Molecular phylogeny and taxonomy of Fibroporia (Basidiomycota) in China

Taxonomic and phylogenetic studies on the Chinese species of Fibroporia were carried out. Fibroporia albicans sp. nov. is described and illustrated on the basis of collections originating from Jiangxi and Xizang provinces, based on morphology and phylogenetic analysis of ITS rDNA sequences. Morphologically, it is characterized by resupinate, annual basidiocarps, white to cream-colored pore surface when fresh, becoming cream to cream-buff upon drying, small pores (6–8 per mm), presence of white to cream rhizomorphs, a dimitic hyphal system with clamped generative hyphae, fusoid cystidioles, and oblong to ellipsoid basidiospores; moreover, it causes a brown rot. Molecular data suggested a close relationship between Fibroporia albicans and F. citrina. Six species of Fibroporia form a monophyletic entity with 100% MP and 1.00 BPP supports. An identification key to the Chinese species of Fibroporia is provided.

Download Full-text

Molecular phylogeny of Pemphiginae (Hemiptera: Aphididae) inferred from nuclear gene EF-1α sequences

Bulletin of Entomological Research ◽

10.1017/s0007485308005828 ◽

2008 ◽

Vol 98 (5) ◽

pp. 499-507 ◽

Cited By ~ 13

Author(s):

H.C. Zhang ◽

G.X. Qiao

Keyword(s):

Phylogenetic Analysis ◽

Molecular Phylogeny ◽

Host Specificity ◽

Nuclear Gene ◽

Molecular Data ◽

Molecular Phylogenetic Analysis ◽

Phylogenetic Study ◽

Primary Host ◽

Molecular Phylogenetic Study ◽

Molecular Phylogenetic

AbstractThree traditional tribes of Fordini, Pemphigini and Eriosomatini comprise Pemphiginae, and there are two subtribes in Fordini and Pemphigini, respectively. Most of the species in this subfamily live heteroecious holocyclic lives with distinct primary host specificity. The three tribes of Pemphigini (except Prociphilina), Eriosomatini and Fordini use three families of plants, Salicaceae (Populus), Ulmaceae (Ulums) and Anacardiaceae (Pistacia and Rhus), as primary hosts, respectively, and form galls on them. Therefore, the Pemphigids are well known as gall makers, and their galls can be divided into true galls and pseudo-galls in type. We performed the first molecular phylogenetic study of Pemphiginae based on molecular data (EF-1α sequences). Results show that Pemphiginae is probably not a monophylum, but the monophyly of Fordini is supported robustly. The monophyly of Pemphigini is not supported, and two subtribes in it, Pemphigina and Prociphilina, are suggested to be raised to tribal level, equal with Fordini and Eriosomatini. The molecular phylogenetic analysis does not show definite relationships among the four tribes of Pemphiginae, as in the previous phylogenetic study based on morphology. It seems that the four tribes radiated at nearly the same time and then evolved independently. Based on this, we can speculate that galls originated independently four times in the four tribes, and there is no evidence to support that true galls are preceded by pseudo-galls, as in the case of thrips and willow sawflies.

Download Full-text

Vanderbylia cinnamomea sp. nov. from southwestern China

Mycotaxon ◽

10.5248/135.371 ◽

2020 ◽

Vol 135 (2) ◽

pp. 371-382

Author(s):

Jun-Zhu Chen ◽

Xiong Yang ◽

Chang-Lin Zhao

Keyword(s):

Phylogenetic Analysis ◽

Morphological Characters ◽

Southwestern China ◽

Pore Surface ◽

Sequence Analyses ◽

Hyphal System ◽

High Support

Vanderbylia cinnamomea is proposed as a new wood-inhabiting polypore species based on morphological characters supported by phylogenetic analysis. The species is characterized by an annual, pileate basidiocarp, a brown to black pileal surface, an olivaceous buff to smoke grey pore surface, a dimitic hyphal system with clamped generative hyphae, and subglobose to amygdaliform, hyaline, thick-walled, smooth, dextrinoid, and cyanophilous basidiospores. ITS+nLSU sequence analyses place V. cinnamomea in Vanderbylia within a subclade with a high support (100% BS, 100% BP, 1.00 BPP) sister to a subclade comprising V. fraxinea and V. robiniophila.

