Identification of Giardia species and Giardia duodenalis assemblages by sequence analysis of the 5.8S rDNA gene and internal transcribed spacers

SUMMARYPCR assays have been developed mainly to assist investigations into the epidemiology of Giardia duodenalis, the only species in the Giardia genus having zoonotic potential. However, a reliable identification of all species is of practical importance, particularly when water samples and samples from wild animals are investigated. The aim of the present work was to genotype Giardia species and G. duodenalis assemblages using as a target the region spanning the 5.8S gene and the 2 flanking internal transcribed spacers (ITS1 and ITS2) of the ribosomal gene. Primers were designed to match strongly conserved regions in the 3′ end of the small subunit and in the 5′ end of the large subunit ribosomal genes. The corresponding region (about 310 bp) was amplified from 49 isolates of both human and animal origin, representing all G. duodenalis assemblages as well as G. muris and G. microti. Sequence comparison and phylogenetic analysis showed that G. ardeae, G. muris, G. microti as well as the 7 G. duodenalis assemblages can be easily distinguished. Since the major subgroups within the zoonotic assemblages A and B can be identified by sequence analysis, this assay is also informative for molecular epidemiological studies.

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Integrative Studies on a New Ciliate Campanella sinica n. sp. (Protista, Ciliophora, Peritrichia) Based on the Morphological and Molecular Data, With Notes on the Phylogeny and Systematics of the Family Epistylididae

Frontiers in Microbiology ◽

10.3389/fmicb.2021.718757 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zhe Wang ◽

Tong Wu ◽

Borong Lu ◽

Yong Chi ◽

Xue Zhang ◽

...

Keyword(s):

Ribosomal Dna ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Small Subunit ◽

Internal Transcribed Spacers ◽

Lsu Rdna ◽

5.8S Rdna ◽

Freshwater Pond ◽

The Family

During an investigation on freshwater peritrichs, a new colonial sessilid ciliate, Campanella sinica n. sp., was isolated from aquatic plants in an artificial freshwater pond in Qingdao, China. Specimen observations of this species were performed both in vivo and using silver staining. C. sinica n. sp. is characterized by the appearance of the mature colony, which is up to 2 cm high and contains more than 1,000 zooids, the asymmetric horn-shaped zooids, strongly everted and multi-layered peristomial lip, the slightly convex peristomial disc, and the well-developed haplokinety and polykinety, which make more than four circuits of the peristome before descending into the infundibulum. The small subunit ribosomal DNA (SSU rDNA), 5.8s rDNA and its flank internal transcribed spacers (ITS1-5.8s rDNA-ITS2), and large subunit ribosomal DNA (LSU rDNA) are sequenced and used for phylogenetic analyses which reveal that the family Epistylididae Kahl, 1933 is non-monophyletic whereas the genus Campanella is monophyletic and nests within the basal clade of the sessilids. The integrative results support the assertion that the genus Campanella represents a separate lineage from other epistylidids, suggesting a further revision of the family Epistylididae is needed. We revise Campanella including the transfer into this genus of a taxon formerly assigned to Epistylis, which we raise to species rank, i.e., Campanella ovata (Nenninger, 1948) n. grad. & n. comb. (original combination Epistylis purneri f. ovataNenninger, 1948). In addition, we provide a key to the identification of the species of Campanella.

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Theileria parva ribosomal internal transcribed spacer sequences exhibit extensive polymorphism and mosaic evolution: application to the characterization of parasites from cattle and buffalo

Parasitology ◽

10.1017/s0031182099004321 ◽

1999 ◽

Vol 118 (6) ◽

pp. 541-551 ◽

Cited By ~ 38

Author(s):

N. E. COLLINS ◽

B. A. ALLSOPP

Keyword(s):

