Partial LSU Sequences Research Articles

Further data on Iranian marine nematode diversity, with description of three new Desmodoridae Filipjev, 1922 (Nematoda: Desmodorida) species from the Persian Gulf

Summary The Desmodoridae is a diverse and widespread family of free-living nematodes. Here, we provide the first record of the group in the Persian Gulf and describe three new species: Metachromadoroides sinuspersici sp. n., Zalonema iranicum sp. n. and Z. supplementorum sp. n. Metachromadoroides sinuspersici sp. n. is characterised by finely annulated cuticle, short and stout cephalic sensilla, amphidial fovea on cuticular thickening, pharyngeal bulb well developed and partitioned into three sections, absence of precloacal supplements, and presence of 6-8 pairs of rounded postcloacal papillae. Zalonema iranicum sp. n. is characterised by papilliform subcephalic sensilla (best observed with SEM), convex cephalic capsule, large multispiral amphidial fovea with 4-5 turns in both males and females, buccal cavity with one ventrosublateral and two dorsal teeth and posterior body of males with lateral alae extending from the last third of the body to the cloacal aperture and ventral alae extending 1395-2250 μm anterior to the cloacal aperture, and no precloacal supplements. Zalonema supplementorum sp. n. is characterised by four subcephalic sensilla 1-2 μm long, multispiral amphidial fovea with three turns in both males and females, buccal cavity with one dorsal and two ventrosublateral teeth, males with lateral alae present on each side of body from posterior half of body to cloacal aperture, ventral alae extending 942-1257 μm anterior to cloacal aperture, strongly cuticularised spicules 41-43 μm long, and 12-16 precloacal supplements. Near full length SSU and partial D2-D3 LSU sequences are provided for M. sinuspersici sp. n. and Z. iranicum sp. n., and the COI sequence is provided for Z. iranicum. The SSU phylogeny suggests a close relationship between M. sinuspersici sp. n. and Metachromadora and Metachromadoroides species and the monophyly of Zalonema (after currently available data). The LSU phylogeny suggests an affinity between Metachromadoroides and Zalonema with Spirinia and Acanthopharynx, respectively.

Three Novel Species of Russula Pers. Subg. Compactae (Fr.) Bon from Dinghushan Biosphere Reserve in Southern China

Three novel species of Russula Pers. subg. Compactae (Fr.) Bon from southern China are described with morphological evidence and phylogenetic analyses based on ITS and the concatenated partial LSU, mtSSU, rpb1, rpb2 and tef1 gene sequences. All three species possess sparse and broad lamellae. Russula latolamellata Y.Song & L.H.Qiu, sp. nov., is characterized by its cracking, black-tan pileus, scarlet-turning context on bruising and absence of pileocystidia and caulocystidia. Russula nigrocarpa S.Y.Zhou, Y.Song & L.H.Qiu, sp. nov., can be distinguished by its off-white lamellae, small basidiospores, hymenial cystidia and pileocystidia of various forms, often with forked apices and by its gelatinous pileipellis. Russula ochrobrunnea S.Y.Zhou, Y.Song & L.H.Qiu, sp. nov., is characterized by its cracking, grayish brown pileus with striate margin, light-brown lamellae whose edges turn dark-brown when mature, small basidiospores and slightly flexuous ormoniliform hymenial cystidia. Their detailed morphological features and phylogenetic positions are discussed and compared among closely related species.

