhynchan Hemiptera in general, appears to be of 1.8% per 100 million years (my). The ITS-2 molecular clock rate in Triatominae is estimated to be around 0.4-1% per 1 my, indicating that ITS-2 evolves 23-55 times faster than 18S rDNA. Inferred chronological data about the evolution of Triatominae fit well with current hypotheses on their evolutionary histories, but suggest reconsideration of the current taxonomy of North American species complexes.

The grass parasitic fungus Claviceps purpurea sensu lato produces sclerotia with toxic indole alkaloids. It constitutes several genetic groups with divergent habitat preferences that recently were delimited into separate proposed species. We aimed to 1) analyze genetic variation of C. purpurea sensu lato in Norway, 2) characterize the associated indole alkaloid profiles, and 3) explore relationships between genetics, alkaloid chemistry and ecology. Approximately 600 sclerotia from 14 different grass species were subjected to various analyses including DNA sequencing and HPLC-MS. Molecular results, supported by chemical and ecological data, revealed one new genetic group (G4) in addition to two of the three known; G1 (C. purpurea sensu stricto) and G2 (C. humidiphila). G3 (C. spartinae) was not found. G4, which was apparently con-specific with the recently described C. arundinis sp. nov, was predominantly found in very wet habitats on Molinia caerulea and infrequently in saline habitats on Leymus arenarius. Its indole-diterpene profile resembled G2, while its ergot alkaloid profile differed from G2 in high amounts of ergosedmam. In contrast to G1, indole-diterpenes were consistently present in G2 and G4. Our study supports and complements the newly proposed species delimitation of the C. purpurea complex, but challenges some species characteristics including host spectrum, habitat preferences and sclerotial floating ability. [ABSTRACT FROM AUTHOR]

The world's fourth largest food crop, potato, originates in the Andes. Here, the community composition of arbuscular mycorrhizal fungi (AMF) associated with potato in Andean ecosystems is described for the first time. AMF were studied in potato roots and rhizosphere soil at four different altitudes from 2,658 to 4,075 m above mean sea level (mamsl) and in three plant growth stages (emergence, flowering, and senescence). AMF species were distinguished by sequencing an approx. 1,500 bp nuclear rDNA region. Twenty species of AMF were identified, of which 12 came from potato roots and 15 from rhizosphere soil. Seven species were found in both roots and soil. Interestingly, altitude affected species composition with the highest altitude exhibiting the greatest species diversity. The three most common colonizers of potato roots detected were Funneliformis mosseae, an unknown Claroideoglomus sp., and Rhizophagus irregularis. Notably, the potato-associated AMF diversity observed in this Andean region is much higher than that reported for potato in other ecosystems. Potato plants were colonized by diverse species from 8 of the 11 Glomeromycota families. Identification of the AMF species is important for their potential use in sustainable management practices to improve potato production in the Andean region. [ABSTRACT FROM AUTHOR]

Highlights: [•] A pseudogene is described in the nuclear rDNA 5.8S and ITS-2 of triatomine vectors. [•] It evolves independently from the concerted evolution of the functional rDNA operon. [•] A complete characterization of its primary and secondary structures is made. [•] A pseudogene in many phylogenetically related species appears to be unique in animals. [•] It becomes a valuable new marker opening a new fundamental and applied research field. [ABSTRACT FROM AUTHOR]

Highlights: [•] Determination of the mitochondrial genome and nuclear rRNA cluster of Diurodrilus subterraneus (Diurodrilidae). [•] Nuclear rRNA data placed Diurodrilidae in Annelida. [•] Mitochondrial genome data support placement of Diurodrilidae in Annelida. [•] Diurodrilidae are not closely related to Platyzoa. [•] The origin of interstitial Diurodrilidae occured most likely by progenetic evolution. [ABSTRACT FROM AUTHOR]

