rDNA Sequence Data Research Articles

Deniquelata quercina sp. nov.; a new endophyte species from Persian oak in Iran

In this study, a new endophyte species within the genus Deniquelata (Didymosphaeriaceae) was isolated from the branches of Persian oak trees (Quercus brantii) in Zagros forests, Iran. The maximum parsimony and Bayesian analyses of 18S, 28S and ITS, rDNA sequence data revealed that the isolates were distinct from other species of the Deniquelata. Based on molecular phylogenetic and morphological characteristics, this fungus was demonstrated to be a new species, Deniquelata quercina. Detailed descriptions and illustrations were provided for D. quercina and it was compared with other known species in the genus.

High dispersal levels and lake warming are emergent drivers of cyanobacterial community assembly in peri-Alpine lakes

Disentangling the relative importance of deterministic and stochastic processes in shaping natural communities is central to ecology. Studies about community assembly over broad temporal and spatial scales in aquatic microorganisms are scarce. Here, we used 16S rDNA sequence data from lake sediments to test for community assembly patterns in cyanobacterial phylogenies across ten European peri-Alpine lakes and over a century of eutrophication and climate warming. We studied phylogenetic similarity in cyanobacterial assemblages over spatial and temporal distance, and over environmental gradients, comparing detected patterns with theoretical expectations from deterministic and stochastic processes. We found limited evidence for deviation of lake communities from a random assembly model and no significant effects of geographic distance on phylogenetic similarity, suggesting no dispersal limitation and high levels of stochastic assembly. We detected a weak influence of phosphorus, but no significant effect of nitrogen levels on deviation of community phylogenies from random. We found however a significant decay of phylogenetic similarity for non-random communities over a gradient of air temperature and water column stability. We show how phylogenetic data from sedimentary archives can improve our understanding of microbial community assembly processes, and support previous evidence that climate warming has been the strongest environmental driver of cyanobacterial community assembly over the past century.

Lichens or endophytes? The enigmatic genus Leptosillia in the Leptosilliaceae fam. nov. (Xylariales), and Furfurella gen. nov. (Delonicicolaceae).

Based on DNA sequence data, the genus Leptosillia is shown to belong to the Xylariales. Molecular phylogenetic analyses of ITS-LSU rDNA sequence data and of a combined matrix of SSU-ITS-LSU rDNA, rpb1, rpb2, tef1 and tub2 reveal that the genera Cresporhaphis and Liberomyces are congeneric with Leptosillia. Coelosphaeria fusariospora, Leptorhaphis acerina, Leptorhaphis quercus f. macrospora, Leptorhaphis pinicola, Leptorhaphis wienkampii, Liberomyces pistaciae, Sphaeria muelleri and Zignoëlla slaptonensis are combined in Leptosillia, and all of these taxa except for C. fusariospora, L. pinicola and L. pistaciae are epitypified. Coelosphaeria fusariospora and Cresporhaphis rhoina are lectotypified. Liberomyces macrosporus and L. saliciphilus, which were isolated as phloem and sapwood endophytes, are shown to be synonyms of Leptosillia macrospora and L. wienkampii, respectively. All species formerly placed in Cresporhaphis that are now transferred to Leptosillia are revealed to be non-lichenized. Based on morphology and ecology, Cresporhaphis chibaensis is synonymised with Rhaphidicyrtis trichosporella, and C. rhoina is considered to be unrelated to the genus Leptosillia, but its generic affinities cannot be resolved in lack of DNA sequence data. Phylogenetic analyses place Leptosillia as sister taxon to Delonicicolaceae, and based on morphological and ecological differences, the new family Leptosilliaceae is established. Furfurella, a new genus with the three new species, F. luteostiolata, F. nigrescens and F. stromatica, growing on dead branches of mediterranean fabaceous shrubs from tribe Genisteae, is revealed to be the closest relative of Delonicicola in the family Delonicicolaceae, which is emended. ITS rDNA sequence data retrieved from GenBank demonstrate that the Leptosilliaceae were frequently isolated or sequenced as endophytes from temperate to tropical regions, and show that the genus Leptosillia represents a widely distributed component of endophyte communities of woody plants.