Description of Aporcella minor sp. n. (Dorylaimida: Aporcelaimidae) from Iran, with an updated taxonomy of the genus

Summary A new species belonging to the genus Aporcella, collected in cultivated soils of East Azarbaijan province, Iran, is described and illustrated. The new species is characterised by its 1.08 (1.05-1.15) mm long body, two-layered cuticle, lip region offset by constriction and 12 (11-13) μm broad, odontostyle 13.0 (12.5-14.0) μm long or nearly equal to lip region diam., neck 310 (293-325) μm long, pharyngeal expansion 137 (128-144) μm long, occupying 43-45% of the total neck length, female genital system didelphic-amphidelphic, uterus simple, 34-48 μm long, vulva transverse (V = 59 (58-61)), tail conical with finely rounded terminus (30 (29-33) μm long, c = 34 (33-36), c′ = 1.5 (1.4-1.6)), and male absent. Molecular analyses, using Bayesian inference based on partial LSU sequences, confirm the monophyly of Aporcella as well as its clustering with other dorylaimid taxa characterised by the absence of pars refringens vaginae. The taxonomy of the genus is updated, with an emended diagnosis, list of species, key to their identification, and a compendium of the main morphometrics of species/populations described since the last available revision.

Tree inhabiting gnomoniaceous species from China, with Cryphogonomonia gen. nov. proposed.

Species of Gnomoniaceae are commonly associated with leaf spot diseases of a wide range of plant hosts worldwide. During our investigation of fungi associated with tree diseases in China, several gnomoniaceous isolates were recovered from symptomatic branches and leaves on different woody plants in the Fagaceae, Pinaceae, and Salicaceae families. These isolates were studied by applying a polyphasic approach including morphological, cultural data, and phylogenetic analyses of partial ITS, LSU, tef1, rpb2 and tub2 gene sequences. As a result, three species were identified with characters fitting into the family Gnomoniaceae. One of these species is described herein as Cryphognomonia pinigen. et sp. nov., characterized by developed pseudostromata and ascospores with obvious hyaline sheath; Gnomoniopsis xunwuensissp. nov. is illustrated showing sympodially branched conidiophore, oval or fusiform conidia; and one known species, Plagiostoma populinum. The current study improves the understanding of gnomoniaceous species causing diebacks and leaf spot on ecological and economic forest trees.

Discovery of Cytospora species associated with canker disease of tree hosts from Mount Dongling of China.

Members of Cytospora encompass important plant pathogens, saprobes and endophytes on a wide range of woody hosts with a worldwide distribution. In the current study, we obtained seven representative isolates from six tree hosts of Betulaceae, Juglandaceae, Rosaceae, Tiliaceae and Ulmaceae in Mount Dongling of China. Based on morphological comparison and phylogenetic analyses using partial ITS, LSU, act, rpb2, tef1-α and tub2 gene sequences, we identified two known species (Cytospora leucostoma and C. pruinopsis) and two novel species (C. coryli and C. spiraeicola). These results represent the first study on Cytospora species associated with canker disease from Mount Dongling of China.

Taxonomy of two synnematal fungal species from Rhus chinensis, with Flavignomonia gen. nov. described.

Rhus chinensis represents a commercially and ecologically important tree species in China, but suffers from canker diseases in Jiangxi Province. Synnemata, pycnidia and ascomata were discovered on cankered tissues. Strains were obtained from single ascospore or conidium within the fruiting bodies and identified based on morphological comparison and the phylogenetic analyses of partial ITS, LSU, tef1 and rpb2 gene sequences. As a result, two species were confirmed to represent two kinds of synnemata. One of these species is described herein as Flavignomonia rhoigenagen. et sp. nov.; and Synnemasporella aculeans is illustrated showing ascomata, pycnidia and synnemata. Flavignomonia is distinguished from Synnemasporella by the colour of the synnematal tips. Additionally, Flavignomonia can be distinguished from the other gnomoniaceous genera by the formation of synnemata.

Diaporthalean fungi associated with canker and dieback of trees from Mount Dongling in Beijing, China.