Plasmodiophora brassicae is a soil-borne obligate intracellular parasite in the phylum Cercozoa of the Rhizaria that causes clubroot disease of crucifer crops. To control the disease, understanding the distribution and infection routes of the pathogen is essential, and thus development of reliable molecular markers to discriminate geographic populations is required. In this study, the nuclear ribosomal RNA gene (rDNA) repeat unit of P. brassicae was determined, with particular emphasis on the structure of large subunit (LSU) rDNA, in which polymorphic regions were expected to be present. The complete rDNA complex was 9513bp long, which included the small subunit, 5.8S and LSU rDNAs as well as the internal transcribed spacer and intergenic spacer regions. Among eight field populations collected from throughout Honshu Island, Japan, a 1.1 kbp region of the LSU rDNA, including the divergent 8 domain, exhibited intraspecific polymorphisms that reflected geographic isolation of the populations. Two new group I introns were found in this region in six out of the eight populations, and the sequences also reflected their geographic isolation. The polymorphic region found in this study may have potential for the development of molecular markers for discrimination of field populations/isolates of this organism. [Copyright &y& Elsevier]

a special reference of the nuclear cistron rDNA of cyclopoid copepods, we obtained the entire DNA sequence of a single rDNA repeat unit from Paracyclopina nana (Cyclopoida: Cyclopettidae). The genomic organization of P. nana rDNA (7,974 bp, 51.7% of GC) was observed to be 18S-ITS1-5.8S-ITS2-28S-IGS in order. Comparative analyses of the rDNA between P. nana and other copepods showed that the intergenic spacer (IGS) was highly informative and divergent, while other coding regions are relatively conserved. We detected eleven poly(T) tracts in the IGS, demonstrating the high AT content in this region. In addition, many sub-repeat sequence patterns (e.g., AG, AT, GC, CCG, TC) such as microsatellites were identified from the rDNA IGS of P. nana. In this article, we show the first complete sequence of rDNA from the order Cyclopoida, providing a better understanding of molecular characteristics in molecular taxonomy. [ABSTRACT FROM AUTHOR]

Tricholomopsis flammula, recently validated, was studied by molecular methods to clarify its taxonomic position. Sequences of T. flammulla form a distinct clade sister to a well-supported clade of T. rutilans sequences, whereas T. decora forms a cluster standing apart from them. T. flammula really is a good species separate from T. rutilans and T. decora, well distinguishable both phenotypically and molecularly. The infraspecific variability revealed by molecular methods is expressed in slight differences among some of the collections studied. The brief characteristics, selected descriptions and illustrations, key diagnostic characters and data on habitats and substrates of T. flammula are given. A discussion on variability of its basidiocarps is added. [ABSTRACT FROM AUTHOR]

Phylogenetic analysis, based on nuclear rDNA internal transcribed spacers (ITS) of Arachis species, corroborated a broad sub-classification of the genus. Three clustering algorithms were used to generate dendrograms which showed that Arachis Sections Extranervosae, Heteranthae and Triseminata were most primitive, and Section Arachis was most advanced, with Sections Caulorrhizae, Erectoides, Procumbentes, Rhizomatosae, and Trierectoides intermediate in evolutionary terms, in relation to the genus Stylosanthes, when it was used as the outgroup. [ABSTRACT FROM AUTHOR]

Abstract: Most ‘ambrosia’ fungi are members of a heterogeneous group of ophiostomatoids that includes the anamorph genera Ambrosiella, Raffaelea and Dryadomyces. The taxonomy of these fungi based on morphological features has been complicated by these features being poorly descriptive and having evolved convergently. In this work we report maximum parsimony and Bayesian phylogenetic analysis of a multigene dataset (nSSU rDNA, nLSU rDNA and β-tubulin gene) from sixty-seven taxa that include members of genera Ambrosiella, Raffaelea and Dryadomyces and a diverse set of ophiostomatoid relatives. We discuss the phylogenetic status of genus Ambrosiella and its relationships with representatives of Ophiostomatales teleomorph and anamorph genera. Our analysis shows that ten of the thirteen species that had been assigned to the genus Ambrosiella are related to the teleomorph genera Grosmannia or Ophiostoma, within the Ophiostomatales. The multigene analysis and expanded taxon samplings provide a higher resolution for the species phylogeny and clarify detailed relationships between Ambrosiella associates of ambrosia and bark beetles and the closely related species of genera Raffaelea and Dryadomyces. We discuss difficulties in using the morphology of conidiophores and the mode of conidiogenesis to re-define the phylogenetic classification of Ambrosiella species. Finally, we report a correlation between the molecular classification of Ophiostomatales-related species of Ambrosiella and Raffaelea and their ecological niches. [Copyright &y& Elsevier]

