Diversity in the yeast Cryptococcus albidus and related species as revealed by ribosomal DNA sequence analysis

1999 ◽  
Vol 46 (1) ◽  
pp. 7-27 ◽  
Author(s):  
Álvaro Fonseca ◽  
Gloria Scorzetti ◽  
Jack W Fell
Keyword(s):  
Ribosomal Dna ◽  
Yeast Species ◽  
Sequence Data ◽  
Taxonomic Status ◽  
Molecular Characteristics ◽  
Its2 Region ◽  
Species Delineation ◽  
Cryptococcus Albidus ◽  
Rdna Sequences ◽  
Rdna Sequence Data

Evidence accumulated from studies based on physiological, biochemical, and molecular characteristics has pointed to the heterogeneity of the ubiquitous anamorphic basidiomycetous yeast species Cryptococcus albidus (Saito) Skinner, with its current varieties and synonyms. The taxonomic status of this species has not been reappraised because different studies, mostly involving limited numbers of strains, have not been integrated. To assess species diversity within the clade containing Cryptococcus albidus and other phylogenetically related Cryptococcus and Filobasidium species, we determined ribosomal DNA (rDNA) sequences of 69 strains from the 5prime end of the 26S gene, D1/D2 region, and in some cases, the non-coding ITS2 region. Analysis of the sequence data together with available physiological, biochemical, and molecular characteristics, showed the segregation of C. albidus into at least 12 species, leading to the elevation of former varieties to the rank of species (C. aerius, C. diffluens), the reinstatement of synonyms (C. liquefaciens, C. terricola), and the proposal of new species (C. arrabidensis, C. chernovii, C. cylindricus, C. oeirensis, C. phenolicus, C. saitoi, C. uzbekistanensis, C. wieringae). The overall analyses of the results argue in favour of the use of rDNA sequence data to improve species delineation when integrated with other available physiological and molecular characteristics.Key words: basidiomycetous yeasts, taxonomy, Cryptococcus albidus, ribosomal DNA, molecular systematics.

On the phylogeny of Ophiostoma, Ceratocystis s.s., and Microascus, and relationships within Ophiostoma based on partial ribosomal DNA sequences

1993 ◽  
Vol 71 (9) ◽  
pp. 1249-1265 ◽  
Author(s):  
G. Hausner ◽  
J. Reid ◽  
G. R. Klassen
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Large Subunit ◽  
Small Subunit ◽  
Data Set ◽  
Rdna Sequences ◽  
Morphological Criteria ◽  
Small Subunit Rdna ◽  
Rdna Sequence Data ◽  
Large Subunit Rdna

Phylogenetic analysis of partial rDNA sequences suggests that Ophiostoma should remain the sole genus of the Ophiostomataceae, and this should be the sole family within the Ophiostomatales, whereas Ceratocystis s.s. would be best disposed within the Microascales. Although morphological criteria suggest that the genus Ophiostoma is heterogeneous, analysis of partial small subunit rDNA sequence data shows that Ophiostoma (excluding O. roraimense) represents a monophyletic taxon. Analysis of a partial large subunit rDNA data set, which included sequences from 55 species assignable to Ophiostoma, failed to support the strict subdivision of the genus based on either ascospore characters or the nature of the anamorph. Key words: Ceratocystis, Microascus, Ophiostoma, partial rDNA sequences, phylogeny.

Characterization of Trichuris trichiura from humans and T. suis from pigs in China using internal transcribed spacers of nuclear ribosomal DNA

2012 ◽  
Vol 88 (1) ◽  
pp. 64-68 ◽  
Author(s):  
G.H. Liu ◽  
W. Zhou ◽  
A.J. Nisbet ◽  
M.J. Xu ◽  
D.H. Zhou ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Sequence Variation ◽  
Animal Health ◽  
Trichuris Trichiura ◽  
Its Rdna ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Economic Losses ◽  
Molecular Characteristics ◽  
Rdna Sequences