Diaporthales is a fungal order comprising important plant pathogens, saprobes and endophytes on a wide range of woody hosts. It is often difficult to differentiate the pathogens in this order, since both the morphology and disease symptoms are similar among the various species. In the current study, we obtained 15 representative diaporthalean isolates from six tree hosts belonging to plant families Betulaceae, Fagaceae, Juglandaceae, Rosaceae, and Ulmaceae from Mount Dongling in China. Six species were identified residing in four families of Diaporthales (Diaporthaceae, Erythrogloeaceae, Juglanconidaceae and Melanconidaceae). Based on morphological comparison and the phylogenetic analyses of partial ITS, LSU, cal, his3, rpb2, tef1-α and tub2 gene sequences, we identified five known species (Diaporthe betulina, D. eres, D. rostrata, Juglamconis oblonga and Melanconis stilbostoma) and one novel species (Dendrostoma donglinensis). These results represent the first study of diaporthalean fungi associated with canker and dieback symptoms from Mount Dongling in Beijing, China.

Morphology and phylogeny of an unarmored dinoflagellate, Karlodinium jejuense sp. nov. (Gymnodiniales), isolated from the northern East China Sea

SUMMARYAn unarmored dinoflagellate, Karlodinium jejuense sp. nov., was isolated from the northern East China Sea. The species was characterized by light, fluorescence, and scanning electron microscopy of laboratory cultures, as well as SSU rDNA, ITS region (ITS1‐5.8S‐ITS2) and LSU rDNA gene sequences. Cells were ellipsoid to oval, small‐sized, 9.9–16.0 μm in length and 6.2–12.7 μm in width. The chloroplasts were 7–10 in number and yellow‐green in color. The central nucleus was large, located in the center of the cell. The linear apical groove with outward thick rolled margins was very short, and there was no ventral pore. Small pores were irregularly distributed on the cell surface. The amphiesmal vesicles were hexagonal and pentagonal. Karlodinium jejuense was morphologically similar to K. ballantinum but differed in cell surface characteristics and swimming pattern. The partial LSU sequence of K. jejuense differed by 3.7–4.1% from that of K. ballantinum. Molecular phylogenetic analyses of multi‐gene sequences revealed that K. jejuense was an independent species nested within the Karlodinium clade. Phylogenetic analysis based on partial LSU rDNA gene sequences indicated that K. jejuense was most closely related to K. gentienii and K. ballantinum.

Translucidithyrium thailandicum gen. et sp. nov.: a new genus in Phaeothecoidiellaceae

A sooty blotch and flyspeck fungus with semi-transparent ascomata was discovered in northern Thailand. Its multi-loculate-like ascomata arrangement is similar to species of Lecideopsella (Schizothyriaceae), but ascomata lack a network-like arrangement. The new genus also has ascospores with appendages at both ends. Maximum parsimony, maximum likelihood, and Bayesian inference analyses of a combined ITS and partial LSU sequence dataset revealed that this new taxon is a member of the family Phaeothecoidiellaceae, but it is distinct from any other genera. Therefore, Translucidithyrium thailandicum gen. et sp. nov. is introduced here with descriptions and illustrations. The discovery of this new genus with sexual characters in Capnodiales will make contributions to the further understanding of sooty blotch and flyspeck fungal group.

Two novel species of Neoaquastroma (Parabambusicolaceae, Pleosporales) with their phoma-like asexual morphs.

The monotypic genus Neoaquastroma (Parabambusicolaceae, Pleosporales) was introduced for a microfungus isolated from a collection of dried stems of a dicotyledonous plant in Thailand. In this paper, we introduce two novel species, N. bauhiniae and N. krabiense, in this genus. Their asexual morphs comprise conidiomata with aseptate and hyaline conidia. Neoaquastroma bauhiniae has ascomata, asci and ascospores that are smaller than those of N. krabiense. Descriptions and illustrations of N. bauhiniae and N. krabiense are provided and the two species compared with the type species of the genus, N. guttulatum. Evidence for the introduction of the new taxa is also provided from phylogenetic analysis of a combined dataset of partial LSU, SSU, ITS and tef1 sequence data. The phylogenetic analysis revealed a distinct lineage for N. bauhiniae and N. krabiense within the family Parabambusicolaceae.