Genetic Recombination ◽

Large Subunit ◽

Small Subunit ◽

Internal Transcribed Spacers ◽

Rrna Genes ◽

Gene Pools ◽

Theileria Parva ◽

Causative Agents ◽

Internal Transcribed Spacer Sequences

We sequenced the rRNA genes and internal transcribed spacers (ITS) of several Theileria parva isolates in an attempt to distinguish between the causative agents of East coast fever and Corridor disease. The small subunit (SSU) and large subunit (LSU) rRNA genes from a cloned T. p. lawrencei parasite were sequenced; the former was identical to that of T. p. parva Muguga, and there were minor heterogeneities in the latter. The 5·8S gene sequences of 11 T. parva isolates were identical, but major differences were found in the ITS. Six characterization oligonucleotides were designed to hybridize within the variable ITS1 region; 93·5% of T. p. parva isolates examined were detected by probe TPP1 and 81·8% of T. p. lawrencei isolates were detected by TPL2 and/or TPL3a. There was no absolute distinction between T. p. parva and T. p. lawrencei and the former hybridized with fewer of the probes than did the latter. It therefore seems that a relatively homogenous subpopulation of T. parva has been selected in cattle from a more diverse gene pool in buffalo. The ITSs of both T. p. parva and T. p. lawrencei contained different combinations of identifiable sequence segments, resulting in a mosaic of segments in any one isolate, suggesting that the two populations undergo genetic recombination and that their gene pools are not completely separate.

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The Evolution of Life Modes in Stictidaceae, with Three Novel Taxa

Journal of Fungi ◽

10.3390/jof7020105 ◽

2021 ◽

Vol 7 (2) ◽

pp. 105

Author(s):

Vinodhini Thiyagaraja ◽

Robert Lücking ◽

Damien Ertz ◽

Samantha C. Karunarathna ◽

Dhanushka N. Wanasinghe ◽

...

Keyword(s):

New Species ◽

Large Scale ◽

Sequence Data ◽

Large Subunit ◽

Monte Carlo Sampling ◽

Small Subunit ◽

Sensu Stricto ◽

Internal Transcribed Spacers ◽

Character State ◽

Phenotypic Data

Ostropales sensu lato is a large group comprising both lichenized and non-lichenized fungi, with several lineages expressing optional lichenization where individuals of the same fungal species exhibit either saprotrophic or lichenized lifestyles depending on the substrate (bark or wood). Greatly variable phenotypic characteristics and large-scale phylogenies have led to frequent changes in the taxonomic circumscription of this order. Ostropales sensu lato is currently split into Graphidales, Gyalectales, Odontotrematales, Ostropales sensu stricto, and Thelenellales. Ostropales sensu stricto is now confined to the family Stictidaceae, which includes a large number of species that are poorly known, since they usually have small fruiting bodies that are rarely collected, and thus, their taxonomy remains partly unresolved. Here, we introduce a new genus Ostropomyces to accommodate a novel lineage related to Ostropa, which is composed of two new species, as well as a new species of Sphaeropezia, S. shangrilaensis. Maximum likelihood and Bayesian inference analyses of mitochondrial small subunit spacers (mtSSU), large subunit nuclear rDNA (LSU), and internal transcribed spacers (ITS) sequence data, together with phenotypic data documented by detailed morphological and anatomical analyses, support the taxonomic affinity of the new taxa in Stictidaceae. Ancestral character state analysis did not resolve the ancestral nutritional status of Stictidaceae with confidence using Bayes traits, but a saprotrophic ancestor was indicated as most likely in a Bayesian binary Markov Chain Monte Carlo sampling (MCMC) approach. Frequent switching in nutritional modes between lineages suggests that lifestyle transition played an important role in the evolution of this family.

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Spegazzinia camelliae sp. nov. (Didymosphaeriaceae, Pleosprales), a new endophytic fungus from northern Thailand

Phytotaxa ◽

10.11646/phytotaxa.483.2.4 ◽

2021 ◽

Vol 483 (2) ◽

pp. 117-128

Author(s):

NAKARIN SUWANNARACH ◽

JATURONG KUMLA ◽

SAISAMORN LUMYONG

Keyword(s):