AbstractTrichuris trichiura and Trichuris suis parasitize (at the adult stage) the caeca of humans and pigs, respectively, causing trichuriasis. Despite these parasites being of human and animal health significance, causing considerable socio-economic losses globally, little is known of the molecular characteristics of T. trichiura and T. suis from China. In the present study, the entire first and second internal transcribed spacer (ITS-1 and ITS-2) regions of nuclear ribosomal DNA (rDNA) of T. trichiura and T. suis from China were amplified by polymerase chain reaction (PCR), the representative amplicons were cloned and sequenced, and sequence variation in the ITS rDNA was examined. The ITS rDNA sequences for the T. trichiura and T. suis samples were 1222–1267 bp and 1339–1353 bp in length, respectively. Sequence analysis revealed that the ITS-1, 5.8S and ITS-2 rDNAs of both whipworms were 600–627 bp and 655–661 bp, 154 bp, and 468–486 bp and 530–538 bp in size, respectively. Sequence variation in ITS rDNA within and among T. trichiura and T. suis was examined. Excluding nucleotide variations in the simple sequence repeats, the intra-species sequence variation in the ITS-1 was 0.2–1.7% within T. trichiura, and 0–1.5% within T. suis. For ITS-2 rDNA, the intra-species sequence variation was 0–1.3% within T. trichiura and 0.2–1.7% within T. suis. The inter-species sequence differences between the two whipworms were 60.7–65.3% for ITS-1 and 59.3–61.5% for ITS-2. These results demonstrated that the ITS rDNA sequences provide additional genetic markers for the characterization and differentiation of the two whipworms. These data should be useful for studying the epidemiology and population genetics of T. trichiura and T. suis, as well as for the diagnosis of trichuriasis in humans and pigs.

A new entomopathogenic nematode, Steinernema colombiense n. sp. (Nematoda: Steinernematidae), from Colombia

Nematology ◽  
2008 ◽  
Vol 10 (4) ◽  
pp. 561-574 ◽  
Author(s):  
Juan Carlos López-Núñez ◽  
Kathryn Plichta ◽  
Carmenza E. Góngora-Botero ◽  
S. Patricia Stock
Keyword(s):  
Excretory Pore ◽  
Sequence Data ◽  
Entomopathogenic Nematode ◽  
Tail Length ◽  
Rdna Sequence ◽  
Its Rdna ◽  
Infective Juvenile ◽  
Diagnostic Features ◽  
Rdna Sequences ◽  
Rdna Sequence Data

Abstract A new entomopathogenic nematode, Steinernema colombiense n. sp., is described from Colombia. Morphological, molecular (28S and ITS rDNA sequence data) and cross-hybridisation studies were used for diagnostics and identification purposes. In addition, 28S and ITS rDNA sequence data were used to assess evolutionary relationships of the new species with other Steinernema spp. Morphological diagnostic features for S. colombiense n. sp. include morphometric features of the third-stage infective juvenile, including body length of 636 (549-732) μm, narrow body diam. (31 (22-36) μm), position of the excretory pore (35 (31-40) μm), tail length (41 (32-53) μm), D% = 29 (25-33) and E% = 205 (138-284). In addition, males of first and second generations are characterised by the morphology of the spicules and gubernaculum, the number and arrangement of the genital papillae and the excretory pore position (at 67 (56-76) and 54 (46-63) μm, for first and second generations, respectively). In addition to these traits, 28S and ITS rDNA sequences analyses both showed this species to be a distinct and unique entity.

scholarly journals The molecular phylogenetic status of <i>Elphidium williamsoni</i> (Haynes, 1973) as inferred from partial 18S-rDNA sequences

2001 ◽  
Vol 20 (2) ◽  
pp. 183-183 ◽  
Author(s):  
Martin R. Langer
Keyword(s):  
North Sea ◽  
Sequence Data ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Small Subunit ◽  
The North ◽  
Rdna Sequences ◽  
Molecular Phylogenetic ◽  
The North Sea ◽  
Muddy Sediments

Abstract. Comparative studies on DNA nucleotide sequences have revolutionized our understanding of the phylogenetic relationships of many organisms and have become an important tool in evolutionary, ecological and palaeobiological inquiry. We have analysed partial small-subunit 18S sequences (srDNA) of Elphidium williamsoni (Haynes, 1973), a common intertidal benthic foraminiferid from the North Sea. The molecular phylogenetic analysis of the ribosomal rDNA sequence data indicate that E. williamsoni constitutes a well-defined genetic entity that is closely related to Elphidium aculeatum.Elphidium williamsoni is a prominent and frequently encountered foraminiferid in the North Sea and other tidal flats. It was originally described by Williamson (1858) as Polystomella umbilicata and subsequently renamed by Haynes (1973). Because of its phenotypic similarities with other elphidiids, this species has been frequently confused with, for example E. excavatum or Cribrononion alvarezianum (see Haynes for discussion). The molecular data provided here, and their direct comparison to other benthic foraminifera including one elphidiid, may therefore provide additional insight into the taxonomic status and the validity of this species.Individuals of the foraminiferid Elphidium williamsoni were collected in October 1997 from the intertidal mud flats of the Crildumersiel at the outer Jade Bay near Wilhelmshaven, North Sea (see Langer et al., 1989 for details). The mud flats are characterized by fine-grained, muddy sediments containing high contents of organic material. In the laboratory, specimens were transferred into petri dishes, examined and cleaned under a stereo microscope. Living specimens of E. williamsoni were picked out separately and placed into clean glass dishes containing filtered. . .