Abstract: In Chagas disease, triatomine vectors are the main target for control measures because of the absence of effective drugs. The broad usefulness of nuclear rDNA and mtDNA sequences explains why triatomine studies using these markers have increased so pronouncedly in recent years. This indicates the appropriateness of an updated review about these molecular markers, concentrating on aspects useful for research on Chagas disease vectors. A comparative analysis is presented on the efficiency, weight of their different characteristics, limitations and problems of each of the different DNA markers in the light of the results obtained in studies on populations, hybrids, subspecies and species of the subfamily Triatominae. The use of a standardized composite haplotype code nomenclature for both nuclear rDNA and mtDNA markers is strongly encouraged to avoid difficulties in comparative studies. Triatomine aspects related to concerted evolution, microsatellites, minisatellites and insertions/deletions in nuclear rDNA and silent/non-silent mutations, pseudogenes and weaknesses of partial sequences in mtDNA are analysed. Introgression and hybrids, nuclear and mitochondrial DNA strengths, and compared evolutionary rates of nuclear rDNA and mtDNA in triatomines are discussed. Many conclusions are obtained thanks to the availability, for the first time in triatomines, of a complete sequence of a protein-coding mtDNA gene as ND1 from very numerous triatomine species covering from different populations of a species up to members belonging to different tribes. The evolutionary rates of each nuclear rDNA marker and mtDNA marker are analysed by comparison at subspecies level (intrapopulational, interpopulational, between morphs, and between subspecies) and species level (close and distant species of the same genus, species of different genera, and species of different tribes). Weaknesses of mtDNA for systematic–taxonomic purposes detected recently and newly in insects and triatomines, respectively, are discussed in detail. Emphasis is given to taxonomic units and biological entities presenting well-known problematics, both from the systematic–taxonomic and/or epidemiological-control points of view, as well as to molecular situations which can give rise to erroneous conclusions. All these aspects constitute the background on which the key question about the systematic concepts of species and subspecies in triatomines is focused. The global purpose is to facilitate future work on triatomines by highlighting present gaps, how better choice the appropriate markers, and marker aspects which should be taken into account. Key characteristics as α, CI and transformation rate matrices ought to be obtained and noted to get appropriate results and allow correct interpretations. The main aim is to offer a baseline for future fundamental research on triatomines and applied research on transmission, epidemiology and control measures related to Chagas disease vectors. [Copyright &y& Elsevier]

The molecular phylogeny of nuclear LSU rDNA sequences (D1/D2 domain), ITS regions, and beta-tubulin gene ( tub2) showed that the seven strains of Shiraia-like fungi obtained from fresh bamboo tissues as endophytes were closely related to Shiraia bambusicola and had three distinctive lineages (groups A-C). The closest group (group A) to S. bambusicola produced distinctive prawn-shaped conidioma-like structures that differed from conidiomata in the anamorph of S. bambusicola. Currently, none of the morphological structures and molecular database records were compatible with our Shiraia-like fungi. These results reveal that Shiraia-like fungi group A is supposed to be a new species that should be assigned into a novel genus/species related to S. bambusicola. [ABSTRACT FROM AUTHOR]