Families and genera of diaporthalean fungi associated with canker and dieback of tree hosts

In this study we accept 25 families in Diaporthales based on phylogenetic analyses using partial ITS, LSU, rpb2 and tef1-α gene sequences. Four different families associated with canker and dieback of tree hosts are morphologically treated and phylogenetically compared. These include three new families (Diaporthostomataceae, Pseudomelanconidaceae, Synnemasporellaceae), and one new genus, Dendrostoma (Erythrogloeaceae). Dendrostoma is newly described from Malus spectabilis, Osmanthus fragrans and Quercus acutissima having fusoid to cylindrical, bicellular ascospores, with three new species namely D. mali, D. osmanthi and D. quercinum. Diaporthostomataceae is characterised by conical and discrete perithecia with bicellular, fusoid ascospores on branches of Machilus leptophylla. Pseudomelanconidaceae is defined by conidiogenous cells with apical collarets and discreet annellations, and the inconspicuous hyaline conidial sheath when mature on Carya cathayensis, compared to morphologically similar families Melanconidaceae and Juglanconidaceae. Synnemasporellaceae is proposed to accommodate fungi with synnematous conidiomata, with descriptions of S. toxicodendri on Toxicodendron sylvestre and S. aculeans on Rhus copallina.

Molecular characterization of Ichtyobronema hamulatum (Moulton, 1931) (Nematoda: Quimperiidae), a common parasite of burbot Lota lota (Linnaeus) (Actinopterygii: Lotidae)

Summary The phylogenetic analysis of partial SSU, LSU (rDNA) and COI (mtDNA) sequences was performed for the quimperiid nematode Ichtyobronema hamulatum, a common parasite of the burbot Lota lota. The study of SSU (for 2007 bp long alignment) has shown that in all kinds of analyses I. hamulatum cluster with Paraquimperia africana (Quimperiidae), while another quimperiid, Paraseuratum sp., unites in a separate clade with Spectatus spectatus (Kathlaniidae). Both groups do not form direct phylogenetic links with the rest of seuratoid nematodes (i.e. Cucullanidae and Seuratidae). Obtained data (for 1080 bp long alignment) exhibit the phylogenetic affinity of I. hamulatum and P. africana with kathlaniids of the genus Falcaustra. The analysis of LSU sequences has revealed that I. hamulatum occupies the basal position in relation to all other members of Spirurina and Rhabditina.

Phylogeny of anaerobic fungi (phylum Neocallimastigomycota), with contributions from yak in China

The phylum Neocallimastigomycota contains eight genera (about 20 species) of strictly anaerobic fungi. The evolutionary relationships of these genera are uncertain due to insufficient sequence data to infer their phylogenies. Based on morphology and molecular phylogeny, thirteen isolates obtained from yak faeces and rumen digesta in China were assigned to Neocallimastix frontalis (nine isolates), Orpinomyces joyonii (two isolates) and Caecomyces sp. (two isolates), respectively. The phylogenetic relationships of the eight genera were evaluated using complete ITS and partial LSU sequences, compared to the ITS1 region which has been widely used in this phylum in the past. Five monophyletic lineages corresponding to six of the eight genera were statistically supported. Isolates of Caecomyces and Cyllamyces were present in a single lineage and could not be separated properly. Members of Neocallimastigomycota with uniflagellate zoospores represented by Piromyces were polyphyletic. The Piromyces-like genus Oontomyces was consistently closely related to the traditional Anaeromyces, and separated the latter genus into two clades. The phylogenetic position of the Piromyces-like genus Buwchfawromyces remained unresolved. Orpinomyces and Neocallimastix, sharing polyflagellate zoospores, were supported as sister genera in the LSU phylogeny. Apparently ITS, specifically ITS1 alone, is not a good marker to resolve the generic affinities of the studied fungi. The LSU sequences are easier to align and appear to work well to resolve generic relationships. This study provides a comparative phylogenetic revision of Neocallimastigomycota isolates known from culture and sequence data.