Phylogenetic Analyses ◽

Large Subunit ◽

Elongation Factor ◽

Small Subunit ◽

Internal Transcribed Spacers ◽

Nuclear Ribosomal Dna ◽

Full Description ◽

Translation Elongation ◽

Spine Length ◽

Elongation Factor 1 Alpha

A new endophytic ascomycete, described herein as Spegazzinia camelliae, was isolated from leaves of Camellia sinensis var. assamica collected from Nan Province, Thailand. This species is characterized by basauxic conidiophores and dark brown to blackish brown α and β conidia. It can be distinguished from previously described Spegazzinia species by the spine length of the α conidia and the size of the β conidia. Multi-gene phylogenetic analyses of the small subunit (SSU), large subunit (LSU) and internal transcribed spacers (ITS) of the nuclear ribosomal DNA (rDNA) and the translation elongation factor 1-alpha (tef1) genes also support S. camelliae is a distinct new species within Spegazzinia. A full description, color photographs, illustrations and a phylogenetic tree showing the position of S. camelliae are provided.

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Ciliate Environmental Diversity Can Be Underestimated by the V4 Region of SSU rDNA: Insights from Species Delimitation and Multilocus Phylogeny of Pseudokeronopsis (Ciliophora, Spirotrichea)

Microorganisms ◽

10.3390/microorganisms7110493 ◽

2019 ◽

Vol 7 (11) ◽

pp. 493 ◽

Cited By ~ 2

Author(s):

Zhan ◽

Li ◽

Keyword(s):

Species Delimitation ◽

High Throughput Sequencing ◽

Sequence Similarity ◽

Large Subunit ◽

Small Subunit ◽

Base Change ◽

Published Data ◽

Environmental Diversity ◽

5.8S Rdna ◽

Eukaryotic Microorganisms

Metabarcoding and high-throughput sequencing methods have greatly improved our understanding of protist diversity. Although the V4 region of small subunit ribosomal DNA (SSU-V4 rDNA) is the most widely used marker in DNA metabarcoding of eukaryotic microorganisms, doubts have recently been raised about its suitability. Here, using the widely distributed ciliate genus Pseudokeronopsis as an example, we assessed the potential of SSU-V4 rDNA and four other nuclear and mitochondrial markers for species delimitation and phylogenetic reconstruction. Our studies revealed that SSU-V4 rDNA is too conservative to distinguish species, and a threshold of 97% and 99% sequence similarity detected only one and three OTUs, respectively, from seven species. On the basis of the comparative analysis of the present and previously published data, we proposed the multilocus marker including the nuclear 5.8S rDNA combining the internal transcribed spacer regions (ITS1-5.8S-ITS2) and the hypervariable D2 region of large subunit rDNA (LSU-D2) as an ideal barcode rather than the mitochondrial cytochrome c oxidase subunit 1 gene, and the ITS1-5.8S-ITS2 as a candidate metabarcoding marker for ciliates. Furthermore, the compensating base change and tree-based criteria of ITS2 and LSU-D2 were useful in complementing the DNA barcoding and metabarcoding methods by giving second structure and phylogenetic evidence.

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Phylogenetic placement of Hanseniaspora–Kloeckera species using multigene sequence analysis with taxonomic implications: descriptions of Hanseniaspora pseudoguilliermondii sp. nov. and Hanseniaspora occidentalis var. citrica var. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64052-0 ◽

2006 ◽

Vol 56 (5) ◽

pp. 1157-1165 ◽

Cited By ~ 23

Author(s):

Neza Cadez ◽

Peter Raspor ◽

Maudy Th. Smith

Keyword(s):