Download Full-text

Phylogeny of Echiura updated, with a revised taxonomy to reflect their placement in Annelida as sister group to Capitellidae

Invertebrate Systematics ◽

10.1071/is19020 ◽

2020 ◽

Vol 34 (1) ◽

pp. 101 ◽

Cited By ~ 1

Author(s):

Ryutaro Goto ◽

James Monnington ◽

Marija Sciberras ◽

Isao Hirabayashi ◽

Greg W. Rouse

Keyword(s):

Molecular Phylogeny ◽

Deep Sea ◽

Sister Group ◽

Molecular Data ◽

Monterey Bay ◽

Phylogenetic Studies ◽

Littoral Zones ◽

Family Level ◽

Relationship Of ◽

The Relationship

Echiura (commonly called spoon worms) are derived annelids that have an unsegmented sausage-shaped body with a highly extensible anterior end (i.e. a proboscis). Echiura currently contains two superfamilies: Echiurioidea (with Echiuridae, Urechidae and Thalassematidae) and Bonellioidea (with Bonelliidae, and Ikedidae). Ikedidae contains only Ikeda, which is distinctive in having a huge trunk, a highly elongate proboscis with stripes or dots, and numerous gonoducts. A recent molecular phylogeny of Echiura recovered Ikedidae as the sister group to Bonelliidae. However, due to relatively low support values for the monophyly of Bonelliidae, this relationship remains problematic. In this study, we reinvestigated the relationship of Bonelliidae and Ikedidae using an expanded dataset with more taxa and genes. In contrast to the previous results, our analyses strongly support that Ikeda is nested within Bonelliidae due to the placement of Maxmuelleria. On the basis of this result, we synonymise Ikedidae with Bonelliidae and transfer Ikeda to the latter, the diagnosis of which is amended. In addition, we synonymise Urechidae with its sister group Echiuridae because they share the synapomorphy of having anal chaetae rings. Furthermore, considering that recent phylogenetic studies have consistently recovered Echiura as the sister group to Capitelliidae within Annelida, we drop the rank of the echiuran clade to family-level and propose a revised classification: Thalassematidae with two subfamilies, Thalassematinae (with two tribes Echiurini and Thalassematini) and Bonelliinae. In addition, we identified a sample collected from the deep sea (~1820 m) of Monterey Bay, California, based on its molecular data. This terminal unexpectedly formed the sister group to the eight genera of Thalassematini, most members of which are inhabitants of littoral zones.

Download Full-text

Veluticeps fasciculata sp. nov. (Gloeophyllaceae, Basidiomycota), a close relative to V. berkeleyi

Phytotaxa ◽

10.11646/phytotaxa.243.2.6 ◽

2016 ◽

Vol 243 (2) ◽

pp. 163 ◽

Cited By ~ 3

Author(s):

Jiao Yang ◽

Karen K. Nakasone ◽

Shuang-Hui He

Keyword(s):

Southern China ◽

Brown Rot ◽

Distinct Species ◽

Fungal Species ◽

Its Rdna ◽

Close Relative ◽

Rdna Sequences ◽

First Time

A new brown-rot fungal species, Veluticeps fasciculata, is described from southern China. It is characterized by perennial effused basidiocarps with smooth or tuberculose hymenophore, nodose-septate generative hyphae, fasciculate cystidia (as hyphal pegs in hymenophore) and relatively small basidiospores. It occurs on wood of Cunninghamia and Cryptomeria. Although similar to Veluticeps berkeleyi, morphological and molecular (ITS rDNA sequences) data show that V. fasciculata is a distinct species. Complete description and illustrations are provided for the V. fasciculata. In addition, V. fimbriata is reported from China for the first time.

Download Full-text

Use of nuclear genes for phylogeny reconstruction in plants

Australian Systematic Botany ◽

10.1071/sb03015 ◽

2004 ◽

Vol 17 (2) ◽

pp. 145 ◽

Cited By ~ 246

Author(s):

Randall L. Small ◽

Richard C. Cronn ◽

Jonathan F. Wendel

Keyword(s):