Tamhinispora saraburiensis sp. nov. (Tubeufiaceae, Dothideomycetes) on bamboo in Thailand based on morphology & phylogenetic analysis

Tamhinispora saraburiensis sp. nov. was collected on decaying culms of bamboo in Saraburi Province, Thailand. Tamhinispora saraburiensis is characterized as dark brown to black, obpyriform, and dictyoseptate and has conidia with long appendages arising from the conidial tip. Phylogenetic analyses of the combined ITS and LSU rDNA sequence data demonstrated that this species formed distinctly from other species and that it belongs in the family Tubeufiaceae. Tamhinispora saraburiensis is therefore introduced here with a description, morphological illustrations and molecular data. A key to the species of Tamhinispora is provided.

A New Species of Pentaloculum (Cestoda: “Tetraphyllidea”) from the Taiwan Saddled Carpetshark, Cirrhoscyllium formosanum (Orectolobiformes: Parascylliidae)

Collection of cestodes from the Taiwan saddled carpetshark, Cirrhoscyllium formosanum, for the first time led to the discovery of Pentaloculum hoi n. sp. This species provided important insights into the identity of the heretofore monotypic Pentaloculum-known previously only from the blind electric ray, Typhlonarke aysoni, in New Zealand. The new species differs from Pentaloculum macrocephalum in testis number, vitelline follicle and cirrus sac configuration, and in that it is hyperapolytic rather than euapolytic. Maximum-likelihood analysis of sequence data generated for the D1-D3 region of the 28S rDNA gene not only confirmed this generic placement but also confirmed the close affinities between both species of Pentaloculum and specimens previously referred to in the literature as new genus 7 n. sp. 1. Examination of limited material of the latter, including that of a second specimen from which partial 28S rDNA sequence data were generated here, led to the realization that new genus 7 n. sp. 1 represents an undescribed species of Pentaloculum, referred to here as Pentaloculum n. sp. 2. All 3 species share bothridia divided into 1 anterior and 2 consecutive pairs of loculi. Given that Pentaloculum n. sp. 2 parasitizes a member of the second and only other genus of parascylliid sharks (i.e., Parascyllium), we predict that the 4 other species of Parascyllium and the 2 other species of Cirrhoscyllium are likely to host other species of Pentaloculum. The factors that might account for the eclectic host associations of Pentaloculum, which include a torpediniform ray and 2 species of orectilobiform sharks, are currently unclear. The compilation of diet data for these elasmobranchs and determination of the final intermediate hosts for these cestodes would be interesting avenues of further investigation given that cestodes are trophically transmitted between their intermediate and definitive hosts. The phylogenetic affinities of Pentaloculum among elasmobranch cestodes remain unresolved.

Masenia nkomatiensis n. sp. (Digenea: Cephalogonimidae) from Clarias gariepinus (Burchell) (Clariidae) in Incomati Basin, Mozambique

A new species of Masenia Chatterji, 1933 is described based on material from the intestine of Clarias gariepinus (Burchell) in the Incomati River, Mozambique. The combination of morphological characteristics and analysis of 18S and 28S rDNA sequences delineated the specimens found in the present study as a distinct species. The new form is distinguished from other Masenia spp. in having a large reniform seminal receptacle, a cirrus-sac ending anterior to the ventral sucker, intestinal caeca extending into the hindbody to the level of the posterior testis, and the vitelline fields extending anteriorly to the ventral sucker and posteriorly to the middle of the ovary. Notably, the new form is the only record of African species having a sac-shaped excretory vesicle. Analysis of 28S rDNA sequence data supported its placement in the Cephalogonimidae Looss, 1899. 18S analyses also supported its placement in this family but showed it was not closely related to Masenia bangweulensis (Beverley-Burton, 1962), the sole other African species for which genetic data is currently accessible. The total pairwise differences for 18S and 28S sequences showed the new form differing from other cephalogonimids. Thus, both morphological and genetic characteristics indicate that the present form represents a distinct species, here described as Masenia nkomatiensis n. sp. An updated key to African Masenia spp., now five, is provided.

Four new monorchiids from the golden trevally, Gnathanodon speciosus (Forsskål) (Perciformes: Carangidae), in Moreton Bay, Australia.