Abstract: The toxic Heterosigma akashiwo has been found in coastal environments and its algal blooms have been associated with mass mortality in marine organisms and farmed fish. Over the last two decades, H. Akashiwo has expanded its geographical range on a worldwide scale, though all populations are suspected to be a single species. To find strong molecular evidence, supporting this hypothesis we determined nuclear 18S, ITS and LSU rDNA, and chloroplast rbcL, rbcS and flanking IGS sequences from six isolates located in North America, Japan and Korea. We compared individual loci from molecular regions (e. G. , 26. 7kbp of DNA sequence) and found all the isolates to have an identical genotype. Further, the long sequences allow us to compare all the partial sequences that have been reported from samples obtained in ten countries. All these sequence are nearly identical. This suggests that they have dispersed recently from one location. The sequences revealed here can be used as an additional option for making molecular comparisons of sequences from the same isolate. [Copyright &y& Elsevier]

We use data from the internal transcribed spacer (ITS) region of the nuclear rDNA cistron and the chloroplast psbA-trnH intergenic spacer to reconstruct the phylogenetic relationships among southern African species of Euphorbia. The results indicate that major re-organization is necessary of the groupings within Euphorbia that have been recognised in the past, since most of them turn out to be polyphyletic. Furthermore, in its present circumscription, Euphorbia itself is not monophyletic, nor do the southern African species form a monophyletic group. Both datasets show that the southern African species fall into four major groups, which we recognise as subgenera: Chamaesyce Raf., Esula Pers., Euphorbia and Rhizanthium (Boiss.) Wheeler. To accommodate the southern African species, subg. Chamaesyce is divided into sect. Chamaesvce, sect. Frondosae Bruyns, sect. nov., sect. Articulofruticosae Bruyns, sect. nov. and sect. Espinosae Pax & Hoffm. Subgenus Euphorbia is divided into sect. Euphorbia, sect. Monadenium (Pax) Bruyns, sect. Goniostema: H. Baill. ex Boiss. and sect. Tirucalli Boiss. To re-establish the monophyly of Euphorbia, the genera Endadenium L.C. Leach, Monadenium Pax and Synadenium Boiss. are reduced to synonymy under Euphorbia subg. Euphorbia sect. Monadenium and the species are all transferred to Euphorbia. Consequently the subtribe Euphorbiinae now consists of the single, very large, very widely distributed and very diverse genus Euphorbia. Three of the subgenera (Chamaesyce, Esula, Euphorbia) are nearly cosmopolitan, showing the great age and wide extent of the radiation that has occurred within Euphorbia. The remaining subg. Rhizanthium is mainly African. [ABSTRACT FROM AUTHOR]

BrazilianFusariumisolates causing soybean sudden death syndrome (SDS) were characterized by comparing them with otherFusariumisolates associated with soybean root rot, as well asF. solanif.sp.glycinesisolates associated with the disease in the USA, using molecular (mitochondrial and nuclear rDNA), morphological, cultural and pathogenic characteristics. On the basis of pathogenicity data, and restriction fragment length polymorphism and sequence analysis of the rDNA internal transcribed spacer (ITS) regions, isolates formed a group distinct from nonSDSF. solaniisolates, as well as otherFusariumspecies. ITS sequence analysis also revealed that Brazilian isolates were distinct from the majority of SDS pathogens from the USA (Fusarium virguliforme) and conformed toFusarium tucumaniae. [ABSTRACT FROM AUTHOR]

Many homobasidiomycetes are characterized by a combination of gloeocystidia and amyloid basidiospores. They display a great variation in basidioma morphology, including erect and effused forms and gilled and nongilled forms. Earlier studies have shown these taxa to be related, and the group has been named the russuloid clade. Phylogenetic relationships among russuloid basidiomycetes were investigated using sequence data from the nuclear 5.8S, ITS2 and large-subunit rDNA genes. A dataset including 127 ingroup sequences representing 43 genera and ca 120 species were analyzed by maximumparsimony and neighbor-joining methods. The sampling of taxa had an emphasis on nongilled taxa and two-thirds of the species possessed corticioid basidiomata. Thirteen major well-supported clades were identified within the russuloid clade. All clades except one include corticioid species. Ten characters from basidioma morphology and cultured mycelium were observed and evaluated. Results suggest that gloeocystidia are a synapomorphy for taxa within the russuloid clade while the amyloidity of spores is inconsistent. The ornamentation of spores and type of nuclear behavior seems to be informative characters at genus level. The agaricoid genera Lactarius and Russula are nested in a clade with corticioid species at the basal position. The new combinations Boidinia aculeata, Gloeodontia subasperispora, Gloeocystidiopsis cryptacantha and Megalocystidium wakullum are proposed. [ABSTRACT FROM AUTHOR]