Type Strain ◽

Large Subunit ◽

Elongation Factor ◽

Sequence Divergence ◽

Species Group ◽

Ribosomal Gene ◽

Internal Transcribed Spacers ◽

Polymorphism Analysis ◽

Protein Coding ◽

Protein Coding Genes

Two protein-coding genes, actin and translation elongation factor-1α (EF-1α), as well as two ribosomal gene regions, D1/D2 domains of the large subunit and both internal transcribed spacers including the 5.8S gene region, were evaluated regarding their usefulness for reconstruction of phylogenetic relationships in the Hanseniaspora–Kloeckera species group. This included analyses of sequence divergence values, heterogeneity of evolutionary rates and the reliability of the inferred trees. Both protein-coding genes showed greater capacities to resolve at the strain level and between the closely related species of Hanseniaspora–Kloeckera, compared with the ribosomal gene regions. However, to obtain a fully resolved and reliable phylogenetic tree that reflected the biological relationships it was necessary to combine three congruent sequence datasets. The novel species Hanseniaspora pseudoguilliermondii sp. nov. (type strain CBS 8772T) is described as a result of the application of various molecular approaches to delimit species. Furthermore, incongruent gene genealogies of genetically divergent strains of Hanseniaspora occidentalis, as determined by amplified fragment length polymorphism analysis and DNA–DNA reassociation measurements, indicated the presence of two novel varieties, H. occidentalis var. occidentalis (type strain CBS 2592T) and H. occidentalis var. citrica var. nov. (type strain CBS 6783T), which could be distinguished by habitat preference.

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Spissiomyces endophytica (Dothideomycetes, Ascomycota), a new endophytic fungus from Thailand

Phytotaxa ◽

10.11646/phytotaxa.333.2.5 ◽

2018 ◽

Vol 333 (2) ◽

pp. 219 ◽

Cited By ~ 1

Author(s):

NAKARIN SUWANNARACH ◽

JATURONG KUMLA ◽

SAISAMORN LUMYONG

Keyword(s):

Phylogenetic Analysis ◽

Large Subunit ◽

Small Subunit ◽

Internal Transcribed Spacers ◽

Nuclear Ribosomal Dna ◽

Full Description ◽

Morphological Investigation ◽

Lampang Province ◽

A New Species ◽

Β Tubulin

A new species of endophytic fungi, described herein as Spissiomyces endophytica, was isolated from tubers of Balanophora fungosa in Lampang Province, Thailand. A morphological investigation revealed that this species was distinguished from the previously described Spissiomyces species by its lager conidial size. Phylogenetic analysis was performed using combined sequence datasets of the small subunit (SSU), large subunit (LSU) and internal transcribed spacers (ITS) of the nuclear ribosomal DNA (rDNA), a part of the RNA polymerase (RPB2) and β-tubulin (TUB) genes, in order to support the morphological results. A full description, illustrations, phylogenetic tree and key to the species are provided.

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Morosphaeria muthupetensis sp. nov. (Morosphaeriaceae) from India: morphological characterization and multigene phylogenetic inference

Botanica Marina ◽

10.1515/bot-2017-0124 ◽

2018 ◽

Vol 61 (4) ◽

pp. 395-405 ◽

Cited By ~ 7

Author(s):

Bandarupalli Devadatha ◽

Vemuri Venkateswara Sarma ◽

Rajesh Jeewon ◽

E.B. Gareth Jones

Keyword(s):

Tamil Nadu ◽

Large Subunit ◽

Elongation Factor ◽

Small Subunit ◽

Morphological Characterization ◽

Internal Transcribed Spacers ◽

Translation Elongation ◽

Elongation Factor 1 Alpha ◽

Elongation Factor 1 ◽

Mangrove Wood

Abstract A novel species of Morosphaeria, Morosphaeria muthupetensis, saprobic on intertidal mangrove wood of Rhizophora mucronata from Muthupet mangroves on Kaveri River Delta, Tamil Nadu along the East coast of India, is described in this paper. Morosphaeria muthupetensis is characterized by large sub-globose to lenticular ascomata; long cylindrical to clavate, short pedicellate asci; small, fusiform to ellipsoidal ascospores with acute ends when compared to other Morosphaeria species. A multigene phylogeny obtained from a combined nuclear large subunit, small subunit, internal transcribed spacers rDNA and translation elongation factor 1-alpha sequence analysis revealed that M. muthupetensis is phylogenetically distinct and nested in between Morosphaeria velatispora and Morosphaeria ramunculicola and all these species constitute a strongly supported monophyletic clade sister to the genus Helicascus. Detailed descriptions and illustrations of M. muthupetensis are presented and compared with other Morosphaeria species.