Setting the Record Straight on North AmericanCantharellus

Abstract The authors assembled for the first time a sequence dataset representative of all 29 presently described North American Cantharellus species, including not only all six newly described North American species presented in this special issue, but very importantly, also newly obtained partial ITS and LSU sequence data from the type specimens of C. camphoratus and C. septentrionalis, two species that supposedly had never been recollected in the United States since their original description. As such, they hope to put the record straight for future research on Cantharellus in North America and to allow for a more precise identification and appreciation of newly collected, sequenced specimens.

Reconstruction of phylogenetic relationships in dermatomycete genus Trichophyton Malmsten 1848 based on ribosomal internal transcribed spacer region, partial 28S rRNA and beta-tubulin genes sequences.

Trichophyton spp. are important causative agents of superficial mycoses. The phylogeny of the genus and accurate strain identification, based on the ribosomal ITS region sequencing, are still under development. The present work is aimed at (i) inferring the genus phylogeny from partial ITS, LSU and BT2 sequences (ii) description of ribosomal ITS region polymorphism in 15 strains of Trichophyton interdigitale. We performed DNA sequence-based species identification and phylogenetic analysis on 48 strains belonging to the genus Trichophyton. Phylogenetic relationships were inferred by maximum likelihood and Bayesian methods on concatenated ITS, LSU and BT2 sequences. Ribosomal ITS region polymorphisms were assessed directly on the alignment. By phylogenetic reconstruction, we reveal major anthropophilic and zoophilic species clusters in the genus Trichophyton. We describe several sequences of the ITS region of T. interdigitale, which do not fit in the traditional polymorphism scheme and propose emendations in this scheme for discrimination between ITS sequence types in T. interdigitale. The new polymorphism scheme will allow inclusion of a wider spectrum of isolates while retaining its explanatory power. This scheme was also found to be partially congruent with NTS typing technique.

Ligninsphaeria jonesii gen. et. sp. nov., a remarkable bamboo inhabiting ascomycete

A new ascomycete species, inhabiting decaying bamboo culms, is introduced in this paper based on morphology and molecular evidence. Analyses of partial LSU sequence data place the taxon in a monophyletic clade within the order Pleosporales. Morphological characters of the taxon are also distinct from other members of Pleosporales. Ligninsphaeria jonesii gen. et sp. nov. is therefore introduced to accommodate the new taxon, which is characterized by its clypeate, scattered, deeply immersed ascomata, with a slit-like opening, long ostioles, cellular pseudoparaphyses, clavate asci containing broad-fusiform and 1-septate ascospores surrounded by a gelatinous cap at both ends. The phylogenetic analyses show that the new taxon is phylogenetically close but distinct from the families Amniculicolaceae and Testudinaceae, and forms a distinct clade from other taxa in Pleosporales. The new taxon is described and compared with similar taxa. A new genus Ligninsphaeria (Pleosporales, incertae sedis) is introduced to accommodate this distinct lineage.

Phylogeography of the freshwater raphidophyte Gonyostomum semen confirms a recent expansion in northern Europe by a single haplotype.

Gonyostmum semen is a freshwater raphidophyte that has increased in occurrence and abundance in several countries in northern Europe since the 1980s. More recently, the species has expanded rapidly also in north‐eastern Europe, and it is frequently referred to as invasive. To better understand the species history, we have explored the phylogeography of G. semen using strains from northern Europe, United States, and Japan. Three regions of the ribosomal RNA gene (small subunit [SSU], internal transcribed spacer [ITS] and large subunit [LSU]) and one mitochondrial DNA marker (cox1) were analyzed. The SSU and partial LSU sequences were identical in all strains, confirming that they belong to the same species. The ITS region differentiated the American from the other strains, but showed high intra‐strain variability. In contrast, the mitochondrial marker cox1 showed distinct differences between the European, American, and Japanese strains. Interestingly, only one cox1 haplotype was detected in European strains. The overall low diversity and weak geographic structure within northern European strains supported the hypothesis of a recent invasion of new lakes by G. semen. Our data also show that the invasive northern European lineage is genetically distinct from the lineages from the other continents. Finally, we concluded that the mitochondrial cox1 was the most useful marker in determining large‐scale biogeographic patterns in this species.