Four new monorchiid trematodes are reported from Moreton Bay, Australia; three new species of Provitellus Dove & Cribb, 1998 and one species of Ovipusillus Dove & Cribb, 1998, are described from Gnathanodon speciosus (Forsskål) (Carangidae), the golden trevally. Provitellus chaometra n. sp., Provitellus infrequens n. sp. and Provitellus infibrova n. sp. differ significantly from the only other species of this genus, Provitellus turrum Dove & Cribb, 1998, in the structure of the eggs, vitelline follicles and terminal organ. The four species are united, however, in the possession of short caeca and a long genital atrium, a combination not reported previously. Ovipusillus geminus n. sp. strongly resembles its only congener, Ovipusillus mayu Dove & Cribb, 1998, but differs in the morphology of the diverticulum in the cirrus-sac and the shape of the pharynx. Complete ITS2 and partial 28S rDNA sequence data were generated for all four species, as well as for two known species of Hurleytrematoides Yamaguti, 1953, Hurleytrematoides galzini McNamara & Cribb, 2011 and Hurleytrematoides loi McNamara & Cribb, 2011. These sequences were analysed with those for other monorchiids available on GenBank, and phylogenetic analyses showed that the four species of Provitellus and two species of Ovipusillus each form strongly supported clades. As with previous monorchiid phylogenetic studies, however, the overall resolution of the phylogeny of the Monorchiidae is poor.

Revisiting a poorly known powdery mildew species: Morphology and molecular phylogeny of Erysiphe longissima

Abstract Erysiphe longissima is a species of Erysiphe sect. Microsphaera endemic to China. Its asexual morph is poorly known and DNA sequence data are unrecorded since its first description in 1977. In 2016 and 2017, two powdery mildew samples with asexual and sexual morphs were collected on Caragana rosea at Jilin Agricultural University, Jilin Province, China. The morphological observations suggested that the two samples belonged to E. longissima. To study the phylogenetic position of E. longissima, a phylogenetic tree was constructed based on the combined ITS and 28S rDNA sequence data. This fungus was close to E. palczewskii in phylogeny and clearly distinguished from other species of Erysiphe sect. Microsphaera. To our knowledge, this is the first detailed record of the asexual morph and molecular data of E. longissima.

Morphogenesis and Molecular Phylogeny of the Soil Ciliate Holostichides chardezi (Ciliophora, Hypotrichia, Bakuellidae), with Redefinition of Holostichides Foissner, 1987 and Establishment of a New Genus Anteholostichides

Morphogenesis of the soil hypotrich ciliate, Holostichides chardezi Foissner, 1987, collected from southeastern China, was investigated using the protargol staining method. The main morphogenetic events follow a similar process with that of its congeners. Phylogenetic analyses based on the SSU rDNA sequence data indicate that Holostichides is nonmonophyletic; H.chardezi, the type species of Holostichides, clusters with H.heterotypicus, while H.terrae is distinctly separate from these species. H.terrae can be distinguished from H.chardezi (type species of Holostichides) and H.heterotypicus by undulating membranes relatively long and distinctly curved (vs. relatively short and straight), pharynx with (vs. without) rod-shaped structure, and two (vs. more than two) frontoterminal cirri. Therefore, a new genus, Anteholostichides nov. gen., has been proposed for H.terrae. Further, the diagnosis of the genus Holostichides is improved.

Hermatomyces trangensis sp. nov., a new dematiaceous hyphomycete (Hermatomycetaceae, Pleosporales) on sugar palm in Thailand

A new species of a hyphomycetous fungus, Hermatomyces trangensis, was collected during an investigation of the diversity of palm fungi in Na Yong district, Trang province, Southern Thailand, and is introduced in this paper based on morphological and molecular evidence. The fungus is characterized by the production of only one type of conidia, globose or subglobose in front view, broadly ellipsoidal or oblong in lateral view, with dark brown to black central cells and subhyaline to pale brown peripheral cells and sporulation in culture. Phylogenetic analyses of combined SSU rDNA, LSU rDNA, ITS rDNA, TEF1 and RPB2 sequence data using maximum parsimony, maximum likelihood and Bayesian inference approaches placed the fungus within a strongly supported clade with other Hermatomyces species within the family Hermatomycetaceae (Pleosporales, Dothideomycetes). Morphologically, it is similar to other taxa with only one type of conidia such as H. sphaericus, H. sphaericoides and H. verrucosus but molecular data clearly support H. trangensis as distinct from those species.

