High intra-individual sequence variation in the nuclear rDNA LSU-5S intergenic spacer in the Sargassaceae (Fucales, Phaeophyceae)

SUMMARYCyathostomins comprise a group of 50 species of parasitic nematodes that infect equids. Ribosomal DNA sequences, in particular the intergenic spacer (IGS) region, have been utilized via several methodologies to identify pre-parasitic stages of the commonest species that affect horses. These methods rely on the availability of accurate sequence information for each species, as well as detailed knowledge of the levels of intra- and inter-specific variation. Here, the IGS DNA region was amplified and sequenced from 10 cyathostomin species for which sequence was not previously available. Also, additional IGS DNA sequences were generated from individual worms of 8 species already studied. Comparative analysis of these sequences revealed a greater range of intra-specific variation than previously reported (up to 23%); whilst the level of inter-specific variation (3–62%) was similar to that identified in earlier studies. The reverse line blot (RLB) method has been used to exploit the cyathostomin IGS DNA region for species identification. Here, we report validation of novel and existing DNA probes for identification of cyathostomins using this method and highlight their application in differentiating life-cycle stages such as third-stage larvae that cannot be identified to species by morphological means†.

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Sequence diversity of two chloroplast genes: rps4 and tRNAGly (UCC), in the liverwort Marchantia polymorpha, an emerging plant model system

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.3573 ◽

2018 ◽

Vol 87 (1) ◽

Cited By ~ 2

Author(s):

Hanna Kijak ◽

Weronika Łodyga ◽

Ireneusz J. Odrzykoski

Keyword(s):

Chloroplast Genome ◽

Sequence Variation ◽

Sequence Divergence ◽

Intergenic Spacer ◽

Marchantia Polymorpha ◽

Homologous Sequences ◽

Clonal Lines ◽

Suspension Line ◽

Marchantia Paleacea ◽

Almost All

The primary purpose of this study is to evaluate the sequence variation for two regions of chloroplast DNA in a collection of 27 taxonomically well-annotated clonal lines of Marchantia polymorpha sensu lato derived from European populations. We attempted to develop molecular markers so as to identify three taxa usually recognized as subspecies. We sequenced two regions: the rps4 gene along with the rps4-trnT intergenic spacer and an intron of the tRNAGly (UCC) gene. Samples of Marchantia paleacea ssp. diptera from Japan were used for comparative purposes.Three haplotypes (MA, MB, and MC) were identified for the species, and almost all sequence divergence between subspecies was found to occur at the level of 0.0023–0.0032 substitutions per site. The sequence divergence between M. polymorpha and M. paleacea was tenfold greater (0.0331–0.0340). We did not detect any differences between M. paleacea and homologous sequences from the reference chloroplast genome of M. polymorpha obtained from the GeneBank (NC_001319). It was confirmed that the cell suspension line A-18 used for the sequencing of the full chloroplast genome in 1986 was incorrectly taxonomically annotated.

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Revised generic delimitations for Oxypolis and Ptilimnium (Apiaceae) based on leaf morphology, comparative fruit anatomy, and phylogenetic analysis of nuclear rDNA ITS and cpDNA trnQ -trnK intergenic spacer sequence data

Taxon ◽

10.1002/tax.612011 ◽

2012 ◽

Vol 61 (2) ◽

pp. 402-418 ◽

Cited By ~ 12

Author(s):

Mary Ann E. Feist ◽

Stephen R. Downie ◽

Anthony R. Magee ◽

Mei Rebecca Liu

Keyword(s):

Phylogenetic Analysis ◽

Leaf Morphology ◽

Sequence Data ◽

Intergenic Spacer ◽

Nuclear Rdna ◽

Fruit Anatomy ◽

Rdna Its

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Genetic polymorphism of natural isolates of Nosema Pyrausta (Microsporidia: Nosematidae)

Ecological genetics ◽

10.17816/ecogen15138-43 ◽

2017 ◽

Vol 15 (1) ◽

pp. 38

Author(s):

Inna V Grushevaya ◽

Anastasia N Ignatieva ◽

Julia M Malysh ◽

Lyudmila I Trepashko ◽

Yuri S Tokarev ◽

...