Sequence Data ◽

Molecular Data ◽

Nuclear Genes ◽

Universal Primers ◽

Plant Systematics ◽

Dna Sequence Data ◽

Rdna Sequences ◽

Phylogenetic Studies ◽

Molecular Phylogenetic ◽

Orthologous Loci

Molecular data have had a profound impact on the field of plant systematics, and the application of DNA-sequence data to phylogenetic problems is now routine. The majority of data used in plant molecular phylogenetic studies derives from chloroplast DNA and nuclear rDNA, while the use of low-copy nuclear genes has not been widely adopted. This is due, at least in part, to the greater difficulty of isolating and characterising low-copy nuclear genes relative to chloroplast and rDNA sequences that are readily amplified with universal primers. The higher level of sequence variation characteristic of low-copy nuclear genes, however, often compensates for the experimental effort required to obtain them. In this review, we briefly discuss the strengths and limitations of chloroplast and rDNA sequences, and then focus our attention on the use of low-copy nuclear sequences. Advantages of low-copy nuclear sequences include a higher rate of evolution than for organellar sequences, the potential to accumulate datasets from multiple unlinked loci, and bi-parental inheritance. Challenges intrinsic to the use of low-copy nuclear sequences include distinguishing orthologous loci from divergent paralogous loci in the same gene family, being mindful of the complications arising from concerted evolution or recombination among paralogous sequences, and the presence of intraspecific, intrapopulational and intraindividual polymorphism. Finally, we provide a detailed protocol for the isolation, characterisation and use of low-copy nuclear sequences for phylogenetic studies.

Download Full-text

A framework for a phylogenetic classification in the genus Cortinarius (Basidiomycota, Agaricales) derived from morphological and molecular data

Canadian Journal of Botany ◽

10.1139/b05-107 ◽

2005 ◽

Vol 83 (11) ◽

pp. 1457-1477 ◽

Cited By ~ 47

Author(s):

Sigisfredo Garnica ◽

Michael Weiß ◽

Bernhard Oertel ◽

Franz Oberwinkler

Keyword(s):

Phylogenetic Analysis ◽

Molecular Data ◽

Internal Transcribed Spacers ◽

Molecular Phylogenetic Analysis ◽

Nuclear Rdna ◽

Ecological Data ◽

Natural Classification ◽

Geographical Patterns ◽

Rdna Sequences ◽

Molecular Phylogenetic

Phylogenetic relationships in the genus Cortinarius with emphasis on European species were studied by integrating a molecular phylogenetic analysis of nuclear rDNA sequences with morphological, chemical, and ecological data. Internal transcribed spacers (ITS1 and ITS2, including 5.8S) and the D1–D2 regions of nuclear rDNA of 262 Cortinarius species including most of the recognised subgenera from Europe, South America, Australia, Tasmania, New Zealand, and Asia were sequenced and analysed by maximum likelihood and neighbour joining. Our morphological and molecular analyses showed considerable disagreement with earlier morphology-based hypotheses concerning the infrageneric delimitations in Cortinarius. We propose a new base for a more natural classification system in Cortinarius involving the taxonomic rearrangement of the species into the following major lineages that we informally designate as “clades” at this time: (1) phlegmacioid species are included in Alluti, Amarescentes, Arguti, Calochroi, Caerulescentes, Percomes, Phlegmacioides, Phlegmacium, Purpurascentes, Scauri, and Vulpini; (2) the Heterocliti clade includes species of the subgenera Leprocybe and Cystogenes ; (3) most of the Myxacium species are included in the Delibuti and Myxacium clades; (4) part of Rozites are included in the Rozites clade; (5) the north-hemispheric species of subgenus Dermocybe are included in the Dermocybe clade and part of the south-hemispheric species in the Splendidi clade; (6) part of Sericeocybe are integrated in the Anomali and Telamonia clades; (7) members of subgenus Cortinarius are assigned to the Cortinarius clade; (8) telamonioid taxa are included in the Obtusi, Renidentes, and Telamonia clades. Several Cortinarius species with peculiar patterns of morphology and basidiome coloration had isolated positions in the sequence analysis, and the evolutionary relationships among the major lineages remained unresolved. Our results suggest the convergent evolution of certain morphological traits across phylogenetically divergent lineages in Cortinarius. However, combinations of features such as pileipellis anatomy, spore shape, veil coloration, basidiome pigments, and stipe shape appear useful to circumscribe clades. Our molecular phylogenetic analysis allows insights in global geographical patterns of species distribution within the major lineages in the genus Cortinarius. The clade structure proposed here could be used as backbone for further more detailed systematic studies.