Comparative ultrastructural data have shown that atleast two distinct groups exist within Carteria. Similarly, interpretations of variation in gross morphological features have led to the discovery of morphologically distinct groups within the genus. Partial sequences from the nuclear-encoded small and large subunit ribosomal RNA molecules of selected Carteria taxa were studied as a means of 1)testing hypotheses that distinct groups of species exist within the genus and 2)assessing monophyly of the genus. Parsimony analysis of the sequence data suggests that three Carteria species, C.lunzenis, C. crucifera, and C.oliveri, form a monophyletic group that is the basal sister group to all other ingroup flagellate taxa (including species of Chlamydomonas, Haematococcus, Stephanosphaera, Volvox and Eudorina). Two other Carteria taxa, C.radiosa and Carteria sp. (UTEX isolate LB 762), form a clade that is the sister group to a clade that includes Haematococcus spp., Chlamydomonas spp., and Stephanosphaera. Thus, the sequence data support the interpretation of ultrastructural evidence that described two distinct Carteria lineages. Moreover, the sequence data suggest that these two Carteria groups do not form a monophyletic assemblage. Parsimony analysis of a suite of organismal (morphologica, ultrastructural, life history and biochemical) character data also suggest two distinct lineages among the five Carteria taxa; however, the organismal data are ambiguous regarding monopophyly of these Carteria taxa. When the two independent data sets are pooled, monophyly of Carteria is not supported; therefore, the weight of available evidence, both molecular and organismal, fails to support the concept of Carteria as a natural genus. [ABSTRACT FROM AUTHOR]

The ribosomal DNA repeat units of two closely related species of the genus Fraxinus, F. excelsior and F. oxyphylla, were characterized. The physical maps were constructed from DNA digested with BamHI, EcoRI, EcoRV and SacI, and hybridized with three heterologous probes. The presence or the absence of an EcoRV restriction site in the 18 s RNA gene characterizes two ribosomal DNA unit types found in both species and which coexist in all individuals. A third unit type appeared unique to all individuals of F. oxyphylla. It carries an EcoRI site in the intergenic spacer. Each type of unit displayed length variations. The rDNA unit length of F. excelsior and F. oxyphylla was determined with EcoRV restriction. It varied between 11kb and 14.5kb in F. excelsior and between 11.8kb to 13.8kb in F. oxyphylla. Using SacI restriction, at least ten spacer length variants were observed in F. excelsior, for which a detailed analysis was conducted. Each individual carries 2-4 length variants which vary by a 0.3-kb step multiple. This length variation was assigned to the intergenic spacer. By using the entire rDNA unit of flax as probe in combination with EcoRI restriction, each species can be unambiguously discriminated. The species-specific banding pattern was used to compare trees from a zone of sympatry between the two species. In some cases, a conflicting classification was obtained from morphological analysis and the use of the species-specific rDNA polymorphism. Implications for the genetic management of both species are discussed. [ABSTRACT FROM AUTHOR]

