Myosporidium ladogensis n. comb. in burbot Lota lota from Finland: fine structure and microsporidian taxonomy

2020 ◽  
Vol 139 ◽  
pp. 15-23
Author(s):  
SRM Jones ◽  
H Ahonen ◽  
J Taskinen
Keyword(s):  
Host Cell ◽  
Ribosomal Rna ◽  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Cell Cytoplasm ◽  
Lota Lota ◽  
Host Cell Cytoplasm ◽  
Pike Perch ◽  
Rrna Sequences

Infections with microsporidian parasites are described in skeletal muscle of burbot Lota lota from Lake Haukivesi, Finland. Infected myocytes contained spores within sporophorous vesicles (SPVs) in contact with host cell cytoplasm, similar to Pleistophora ladogensis in L. lota and smelt Osmerus eperlanus in western Russia and northern Germany. Analysis of small subunit ribosomal RNA (SSU rRNA) gene sequences indicated identity with Myosporidium spraguei in burbot and pike-perch from this lake. The latter is considered a junior synonym of P. ladogensis. Phylogenetic analysis of SSU rRNA sequences resolved the burbot parasite apart from a clade containing the type species P. typicalis, but together with M. merluccius. The parasite is renamed Myosporidium ladogensis (Voronin, 1978) n. comb. Networks of tubular appendages arising from developing meronts and SPVs were associated with degradation of host cell cytoplasm.

scholarly journals An ITS-based phylogenetic framework for the genus Vorticella : finding the molecular and morphological gaps in a taxonomically difficult group

2013 ◽  
Vol 280 (1771) ◽  
pp. 20131177 ◽  
Author(s):  
Ping Sun ◽  
John C. Clamp ◽  
Dapeng Xu ◽  
Bangqin Huang ◽  
Mann Kyoon Shin ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Branching Order ◽  
Close Relationship ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework

Vorticella includes more than 100 currently recognized species and represents one of the most taxonomically challenging genera of ciliates. Molecular phylogenetic analysis of Vorticella has been performed so far with only sequences coding for small subunit ribosomal RNA (SSU rRNA); only a few of its species have been investigated using other genetic markers owing to a lack of similar sequences for comparison. Consequently, phylogenetic relationships within the genus remain unclear, and molecular discrimination between morphospecies is often difficult because most regions of the SSU rRNA gene are too highly conserved to be helpful. In this paper, we move molecular systematics for this group of ciliates to the infrageneric level by sequencing additional molecular markers—fast-evolving internal transcribed spacer (ITS) regions—in a broad sample of 66 individual samples of 28 morphospecies of Vorticella collected from Asia, North America and Europe. Our phylogenies all featured two strongly supported, highly divergent, paraphyletic clades (I, II) comprising the morphologically defined genus Vorticella . Three major lineages made up clade I, with a relatively well-resolved branching order in each one. The marked divergence of clade II from clade I confirms that the former should be recognized as a separate taxonomic unit as indicated by SSU rRNA phylogenies. We made the first attempt to elucidate relationships between species in clade II using both morphological and multi-gene approaches, and our data supported a close relationship between some morphospecies of Vorticella and Opisthonecta , indicating that relationships between species in the clade are far more complex than would be expected from their morphology. Different patterns of helix III of ITS2 secondary structure were clearly specific to clades and subclades of Vorticella and, therefore, may prove useful for resolving phylogenetic relationships in other groups of ciliates.

scholarly journals Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Alejandro A. Schäffer ◽  
Richard McVeigh ◽  
Barbara Robbertse ◽  
Conrad L. Schoch ◽  
Anjanette Johnston ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Ribosomal Rna ◽  
Dna Sequences ◽  
Software Package ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Rrna Sequence ◽  
Ssu Rrna Gene ◽  
Taxonomic Groups ◽  
Rrna Sequences