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Intragenomic Heterogeneity and Intergenomic Recombination among Haloarchaeal rRNA Genes

Journal of Bacteriology ◽

10.1128/jb.186.12.3980-3990.2004 ◽

2004 ◽

Vol 186 (12) ◽

pp. 3980-3990 ◽

Cited By ~ 86

Author(s):

Yan Boucher ◽

Christophe J. Douady ◽

Adrian K. Sharma ◽

Masahiro Kamekura ◽

W. Ford Doolittle

Keyword(s):

Hot Spots ◽

Large Subunit ◽

Halophilic Archaea ◽

Small Subunit ◽

Internal Transcribed Spacers ◽

Rrna Genes ◽

Extremely Halophilic Archaea ◽

The Impact ◽

Interspecies Recombination ◽

Archaeal Genus

ABSTRACT More than one copy of rRNA operons, which code for both the small-subunit (SSU) and large-subunit (LSU) rRNA, are often found in prokaryotes. It is generally assumed that all rRNA operons within a single cell are almost identical. A notable exception is the extremely halophilic archaeal genus Haloarcula, most species of which are known to harbor highly divergent rRNA operons that differ at ∼5% of the nucleotide positions in the SSU gene and at 1 to 2% of the nucleotide positions in the LSU gene. We report that such intragenomic heterogeneity is not unique to Haloarcula, as high levels of intragenomic sequence variation have been observed for the SSU genes of two other genera of extreme halophiles, Halosimplex and Natrinema. To investigate this in detail, the two rRNA operons of Halosimplex carlsbadense and the four operons of Natrinema sp. strain XA3-1 were cloned and completely sequenced. The SSU and LSU genes of H. carlsbadense show the highest levels of intragenomic heterogeneity observed so far in archaea (6.7 and 2.6%). The operons of Natrinema sp. strain XA3-1 have additional unusual characteristics, such as identical internal transcribed spacers, while one of four SSU genes is 5% divergent and all LSU genes differ from each other by 0.9 to 1.9%. The heterogeneity among the Natrinema sp. strain XA3-1 LSU genes is localized in hot spots, and one of these regions is shown to be the result of a recombination event with a distantly related halophile. This is the first example of interspecies recombination between rRNA genes in archaea, and the recombination occurred over one of the largest phylogenetic distances ever reported for such an event. We suggest that intragenomic heterogeneity of rRNA operons is an ancient and stable trait in several lineages of the Halobacteriales. The impact of this phenomenon on the taxonomy of extremely halophilic archaea is discussed.

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Phylogenetic classification and generic delineation of Hydeomyces desertipleosporoides gen. et sp. nov., (Phaeosphaeriaceae) from Jebel Akhdar Mountain in Oman

Phytotaxa ◽

10.11646/phytotaxa.391.1.2 ◽

2019 ◽

Vol 391 (1) ◽

pp. 28 ◽

Cited By ~ 4

Author(s):

SAJEEWA S. N. MAHARACHCHIKUMBURA ◽

HIRAN A. ARIYAWANSA ◽

DHANUSHKA N. WANASINGHE ◽

MONIKA C. DAYARATHNE ◽

NADIYA A. AL-SAADY ◽

...

Keyword(s):

Large Subunit ◽

Elongation Factor ◽

Small Subunit ◽

Internal Transcribed Spacers ◽

New Taxon ◽

Small Subunit Rrna ◽

Translation Elongation ◽

The Family ◽

Large Subunit Rrna ◽

Elongation Factor 1

Specimens of a new pleosporalean taxon were obtained on the bark of Juniperus excels from the northern mountains of Oman; from the Jebel Akhdar (‘Green Hills’). Sequence analyses based on the regions of large subunit rRNA (LSU), small subunit rRNA (SSU), translation elongation factor 1-α (TEF) and internal transcribed spacers (ITS) were performed to resolve the phylogenetic relationships of the new taxon in Phaeosphaeriaceae. The data concluded that the taxon represents a novel genus of the family Phaeosphaeriaceae and the generic name Hydeomyces and the species name H. desertipleosporoides are introduced for the new taxon. An outline of the characters which differentiate the new genus from phylogenetically closely related genera Dematiopleospora and Dlhawksworthia is given and its morphology of asexual and sexual morphs is described.

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