Keyword(s):

Ribosomal Rna ◽

Sequence Variation ◽

Intergenic Spacer ◽

Small Subunit ◽

Ssu Rrna ◽

Corn Borer ◽

Corn Borers ◽

Natural Isolates ◽

Disease Agent ◽

Important Disease

Background. Microsporidia are ubiquitous parasites of animals, most abundant in arthropods and fishes. Many species of these parasites are important from standpoints of medicine, veterinary and agriculture. Microsporidium Nosema pyrausta is an important disease agent in corn borer populations causing adverse effect on host fitness. Genotyping of this parasite is necessary for proper species identification and intraspecific polymorphysm studies. Materials and Methods. Microsporidia-infected larvae of corn borers of the genus Ostrinia were recovered from Krasnodar Territory in Russia and Gomel Region in Belarus. Small subunit ribosomal RNA (SSU rRNA) was amplified and sequenced directly, while intergenic spacer (IGS) was amplified, cloned and sequenced (1-5 clones per sample) for four isolates of microsporidia. Sequences were aligned and compared using standard bioinformatics tools (Clustal W and BLAST). Results. SSU rRNA genotyping showed allocation of all four isolates to N. pyrausta with 100% identity to each other and 99.7% similarity to Nosema bombycis, the type species of the genus Nosema. High levels of IGS sequence variation (61-74%) is observed both between isolates of different species and populations of microsporidia as well as between molecular clones within parasite isolates from individual hosts. Conclusion. N. pyrausta is widespread in corn borer populations and its genetic structure is complicated, as in other species of these parasites. Further studies of molecular markers are needed for genetic differentiation of geographic isolates of N. pyrausta.

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Characterization of California Isolates of Fusarium oxysporum f. sp. vasinfectum

Plant Disease ◽

10.1094/pd-89-0366 ◽

2005 ◽

Vol 89 (4) ◽

pp. 366-372 ◽

Cited By ~ 74

Author(s):

Y. Kim ◽

R. B. Hutmacher ◽

R. M. Davis

Keyword(s):

Fusarium Oxysporum ◽

Elongation Factor ◽

Intergenic Spacer ◽

Culture Collection ◽

Nuclear Rdna ◽

Bt Genes ◽

Pathogenicity Tests ◽

Race 4 ◽

Lineage Iv

Thirty isolates of Fusarium oxysporum f. sp. vasinfectum from California, Australia, China, and the American Type Culture Collection were characterized by partial sequences of translational elongation factor (EF-1α), phosphate permase (PHO), and beta-tubulin (BT) genes, restriction digests of the intergenic spacer (IGS) region of nuclear rDNA, and pathogenicity tests. Based on phylogenetic analysis of combined sequences of EF-1α, PHO, and BT genes, California isolates represented four lineages. Lineage I contained race 3, lineage II contained races 1, 2, and 6, lineage III contained race 8, and lineage IV contained race 4. The Australian isolates formed a strongly supported independent clade. There were nine haplotypes based on restriction digests of the IGS region. In greenhouse pathogenicity tests with California isolates, those from the race 4 lineage were highly aggressive on certain Pima cotton (Gossypium barbadense) cultivars and less aggressive on Upland cotton (Gossypium hirsutum) cultivars. All isolates belonging to the other lineages caused relatively mild symptoms on both Pima and Upland cultivars. This is the first report of the occurrence of races 3, 4, and 8 in California.

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Molecular taxonomic clarification of Ptilotus exaltatus and Ptilotus nobilis (Amaranthaceae)

Australian Systematic Botany ◽

10.1071/sb06010 ◽

2007 ◽

Vol 20 (1) ◽

pp. 72 ◽

Cited By ~ 8

Author(s):

Kok K. Lee ◽

Dion K. Harrison ◽

Margaret E. Johnston ◽

Richard R. Williams

Keyword(s):