Abstract Background The DNA sequences encoding ribosomal RNA genes (rRNAs) are commonly used as markers to identify species, including in metagenomics samples that may combine many organismal communities. The 16S small subunit ribosomal RNA (SSU rRNA) gene is typically used to identify bacterial and archaeal species. The nuclear 18S SSU rRNA gene, and 28S large subunit (LSU) rRNA gene have been used as DNA barcodes and for phylogenetic studies in different eukaryote taxonomic groups. Because of their popularity, the National Center for Biotechnology Information (NCBI) receives a disproportionate number of rRNA sequence submissions and BLAST queries. These sequences vary in quality, length, origin (nuclear, mitochondria, plastid), and organism source and can represent any region of the ribosomal cistron. Results To improve the timely verification of quality, origin and loci boundaries, we developed Ribovore, a software package for sequence analysis of rRNA sequences. The and programs are used to validate incoming sequences of bacterial and archaeal SSU rRNA. The program is used to create high-quality datasets of rRNAs from different taxonomic groups. Key algorithmic steps include comparing candidate sequences against rRNA sequence profile hidden Markov models (HMMs) and covariance models of rRNA sequence and secondary-structure conservation, as well as other tests. Nine freely available rRNA databases created and maintained with Ribovore are used for checking incoming GenBank submissions and used by the browser interface at NCBI. Since 2018, Ribovore has been used to analyze more than 50 million prokaryotic SSU rRNA sequences submitted to GenBank, and to select at least 10,435 fungal rRNA RefSeq records from type material of 8350 taxa. Conclusion Ribovore combines single-sequence and profile-based methods to improve GenBank processing and analysis of rRNA sequences. It is a standalone, portable, and extensible software package for the alignment, classification and validation of rRNA sequences. Researchers planning on submitting SSU rRNA sequences to GenBank are encouraged to download and use Ribovore to analyze their sequences prior to submission to determine which sequences are likely to be automatically accepted into GenBank.

scholarly journals Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation

2021 ◽  
Author(s):  
Alejandro A. Schäffer ◽  
Richard McVeigh ◽  
Barbara Robbertse ◽  
Conrad L. Schoch ◽  
Anjanette Johnston ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Ribosomal Rna ◽  
Dna Sequences ◽  
Software Package ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Rrna Sequence ◽  
Ssu Rrna Gene ◽  
Taxonomic Groups ◽  
Rrna Sequences

AbstractBackgroundThe DNA sequences encoding ribosomal RNA genes (rRNAs) are commonly used as markers to identify species, including in metagenomics samples that may combine many organismal communities. The 16S small subunit ribosomal RNA (SSU rRNA) gene is typically used to identify bacterial and archaeal species. The nuclear 18S SSU rRNA gene, and 28S large subunit (LSU) rRNA gene have been used as DNA barcodes and for phylogenetic studies in different eukaryote taxonomic groups. Because of their popularity, the National Center for Biotechnology Information (NCBI) receives a disproportionate number of rRNA sequence submissions and BLAST queries. These sequences vary in quality, length, origin (nuclear, mitochondria, plastid), and organism source and can represent any region of the ribosomal cistron.ResultsTo improve the timely verification of quality, origin and loci boundaries, we developed Ribovore, a software package for sequence analysis of rRNA sequences. The ribotyper and ribosensor programs are used to validate incoming sequences of bacterial and archaeal SSU rRNA. The ribodbmaker program is used to create high-quality datasets of rRNAs from different taxonomic groups. Key algorithmic steps include comparing candidate sequences against rRNA sequence profile hidden Markov models (HMMs) and covariance models of rRNA sequence and secondary-structure conservation, as well as other tests. At least nine freely available blastn rRNA databases created and maintained with Ribovore are used either for checking incoming GenBank submissions or by the blastn browser interface at NCBI or both. Since 2018, Ribovore has been used to analyze more than 50 million prokaryotic SSU rRNA sequences submitted to GenBank, and to select at least 10,435 fungal rRNA RefSeq records from type material of 8,350 taxa.ConclusionRibovore combines single-sequence and profile-based methods to improve GenBank processing and analysis of rRNA sequences. It is a standalone, portable, and extensible software package for the alignment, classification and validation of rRNA sequences. Researchers planning on submitting SSU rRNA sequences to GenBank are encouraged to download and use Ribovore to analyze their sequences prior to submission to determine which sequences are likely to be automatically accepted into GenBank.