Phylogenetic studies on three Helicotylenchus species based on 28S rDNA and mtCOI sequence data

To facilitate the process of spiral nematode species delineation, populations of Helicotylenchus canadensis, H. pseudorobustus, and H. varicaudatus deriving from various locations and diverse natural and anthropogenic environments from Poland were investigated and characterized. For the first time, 28S rDNA sequences are reported for H. canadensis and H. varicaudatus, whereas new mtCOI sequences were acquired for all three analyzed species. A Bayesian phylogenetic analysis of the 28S rDNA fragments revealed that H. canadensis and H. varicaudatus are members of a clade that is a sister group to all other Helicotylenchus species; however, the closest known sister group to H. canadensis is H. vulgaris type A. Both 28S rDNA- and mtCOI-based phylogenetic results suggest that this clade excludes H. pseudorobustus, whose most recent common ancestor with the former species was inferred to be the ancestor of all Helicotylenchus species. Moreover, within the mtCOI sequences obtained from H. pseudorobustus, unlike from the other two, a simultaneous presence of TAG and TAA codons was identified. This may indicate mitochondrial genetic code alterations or other genomic rearrangements in H. pseudorobustus.

Light capture and pigment diversity in marine and freshwater cryptophytes.

Phenotypic traits associated with light capture andphylogenetic relationships were characterized in 34 strains of diversely pigmented marine and freshwater cryptophytes. Nuclear SSU and partial LSU rDNA sequence data from 33 of these strains plus an additional 66 strains produced aconcatenated rooted maximum likelihood tree that classified the strains into 7 distinct clades. Molecular and phenotypic datatogether support: (i) the reclassification of Cryptomonas irregularis NIES 698 tothe genus Rhodomonas, (ii) revision of phycobiliprotein (PBP) diversity within the genus Hemiselmis to include cryptophyte phycocyanin (Cr-PC) 569, (iii) the inclusion of previously unidentified strain CCMP 2293 into the genus Falcomonas, even though it contains cryptophyte phycoerythrin 545 (Cr-PE 545), and (iv) the inclusion of previously unidentified strain CCMP 3175, which contains Cr-PE 545, in aclade with PC-containing Chroomonas species. Adiscriminant analysis-based model of group membership correctly predicted 70.6% of the clades using three traits: PBP concentration · cell-1 , the wavelength of PBP maximal absorption, and habitat. Non-PBP pigments (alloxanthin, chl-a, chl-c2 , α-carotene) did not contribute significantly to group classification, indicating the potential plasticity of these pigments and the evolutionary conservation of the PBPs. Pigment data showed evidence of trade-offs in investments in PBPs vs. chlorophylls (a +c2 ).

A Novel Phagomyxid Parasite Produces Sporangia in Root Hair Galls of Eelgrass (Zostera marina)

The objective of this study was to identify the parasite causing the formation of root hair galls on eelgrass (Zostera marina) in Puget Sound, WA. Microscopic and molecular analyses revealed that a novel protist formed plasmodia that developed into sporangia in root hair tip galls and released biflagellate swimming zoospores. Root hair galls were also observed in the basal section of root hairs, and contained plasmodia or formed thick-walled structures filled with cells (resting spores). Phylogenetic analyses of 18S rDNA sequence data obtained from cells in sporangia indicated that the closest relative of the parasite with a known taxonomic identification was Plasmodiophora diplantherae (86.9% sequence similarity), a phagomyxid parasite that infects the seagrass Halodule spp. To determine the local geographic distribution of the parasite, root and soil samples were taken from four eelgrass populations in Puget Sound and analyzed for root hair galls and parasite DNA using a newly designed qPCR protocol. The percent of root hairs with galls and amount of parasite DNA in roots and sediment varied among the four eelgrass populations. Future studies are needed to establish the taxonomy of the parasite, its effects on Z. marina, and the factors that determine its distribution and abundance.