Description of Ektaphelenchus ibericus n. sp. (Nematoda: Ektaphelenchinae) found in packaging wood from Spain

Ektaphelenchus ibericus n. sp. is described and figured. The new species was isolated from pine packaging wood from Spain that was inspected in Ningbo harbour, China, in 2011. Ektaphelenchus ibericus n. sp. is characterised by lip region without clear constriction, relatively short stylet (11-15 μm) lacking basal knobs, and four lateral lines. The female post-uterine sac is less than one body diam. long, rectum and anus are absent, and the tail is conoid with a sharply pointed terminus. Males are rare and have a conoid tail with a sharply pointed terminus, spicules mitten-shaped, 12.8 μm long (chord) and smoothly curved with a high and bluntly rounded condylus and bluntly pointed rostrum, distal end broadly rounded, and three pairs of ventral caudal papillae present. The separate species status is also supported by molecular phylogenetic analysis based on partial SSU, ITS1/2 and partial LSU sequences.

Fungal communities in soils along a vegetative ecotone

We investigated the community composition and diversity of soil fungi along a sharp vegetative ecotone between coastal sage scrub (CSS) and nonnative annual grassland habitat at two sites in coastal California. USA- We pooled soil samples across 29 m transects on either side of the ecotone at each of the two sites, and. using clone libraries of fungal ribosomal DNA, we identified 280 operational taxonomic units (OTUs) from a total 40 g soil. We combined information from partial LSU and ITS sequences and found that the majority of OTUs belonged to the phylum Ascomycota, followed by Basidiomycota. Within the Ascomycota. a quarter of OTUs were Sordariomycetes. 17% were Leotiomycet.es, 16% were Dothideomycetes and the remaining OTUs were distributed among the classes Eurotiomycetes, Pezizomycetes, Lecanoromycetes, Orbiliomycetes and Arthoniomycetes. Within the Basidiomycota. all OTUs but one belonged to the subphylum Agaricomycotina. We also sampled plant communities at the same sites to offer a point of comparison for patterns in richness of fungal communities. Fungal communities had higher alpha and beta diversity than plant communities; fungal communities were approximately 20 times as rich as plant communities and the majority of OTUs were found in single soil samples. Soils harbored a unique mycoflora that did not reveal vegetative boundaries or site differences. High alpha and beta diversity and possible sampling artifacts necessitate extensive sampling to reveal differentiation in these fungal communities.

Description of Aphelenchoides xui sp. n. (Nematoda: Aphelenchoididae) in packaging wood from South Africa

Aphelenchoides xui sp. n. is described and illustrated from imported packaging wood from South Africa intercepted at Ningbo Port, China. The new species has a body length of 564-820 μm (males) and 549-882 μm (females). The cuticle is weakly annulated with four lines in the lateral field. The stylet is 11-13 μm long and has small basal swellings. The excretory pore is located ca one body diam. posterior to the median bulb, or 75-100 μm from the head. Spicules are relatively large (18-23 μm) with apex and rostrum rounded and well developed and the end of the dorsal limb clearly curved ventrad like a hook. The male tail bears six (2 + 2 + 2) caudal papillae. The spermatheca is axial and oblong and contains disc-like sperm. The female tail is conical, terminating in a complicated step-like projection, usually with many tiny nodular protuberances. The new species is morphologically similar to A. arcticus, A. haguei and A. parasaprophilus in Group 2 sensu Shahina, but is distinguished by spicule shape and form of the female tail terminus. Phylogenetic analysis based on SSU and partial LSU sequences revealed that A. xui sp. n. was closest to A. varicaudatus, although some species of Laimaphelenchus and Schistonchus were also included in the same branch.