Nucleotide sequences from the internal transcribed spacer (ITS) regions of the 18S–26S nuclear ribosomal DNA have been studied from ten species of Quercus (representing four subgenera), Castanea sativa and Fagus sylvatica, as a preliminary molecular contribution to the still poorly understood systematics and evolution of Fagaceae. The resulting matrix has been used to calculate pair-wise sequence divergence indices and to construct a maximum parsimony tree for Quercus coding indels as a fifth state. Divergence is greater for Quercus vs. Fagus than for Quercus vs. Castanea. The tree for the Quercus taxa studied reveals two clearly divergent clades. In clade I the evergreen W Mediterranean Q. suber appears in a basal position as sister to more distal deciduous taxa, i.e. the E Mediterranean Q. macrolepis and the E Asiatic Q. acutissima (all formerly united as different sections under the apparently polyphyletic subg. Cerris), and Q. rubra (a representative of the N American subg. Erythrobalanus), forming a pair with Q. acutissima. In clade II the evergreen southeastern N American Q. virginiana is basal and sister to the remaining three branches, i.e. a pair of evergreen Mediterranean taxa with Q. ilex and Q. coccifera (subg. Sclerophyllodrys), the deciduous but otherwise plesiomorphic SE European/SW Asiatic Q. cerris (type species of subg. Cerris), and the related but more apomorphic European pair Q. petraea and Q. robur (subg. Quercus). These results partly conflict with current taxonomic classification but are supported by some anatomical and morphological characters. They document polyphyletic lines from evergreen to deciduous taxa and suggest Tertiary transcontinental connections within the genus. [ABSTRACT FROM AUTHOR]

We have characterized the nuclear rDNA unit of Euglena gracilis var. bacillaris and compared it to that of the Z strain. We have localized restriction sites for Eco R1, Sal 1, Sma 1, Hind III, Bam H1 and Bgl II on this unit as well as the coding region for 20 S and 25 S rRNAs. For both strains, results suggest an homogeneity of the 11.6 kbp rDNA units. Comparison between strains shows differences characterized by two additional Sal 1 sites in bacillaris and the likely methylation of one Sma 1 site in Z. Both differences are localized in a non-coding region of the rDNA unit. Analyses of 18 Euglena strains from various origins confirm these differences and allow easy recognition of bacillaris and Z type strains. [ABSTRACT FROM AUTHOR]

The nucleotide sequence of a spacer region between rice 17S and 25S rRNA genes (rDNAs) has been determined. The coding regions for the mature 17S, 5.8S and 25S rRNAs were identified by sequencing terminal regions of these rRNAs. The first internal transcribed spacer (ITS1), between 17S and 5.8S rDNAs, is 194-195 bp long. The second internal transcribed spacer (ITS2), between 5.8S and 25S rDNAs, is 233 bp long. Both spacers are very rich in G+C, 72.7% for ITS1 and 77.3% for ITS2. The 5.8S rDNA is 163-164 bp long and similar in primary and secondary structures to other eukaryotic 5.8S rDNAs. The 5.8S rDNA is capable of interacting with the 5′ terminal region of 25S rDNA. [ABSTRACT FROM AUTHOR]

Nuclear ribosomal RNA (rRNA) genes represent the oldest repetitive fraction universal to all eukaryotic genomes. Their deeply anchored universality and omnipresence during eukaryotic evolution reflects in multiple roles and functions reaching far beyond ribosomal synthesis. Merely the copy number of non-transcribed rRNA genes is involved in mechanisms governing e.g., maintenance of genome integrity and control of cellular aging. Their copy number can vary in response to environmental cues, in cellular stress sensing, in development of cancer and other diseases. While reaching hundreds of copies in humans, there are records of up to 20,000 copies in fish and frogs and even 400,000 copies in ciliates forming thus a literal subgenome or an rDNAome within the genome. From the compositional and evolutionary dynamics viewpoint, the precursor 45S rDNA represents universally GC-enriched, highly recombining and homogenized regions. Hence, it is not accidental that both rDNA sequence and the corresponding rRNA secondary structure belong to established phylogenetic markers broadly used to infer phylogeny on multiple taxonomical levels including species delimitation. However, these multiple roles of rDNAs have been treated and discussed as being separate and independent from each other. Here, I aim to address nuclear rDNAs in an integrative approach to better assess the complexity of rDNA importance in the evolutionary context. [ABSTRACT FROM AUTHOR]