Hidden mycota of pine needles: Molecular signatures from PCR-DGGE and Ribosomal DNA phylogenetic characterization of novel phylotypes

Previous studies for enumerating fungal communities on pine needles relied entirely on phenotypic diversity (microscopy) or identification based on DNA sequence data from those taxa recovered via cultural studies. To bypass limitations of the culturing methods and provide a more realistic diversity estimate, we employed and assessed a PCR-DGGE based method coupled with rDNA phylogenetic sequence analyses to characterize fungal taxa associated with pine needles. Fresh (living) and decayed needles from three hosts of the Pinaceae (Keteleeria fortunei, Pinus elliottii and P. massoniana) were examined. Morphological studies reveal that the most abundant species associated with decayed needles were Cladosporium cladosporioides and an unidentified Trichoderma species followed by Gliocephalotrichum sp., Gliocladium sp., Lophodermium pinastri, Paecilomyces varioti, Phaeostalagmus cyclosporus and a Phoma sp, which are commonly occurring fungi. Community genomic data from freshly collected and decayed pine needles recovered 40 operational taxonomic units, which appear to be mostly undetected members of the natural fungal consortium. Sequence analyses revealed a number of phylotypes or “species” that were not recovered using traditional morphological and cultural approaches previously used. Phylogenetic data from partial 18S rDNA sequence data reveal that most phylotypes represent potential novel phylogenetic fungal lineages with affinities to the Dothideomycetes, Leotiomycetes, Lecanoromycetes and Sordariomycetes and were not identical to previously known endophytes or saprobes. Although the major ecological roles of these phylotypes in pine needles are still enigmatic, this study provides new insights in hidden fungal diversity that mycologists are possibly ignoring given the discrepancies associated with available methods. To what extent do previously recovered identified species (either as saprobes or endophytes) from morphological or culturing studies act as pioneer decomposers or constitute an integral part of endophytic community warrants further investigation.

Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics

BackgroundThe Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African countries. H3ABioNet is part of the Human Health and Heredity in Africa program (H3Africa), an African-led research consortium funded by the US National Institutes of Health and the UK Wellcome Trust, aimed at using genomics to study and improve the health of Africans. A key role of H3ABioNet is to support H3Africa projects by building bioinformatics infrastructure such as portable and reproducible bioinformatics workflows for use on heterogeneous African computing environments. Processing and analysis of genomic data is an example of a big data application requiring complex interdependent data analysis workflows. Such bioinformatics workflows take the primary and secondary input data through several computationally-intensive processing steps using different software packages, where some of the outputs form inputs for other steps. Implementing scalable, reproducible, portable and easy-to-use workflows is particularly challenging.ResultsH3ABioNet has built four workflows to support (1) the calling of variants from high-throughput sequencing data; (2) the analysis of microbial populations from 16S rDNA sequence data; (3) genotyping and genome-wide association studies; and (4) single nucleotide polymorphism imputation. A week-long hackathon was organized in August 2016 with participants from six African bioinformatics groups, and US and European collaborators. Two of the workflows are built using the Common Workflow Language framework (CWL) and two using Nextflow. All the workflows are containerized for improved portability and reproducibility using Docker, and are publicly available for use by members of the H3Africa consortium and the international research community.ConclusionThe H3ABioNet workflows have been implemented in view of offering ease of use for the end user and high levels of reproducibility and portability, all while following modern state of the art bioinformatics data processing protocols. The H3ABioNet workflows will service the H3Africa consortium projects and are currently in use. All four workflows are also publicly available for research scientists worldwide to use and adapt for their respective needs. The H3ABioNet workflows will help develop bioinformatics capacity and assist genomics research within Africa and serve to increase the scientific output of H3Africa and its Pan-African Bioinformatics Network.

Crossopsorella, a new tropical genus of rust fungi

Prior phylogenetic studies of rust fungi have shown the Phakopsoraceae as polyphyletic. However, most of the ca. 13 genera currently placed in Phakopsoraceae s.l. have not been the subject of phylogenetic analyses. In this study we examine the placement of several species of Crossopsora (Phakopsoraceae) from newly generated nuc 28S rDNA (28S) sequence data. While the type species, C. ziziphi, cannot be excluded from the Phakopsoraceae s.s., several other species, including C. byrsonimae, are not congeneric with the type. Herein we describe the new genus Crossopsorella, based on C. byrsonimae as the type, to accommodate specimens of this species found in four different Byrsonima species.