Download Full-text

Photobiont flexibility in the lichen Protoparmeliopsis muralis as revealed by ITS rDNA analyses

The Lichenologist ◽

10.1017/s0024282906005068 ◽

2006 ◽

Vol 38 (5) ◽

pp. 469-476 ◽

Cited By ~ 54

Author(s):

Beata GUZOW-KRZEMIŃSKA

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Its Rdna ◽

Single Specimen ◽

Low Level ◽

Rdna Sequences ◽

The World

The genetic diversity of photobionts in the lichen Protoparmeliopsis muralis was examined to determine the identity of the photobiont and the level of selectivity for the photobiont by the mycobiont. Forty ITS rDNA sequences of photobionts from thirty nine specimens of Protoparmeliopsis muralis have been determined. The photobiont species were identified both by direct comparison with the available sequences and by phylogenetic analysis. The sequences obtained from P. muralis specimens belonged to different Trebouxia clades. The most common photobionts were T. incrustata and an unidentified lineage, here named as “muralis I”. Less common photobionts were T. asymmetrica and T. gigantea. Two unidentified Trebouxia spp. and a photobiont that belonged to the clade that includes T. impressa, T. flava and T. potteri were also found to be associated with P. muralis. Such flexibility has not been reported to date. Moreover, two different photobionts were found in a single specimen. They belonged to the T. gigantea clade and “muralis I” lineage. The low level of selectivity with respect to the photobiont may constitute an important aspect in that Protoparmeliopsis muralis is one of the most successful urban lichens in the world.

Download Full-text

Molecular characterization of Fasciola isolates collected from sheep, goats and cattle in Kisumu, Baringo and Narok Counties, Kenya

10.21203/rs.3.rs-930890/v1 ◽

2021 ◽

Author(s):

Cornelius Kibet Kipyegen ◽

Charles I. Muleke ◽

Elick O. Otachi

Keyword(s):

Phylogenetic Analysis ◽

Fasciola Hepatica ◽

Internal Transcribed Spacers ◽

Nuclear Ribosomal Dna ◽

Rdna Sequences ◽

Close Relationship ◽

Control Programmes ◽

Veterinary Importance ◽

Liver Flukes ◽

And Control

Abstract Fasciolosis is a neglected trematode infection of public health and veterinary importance caused by Fasciola gigantica and Fasciola hepatica. Molecular analysis using the internal transcribed spacers’ ITS-1 and ITS-2 of nuclear ribosomal DNA is useful in distinguishing Fasciola species. This study aimed to characterize liver flukes from sheep, goats and cattle using these genetic markers. Fifty nine adult Fasciola specimens were collected from livers of naturally infected sheep, goats and cattle at selected abattoirs in Kisumu, Baringo and Narok Counties. Sequence comparison of ITS-1 and ITS-2 sequences of Fasciola isolates from this study and sequences in Genbank was carried out. A maximum likelihood tree was constructed for phylogenetic analysis. Analysis of ITS-1 and ITS-2 rDNA sequences revealed that F. hepatica and F. gigantica caused infection in both cattle and sheep and in goats only F. gigantica caused infection. The sequenced PCR amplicons showed a close relationship between Fasciola species in this study with Fasciola isolates from other regions in the world. Phylogenetic analysis showed that sequences of F. hepatica are similar to the sequence from Spain, China and Tunisia obtained from GenBank. The sequences of F. gigantica in this study have similarity to the sequence from Iran and Burkina Faso. Data from this study provides information that serves as basis for further studies on the distribution of F. gigantica and F. hepatica in other localities in Kenya, and is also important in designing epidemiological and control programmes for zoonotic fascioliasis.

Download Full-text

Usnea nipparensis and U. sinensis form a ‘species pair ’ presuming morphological, chemical and molecular phylogenetic data

Plant and Fungal Systematics ◽

10.35535/pfsyst-2020-0023 ◽

2020 ◽

pp. 265-271

Author(s):

Yoshihito Ohmura

Keyword(s):

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Its Rdna ◽

Phylogenetic Position ◽

Species Pair ◽

Rdna Sequences ◽

Phylogenetic Data ◽

Close Relationship ◽

Molecular Phylogenetic ◽

Molecular Phylogenetic Data

Phylogenetic relationships between Usnea nipparensis and U. sinensis, caperatic acid containing Usnea species, were examined based on ITS rDNA, and the phylogenetic position of U. nipparensis was inferred based on multi-locus gene analysis using ITS rDNA, nuLSU, and MCM7. Although U. nipparensis and U. sinensis have a sorediate and an esorediate shrubby thallus, respectively, and in general look quite different, other detailed morphological and chemical features are similar. Analysis of the ITS rDNA sequences suggests their close relationship, but also confirms the independence of both species, and that they most likely form a ‘species pair’ based on morphological, chemical and molecular phylogenetic data. Phylogenetic trees based on both multi-locus gene and ITS rDNA alone strongly support that U. nipparensis and U. angulata belong to the same clade.

Download Full-text