Molecular insights into the taxonomic status of Coris atlantica (Pisces: Labridae)

2000 ◽  
Vol 80 (5) ◽  
pp. 929-933 ◽  
Author(s):  
Thomas Guillemaud ◽  
Maria L. Cancela ◽  
Pedro Afonso ◽  
Telmo Morato ◽  
Ricardo S. Santos ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Molecular Genetic ◽  
Taxonomic Status ◽  
Molecular Genetic Analysis ◽  
Maximum Likelihood Analysis ◽  
Rdna Sequence Data ◽  
Likelihood Analysis ◽  
Mitochondrial Rdna

A molecular genetic analysis of Coris julis from different sites in the Mediterranean and the Atlantic and C. atlantica from the Cabo Verde Islands was applied to infer phylogenetic relationships between the taxa. More precisely, partial 12S mitochondrial rDNA sequence data were used in maximum parsimony, neighbour-joining, and maximum likelihood analysis to generate phylogenetic trees. The polymorphism observed indicated an important differentiation between the C. atlantica and C. julis specimens and supported the existence of two different species.

scholarly journals Discovery of Novel Backusella (Backusellaceae, Mucorales) Isolated from Invertebrates and Toads in Cheongyang, Korea

2021 ◽  
Vol 7 (7) ◽  
pp. 513
Author(s):  
Thuong T.T. Nguyen ◽  
Kerstin Voigt ◽  
André Luiz Cabral Monteiro de Azevedo Santiago ◽  
Paul M. Kirk ◽  
Hyang-Burm Lee
Keyword(s):  
Ribosomal Dna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Morphological Characters ◽  
Fungal Species ◽  
Lsu Rdna ◽  
Rdna Sequences ◽  
The Family ◽  
Internal Transcribed Spacer Sequences

Three novel fungal species, Backusella chlamydospora sp. nov., B. koreana sp. nov., and B. thermophila sp. nov., as well as two new records, B. oblongielliptica and B. oblongispora, were found in Cheongyang, Korea, during an investigation of fungal species from invertebrates and toads. All species are described here using morphological characters and sequence data from internal transcribed spacer sequences of ribosomal DNA and large subunit of the ribosomal DNA. Backusella chlamydospora is different from other Backusella species by producing chlamydospores. Backusella koreana can be distinguished from other Backusella species by producing abundant yeast-like cells. Backusella thermophila is characterized by a variable (subglobose to oblong, applanate to oval, conical and ellipsoidal to pyriform) columellae and grows well at 37 °C. Multigene phylogenetic analyses of the combined ITS and LSU rDNA sequences data generated from maximum likelihood and MrBayes analyses indicate that B. chlamydospora, B. koreana, and B. thermophila form distinct lineages in the family Backusellaceae. Detailed descriptions, illustrations, phylogenetic tree, and taxonomic key to the Backusella species present in Korea are provided.

scholarly journals Rapid Differentiation of Phenotypically Similar Yeast Species by Single-Strand Conformation Polymorphism Analysis of Ribosomal DNA

2008 ◽  
Vol 74 (9) ◽  
pp. 2604-2611 ◽  
Author(s):  
Qi-Ming Wang ◽  
Juan Li ◽  
Shi-An Wang ◽  
Feng-Yan Bai
Keyword(s):  
Ribosomal Dna ◽  
Yeast Species ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Sscp Analysis ◽  
Species Differentiation ◽  
Polymorphism Analysis ◽  
Rdna Sequences ◽  
Yeast Strains ◽  
Conformation Polymorphism