Berberis lycium: the newly discovered aecial host of Puccinia striiformoides

Berberis lycium is reported for the first time as the alternate (aecial) host for Puccinia striiformoides from collections in Pakistan. This finding is confirmed by phylogenetic analyses of internal transcribed spacer (ITS) rDNA sequence data, which place our sequences of aecial P. striiformoides on B. lycium in a well-supported clade with GenBank sequences from uredinial P. striiformoides on Dactylis glomerata. Aecia of Puccinia graminis, P. graminis f.sp. tritici, and P. brachypodii that were also collected on B. lycium from Pakistan provide additional evidence of multiple rust species occurring on secondary host plant species.

Three, two, one! Revision of the long-bodied sphaerodorids (Sphaerodoridae, Annelida) and synonymization of Ephesiella, Ephesiopsis and Sphaerodorum.

BackgroundLong-bodied sphaerodorids (Annelida, Sphaerodoridae) is the common name for members of the three closely and morphologically homogenous currently accepted genera of benthic marine bristle worms: Ephesiella, Ephesiopsis and Sphaerodorum. Members of this group share the presence of two dorsal and longitudinal rows of macrotubercles with terminal papillae, and two longitudinal rows of microtubercles, features that are unique among sphaerodorids. Genera are distinguished by the chaetae morphology. Members of Ephesiella are characterised by having compound chaetae (except, sometimes, simple chaetae in the first chaetigers), Sphaerodorum bear only simple chaetae, and Ephesiopsis have both compound and simple chaetae in all parapodia.MethodsMitochondrial (partial COI and 16S rDNA) and nuclear (partial 18S rDNA and 28S rDNA) sequence data of long-bodied sphaerodorids with compound and simple chaetae, and an outgroup of additional seven sphaerodorid species were analysed separately and in combination using Bayesian inference (BA), and Maximum Likelihood (ML) methods. Long-bodied sphaerodorids from around the world (including type specimens) were examined under a range of optical equipment in order to evaluate putative generic and specific diagnostic features, in addition to intraspecific variability.ResultsPhylogenetic analyses of mitochondrial and nuclear DNA sequences of specimens identified as Ephesiella and Sphaerodorum, based on chaeta morphology, were performed. Sphaerodorum and Ephesiella were recovered as paraphyletic and nested within each other. Revision of current nominal species diagnostic features are performed and discussed.DiscussionResults contradict current generic definitions. Recovery of paraphyletic compound and simple chaetae clades urge the synonymization of these two genera of long-bodied sphaerodorids. Morphological data also suggest the synonymization of Ephesiopsis.

Raveneliapiepenbringiae and Raveneliahernandezii, two new rust species on Senegalia (Fabaceae, Mimosoideae) from Panama and Costa Rica.

Two new rust species, Raveneliapiepenbringiae and R.hernandezii (Pucciniales) on Senegalia spp. (Fabaceae) are described from the Neotropics (Panama, Costa Rica). A key to the species on neotropical Senegalia spp. is provided. Molecular phylogenetic analyses based on 28S rDNA sequence data suggest that the representatives of Senegalia rusts distributed in the neotropics evolved independently from species known from South Africa. This is further supported by the teliospore morphology, which is characterised by uniseriate cysts in the neotropical Senegalia rusts and contrasting multiseriate cysts in the paleotropic Ravenelia species that infect this host genus.

A novel marine genus, Halobyssothecium (Lentitheciaceae) and epitypification of Halobyssothecium obiones comb. nov.

A novel marine genus, Halobyssothecium (Lentitheciaceae), is introduced to accommodate Byssothecium obiones (= Halobyssothecium obiones) with evidence from phylogenetic analyses of concatenated LSU, SSU, ITS rDNA, and TEF1 sequence data. We could not locate any type material for this species and there is no molecular data available for the type of this species. Therefore, an epitype is designated for the precise delineation of this taxon. A detailed morphological description and DNA characterization based on LSU, SSU, ITS rDNA, and TEF1 sequence data are provided for the epitype, obtained from Spartina culms in Eastney, Langstone Harbour, Hampshire, UK.