Sequence Variation ◽

Sequence Data ◽

Morphological Characteristics ◽

Morphological Characters ◽

Nuclear Rdna ◽

Monophyletic Clade ◽

Morphological Taxonomy ◽

Molecular Phylogenetic ◽

Morphological Differences ◽

Respective Species

A complete botanical key for the genus Ptilotus R.Brown (family Amarathaceae) has not yet been published. Identifying the 100 or more Ptilotus species using morphological characters has been difficult because plants often exhibit slight morphological differences and intermediate characteristics common to several species, subspecies, varieties and forms. Ptilotus exaltatus Nees and P. nobilis (Lindl) F.Muell share many morphological characteristics, but are classified as different species predominantly based on inflorescence colour. The current study involved a molecular phylogenetic analysis of 14 Ptilotus species using sequence data from the internal transcribed spacer (ITS) regions ITS 1 and ITS 2 within the 18S–26S nuclear rDNA. Of the 39 accessions analysed, all except those identified as P. exaltatus and P. nobilis clustered according to their respective species based on their morphological taxonomy. In contrast, all 18 P. exaltatus and P. nobilis accessions formed a distinct monophyletic clade with 99% bootstrap values and a low level of sequence variation (GD = 0.002). Taking into account the lack of reliable morphological characters for separating P. exaltatus and P. nobilis, together with the ITS sequence data showing little genetic divergence or genetic structure, we propose that P. exaltatus and P. nobilis are conspecific.

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Phylogenetic positions of Actites megalocarpa and Sonchus hydrophilus (Sonchinae: Asteraceae) based on ITS and chloroplast non-coding DNA sequences

Australian Systematic Botany ◽

10.1071/sb03019 ◽

2004 ◽

Vol 17 (1) ◽

pp. 73 ◽

Cited By ~ 13

Author(s):

Seung-Chul Kim ◽

Christina T. Lu ◽

Brendan J. Lepschi

Keyword(s):

New Zealand ◽

Chloroplast Dna ◽

Dna Sequences ◽

Intergenic Spacer ◽

Its Sequences ◽

Monotypic Genus ◽

Nuclear Rdna

Phylogenetic positions of the Australian endemic taxa Actites megalocarpa and Sonchus hydrophilus within the subtribe Sonchinae were determined on the basis of ITS sequences of nuclear rDNA and the psbA–trnH(GUG) intergenic spacer of chloroplast DNA. Both ITS and cpDNA phylogenies suggest that the monotypic genus Actites is not closely related to the members of Sonchus section Asperi, as previously suggested. Rather, this study indicates that it is more closely related to the members of Sonchus sections Maritimi (S.�maritimus) and Arvenses (S. arvensis). It also suggests that S. maritimus from section Maritimi is one of the closest relatives of Actites in Australia, although an alternative origin from section Arvenses is possible. Actites and Embergeria, once treated as congeneric taxa, appear to have originated independently in Australia and New Zealand, respectively. Sonchus hydrophilus is closely related to the S. asper complex, S. oleraceus and S. kirkii. This study suggests that S. kirkii may be involved in the origin of S. hydrophilus in Australia.

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Comparison of ITS and IGS1 regions for strain typing of clinical and non-clinical isolates of Pichia anomala

Journal of Medical Microbiology ◽

10.1099/jmm.0.05436-0 ◽

2004 ◽

Vol 53 (2) ◽

pp. 119-123 ◽

Cited By ~ 5

Author(s):

Rajeshwari Sutar ◽

Joseph K. David ◽

K. Ganesan ◽

Anup K. Ghosh ◽

Sunit Singhi ◽

...

Keyword(s):

Comparative Analysis ◽

Internal Transcribed Spacer ◽

Sequence Variation ◽

Intergenic Spacer ◽

Pichia Anomala ◽

Clinical Isolates ◽

Strain Typing ◽

Nosocomial Pathogen ◽

Its Regions

Pichia anomala is an emerging nosocomial pathogen and there is a need for methods that distinguish between different P. anomala strains. In the typing of several clinical as well as non-clinical P. anomala strains, the sequence variation of the internal transcribed spacer (ITS) was found to be inadequate for typing purposes. The intergenic spacer 1 (IGS1) region of the rDNA of several P. anomala strains was therefore investigated in detail. The IGS1 region (which varied from 1213 to 1231 bp in length) was interspersed with repeats and had more variation than the ITS regions. Comparative analysis in cases where analysis by the ITS was ambiguous clearly revealed the IGS1 region to be a more discriminatory tool in the typing of P. anomala strains.

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