Morphology and phylogeny of a new species, Uroleptus (Caudiholosticha) antarctica n. sp. (Ciliophora, Hypotricha) from Greenwich Island in Antarctica

Zootaxa ◽  
2018 ◽  
Vol 4483 (3) ◽  
pp. 591 ◽  
Author(s):  
KYUNG-MIN PARK ◽  
GI-SIK MIN ◽  
SANGHEE KIM
Keyword(s):  
New Species ◽  
Ribosomal Rna ◽  
Small Subunit ◽  
Phylogenetic Position ◽  
Ssu Rrna ◽  
Cortical Granules ◽  
Standard Methods ◽  
A New Species ◽  
Rrna Sequences

This paper describes the morphological features based on standard methods and estimates their phylogenetic position using small subunit ribosomal RNA (SSU rRNA) sequences of a Uroleptus (Caudiholosticha) antarctica n. sp. population investigated from moss of the Greenwich Island, Antarctica. The morphology of Uroleptus (Caudiholosticha) antarctica n. sp. is characterized as follows: 213.0–238.0×67.5–74.5 μm size in vivo; contractile vacuole located slightly above left of mid-body; cortical granules lacking; three frontal and two frontoterminal cirri; five to six transverse cirri; one pretransverse cirri; one right and one left marginal rows; six to seven dorsal kineties; three caudal cirri. 

scholarly journals Genetic Diversity within Cryptosporidium parvum and Related Cryptosporidium Species

1999 ◽  
Vol 65 (8) ◽  
pp. 3386-3391 ◽  
Author(s):  
Lihua Xiao ◽  
Una M. Morgan ◽  
Josef Limor ◽  
Ananias Escalante ◽  
Michael Arrowood ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cryptosporidium Parvum ◽  
Fragment Length Polymorphism ◽  
Distinct Species ◽  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Specific Host ◽  
Pcr Product ◽  
Rrna Sequences

ABSTRACT To assess the genetic diversity in Cryptosporidium parvum, we have sequenced the small subunit (SSU) rRNA gene of seven Cryptosporidium spp., various isolates of C. parvum from eight hosts, and a Cryptosporidiumisolate from a desert monitor. Phylogenetic analysis of the SSU rRNA sequences confirmed the multispecies nature of the genusCryptosporidium, with at least four distinct species (C. parvum, C. baileyi, C. muris, and C. serpentis). Other species previously defined by biologic characteristics, including C. wrairi, C. meleagridis, and C. felis, and the desert monitor isolate, clustered together or within C. parvum. Extensive genetic diversities were present among C. parvum isolates from humans, calves, pigs, dogs, mice, ferrets, marsupials, and a monkey. In general, specific genotypes were associated with specific host species. A PCR-restriction fragment length polymorphism technique previously developed by us could differentiate mostCryptosporidium spp. and C. parvum genotypes, but sequence analysis of the PCR product was needed to differentiateC. wrairi and C. meleagridis from some of theC. parvum genotypes. These results indicate a need for revision in the taxonomy and assessment of the zoonotic potential of some animal C. parvum isolates.

scholarly journals Detection of Introns in Eukaryotic Small Subunit Ribosomal RNA Gene Sequences

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Dipankar Bachar ◽  
Laure Guillou ◽  
Richard Christen
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Ssu Rrna ◽  
Gene Sequences ◽  
Gene Encoding ◽  
C Program ◽  
Horizontal Transfers ◽  
Sequence Quality ◽  
Rrna Sequences

The gene encoding SSU-rRNA sequences is the tool of choice for phylogenetic analyses and environmental biodiversity analyses of bacteria, Archaea but also unicellular Eukaryota. In Eukaryota, gene sequences may often be interrupted by long or several introns. Searching in GenBank release 188, we found descriptions of 3638 such sequences. Using a database of 180 000 SSU-rRNA sequences well annotated for taxonomy and a C++ program written for that purpose, we computed the presence of 18 691 introns (among which the 3638 described introns). Filtering on length and sequence quality, 3646 sequences were retained. These introns were clustered; clusters were analyzed for the presence of single or multiple clades at various levels of taxonomic depth, allowing future analyses of horizontal transfers. Various analyses of the results are provided as tabulated files as well as FASTA files of described or computed introns. Each sequence is annotated for cellular location (nuclear, chloroplast, and mitochondria), positions at which they were found in the SSU-rRNA sequences and taxonomy as provided by GenBank.

scholarly journals Thousands of primer-free, high-quality, full-length SSU rRNA sequences from all domains of life

2016 ◽  
Author(s):  
Søren M. Karst ◽  
Morten S. Dueholm ◽  
Simon J. McIlroy ◽  
Rasmus H. Kirkegaard ◽  
Per H. Nielsen ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Ribosomal Rna ◽  
Full Length ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Gene Sequences ◽  
Variable Regions ◽  
Domains Of Life ◽  
Rrna Sequences