ABSTRACT Single-strand conformation polymorphism (SSCP) analysis of ribosomal DNA (rDNA) was investigated for rapid differentiation of phenotypically similar yeast species. Sensitive tests indicated that some yeast strains with one, most strains with two, and all strains with three or more nucleotide differences in the internal transcribed spacer 1 (ITS1) or ITS2 region could be distinguished by PCR SSCP analysis. The discriminative power of SSCP in yeast species differentiation was demonstrated by comparative studies of representative groups of yeast species from ascomycetes and basidiomycetes, including Saccharomyces species, medically important Candida species, and phylloplane basidiomycetous yeast species. Though the species within each group selected are closely related and have relatively similar rDNA sequences, they were clearly differentiated by PCR-SSCP analysis of the ITS1 region, given the amplified fragments were less than 350 bp in sizes. By using SSCP analysis for rapid screening of yeast strains with different rDNA sequences, species diversity existing in a large collection of yeast strains from natural sources was effectively and thoroughly investigated with substantially reduced time and cost in subsequent DNA sequencing.

scholarly journals Cyanophycin Production in a Phycoerythrin-Containing Marine Synechococcus Strain of Unusual Phylogenetic Affinity

2002 ◽  
Vol 68 (4) ◽  
pp. 1772-1777 ◽  
Author(s):  
Lauren L. Wingard ◽  
Scott R. Miller ◽  
Jeanne M. L. Sellker ◽  
Erik Stenn ◽  
Mary M. Allen ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Arabian Sea ◽  
Functional Group ◽  
Sequence Data ◽  
Nitrogen Storage ◽  
Filamentous Cyanobacteria ◽  
16S Ribosomal Dna ◽  
Rdna Sequence Data ◽  
Synechococcus Strain

ABSTRACT Thirty-two strains of phycoerythrin-containing marine picocyanobacteria were screened for the capacity to produce cyanophycin, a nitrogen storage compound synthesized by some, but not all, cyanobacteria. We found that one of these strains, Synechococcus sp. strain G2.1 from the Arabian Sea, was able to synthesize cyanophycin. The cyanophycin extracted from the cells was composed of roughly equimolar amounts of arginine and aspartate (29 and 35 mol%, respectively), as well as a small amount of glutamate (15 mol%). Phylogenetic analysis, based on partial 16S ribosomal DNA (rDNA) sequence data, showed that Synechococcus sp. strain G2.1 formed a well-supported clade with several strains of filamentous cyanobacteria. It was not closely related to several other well-studied marine picocyanobacteria, including Synechococcus strains PCC7002, WH7805, and WH8018 and Prochlorococcus sp. strain MIT9312. This is the first report of cyanophycin production in a phycoerythrin-containing strain of marine or halotolerant Synechococcus, and its discovery highlights the diversity of this ecologically important functional group.

Redescription and synonymization of Oscheius citri Tabassum, Shahina, Nasira and Erum, 2016 (Rhabditida, Rhabditidae) from India and its taxonomical consequences

2021 ◽  
Vol 95 ◽  
Author(s):  
A. Rana ◽  
A.H. Bhat ◽  
A.K. Chaubey ◽  
V. Půža ◽  
J. Abolafia
Keyword(s):  
Indian Population ◽  
Uttar Pradesh ◽  
Nematode Species ◽  
Molecular Data ◽  
Molecular Characteristics ◽  
Morphometric Characteristics ◽  
High Similarity ◽  
Rdna Sequences ◽  
Indian Strain ◽  
28S Rdna Sequences

Abstract A population of a nematode species belonging to the genus Oscheius was isolated in western Uttar Pradesh, India. Morphological and morphometrical studies on this species showed its high similarity with six species described previously from Pakistan (Oscheius citri, O. cobbi, O. cynodonti, O. esculentus, O. punctatus and O. sacchari). The molecular analysis of the ITS1-5.8S-ITS2 rDNA sequences of the Indian population and the six species described from Pakistan showed that all the sequences are almost identical. Thus, based on morphological and molecular characteristics, all of the six above-mentioned Pakistani species and Indian strain do not differ from each other, hence can be considered synonyms. The correct name for this taxon is the first described species O. citri. Additionally, the phylogenetic analysis of the 18S rDNA and the 28S rDNA sequences showed that Oscheius citri is sister to the clade formed by O. chongmingensis and O. rugaoensis from China. The high similarity of morphological and morphometric characteristics of O. citri and other species, O. maqbooli, O. nadarajani, O. niazii, O. shamimi and O. siddiqii, suggest their conspecificity; however, lack of molecular data for these species does not allow this hypothesis to be tested.

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