AbstractRibosomal RNA (rRNA) genes are the consensus marker for determination of microbial diversity on the planet, invaluable in studies of evolution and, for the past decade, high-throughput sequencing of variable regions of ribosomal RNA genes has become the backbone of most microbial ecology studies. However, the underlying reference databases of full-length rRNA gene sequences are underpopulated, ecosystem skewed1, and subject to primer bias2, which hamper our ability to study the true diversity of ecosystems. Here we present an approach that combines reverse transcription of full-length small subunit (SSU) rRNA genes and synthetic long read sequencing by molecular tagging, to generate primer-free, full-length SSU rRNA gene sequences from all domains of life, with a median raw error rate of 0.17%. We generated thousands of full-length SSU rRNA sequences from five well-studied ecosystems (soil, human gut, fresh water, anaerobic digestion, and activated sludge) and obtained sequences covering all domains of life and the majority of all described phyla. Interestingly, 30% of all bacterial operational taxonomic units were novel, compared to the SILVA database (less than 97% similarity). For the Eukaryotes, the novelty was even larger with 63% of all OTUs representing novel taxa. In addition, 15% of the 18S rRNA OTUs were highly novel sequences with less than 80% similarity to the databases. The generation of primer-free full-length SSU rRNA sequences enabled eco-system specific estimation of primer-bias and, especially for eukaryotes, showed a dramatic discrepancy between the in-silico evaluation and primer-free data generated in this study. The large amount of novel sequences obtained here reaffirms that there is still vast, untapped microbial diversity lacking representatives in the SSU rRNA databases and that there might be more than millions after all1, 3. With our new approach, it is possible to readily expand the rRNA databases by orders of magnitude within a short timeframe. This will, for the first time, enable a broad census of the tree of life.

The RhopH complex is transferred to the host cell cytoplasm following red blood cell invasion by Plasmodium falciparum

2008 ◽  
Vol 160 (2) ◽  
pp. 81-89 ◽  
Author(s):  
Laetitia Vincensini ◽  
Gamou Fall ◽  
Laurence Berry ◽  
Thierry Blisnick ◽  
Catherine Braun Breton
Keyword(s):  
Plasmodium Falciparum ◽  
Blood Cell ◽  
Host Cell ◽  
Cell Invasion ◽  
Red Blood Cell ◽  
Cell Cytoplasm ◽  
Host Cell Cytoplasm

scholarly journals Brefeldin A inhibits transport of the glycophorin-binding protein from Plasmodium falciparum into the host erythrocyte

1994 ◽  
Vol 300 (3) ◽  
pp. 821-826 ◽  
Author(s):  
J Benting ◽  
D Mattei ◽  
K Lingelbach
Keyword(s):  
Plasmodium Falciparum ◽  
Golgi Apparatus ◽  
Host Cell ◽  
Protein Secretion ◽  
Secretory Pathway ◽  
Binding Protein ◽  
Brefeldin A ◽  
Cell Cytoplasm ◽  
Parasite Cell ◽  
Host Cell Cytoplasm

Plasmodium falciparum, a protozoan parasite of the human erythrocyte, causes the most severe form of malaria. During its intraerythrocytic development, the parasite synthesizes proteins which are exported into the host cell. The compartments involved in the secretory pathway of P. falciparum are still poorly characterized. A Golgi apparatus has not been identified, owing to the lack of specific protein markers and Golgi-specific post-translational modifications in the parasite. The fungal metabolite brefeldin A (BFA) is known to inhibit protein secretion in higher eukaryotes by disrupting the integrity of the Golgi apparatus. We have used the parasite-encoded glycophorin-binding protein (GBP), a soluble protein found in the host cell cytoplasm, as a marker to investigate the effects of BFA on protein secretion in the intracellular parasite. In the presence of BFA, GBP was not transported into the erythrocyte, but remained inside the parasite cell. The effect caused by BFA was reversible, and the protein could be chased into the host cell cytoplasm within 30 min. Transport of GBP from the BFA-sensitive site into the host cell did not require protein synthesis. Similar observations were made when infected erythrocytes were incubated at 15 degrees C. Incubation at 20 degrees C resulted in a reduction rather than a complete block of protein export. The relevance of our findings to the identification of compartments involved in protein secretion from the parasite cell is discussed.

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