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.

Phylogenic analysis of Chinese Leishmania isolates based on small subunit ribosomal RNA (SSU rRNA) and 7 spliced leader RNA (7SL RNA)

2012 ◽  
Vol 57 (2) ◽  
Author(s):  
Wang Guan ◽  
De-Ping Cao ◽  
Ke sun ◽  
Jia-nan Xu ◽  
Jun-rong Zhang ◽  
...  
Keyword(s):  
Bayesian Analysis ◽  
Ribosomal Rna ◽  
Small Subunit ◽  
Ssu Rrna ◽  
Gene Sequences ◽  
Rna Sequences ◽  
Spliced Leader ◽  
Small Subunit Ribosomal Rna ◽  
7Sl Rna ◽  
Spliced Leader Rna

AbstractThe leishmaniases are zoonotic diseases caused by protozoan parasites of the genus Leishmania. Leishmaniases are still endemic in China, especially in the west and northwest froniter regions. To revalue the preliminary phylogenetic results of Chinese Leishmania isolates, we amplified partial fragment of small subunit ribosomal RNA (SSU rRNA) and 7 spliced leader RNA (7SL RNA), then tested the phylogenetic relationships among Chinese Leishmania isolates and their relatives by analyzing SSU rRNA gene sequences and 7SL RNA gene sequences. 19 SSU RNA sequences and 9 7SL RNA sequences were obtained in our study, then analyzed with 42 SSU RNA sequences and 32 7SL RNA sequences retrieved from Genbank, respectively. In the Bayesian analysis of the SSU RNA gene, the isolate MHOM/CN/93/GS7 and the isolate IPHL/CN/77/XJ771 are members of Leishmania donovani complex, while the isolate MHOM/CN/84/JS1 clustered with Leishmania tropica. The other 11 Chinese Leishmania isolates (MHOM/CN/90/WC, MCAN/CN/90/SC11, MHOM/CN/80/XJ801, MHOM/CN/85/GS4, MHOM/CN/84/SD1, MCAN/CN/86/SC7, MHOM/CN/54/#3, MHOM/CN/83/GS2, MHOM/CN/90/SC10H2, MHOM/CN/89/GS6 and MHOM/CN/ 89/GS5) form an unclassified group, defined as Leishmania sp., and the most relative species to this group is L. tarentolae. In the Bayesian analysis of the 7SL RNA gene, 9 Chinese Leishmania isolates also formed an unclassified group with L. tarentolae, including canine isolate 10, MHOM/CN/85/GS4, MHOM/CN/84/SD1, MCAN/CN/86/SC7, MHOM/CN/54/#3, MHOM/ CN/83/GS2, MHOM/CN/90/SC10H2, MHOM/CN/89/GS6 and MHOM/CN/89/GS5. We concluded that: (1) Chinese Leishmania isolates are non-monophyly group; (2) an unclassified group may exist in China, and the most relative species to this group is L. tarentolae; (3) MHOM/CN/84/JS1, which was previously assigned as L. donovani, was most genetically related to L. tropica strain MHOM/SU/74/K27.

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 Morphology and phylogeny of three karyorelictean ciliates (Protista, Ciliophora), including two novel species, Trachelocerca chinensis sp. n. and Tracheloraphis dragescoi sp. n.

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4084-4097 ◽  
Author(s):  
Yuan Xu ◽  
Ying Yan ◽  
Lifang Li ◽  
Khaled A. S. Al-Rasheid ◽  
Saleh A. Al-Farraj ◽  
...  
Keyword(s):  
Intertidal Zone ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Sandy Beaches ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Gene Sequences ◽  
Approximately Unbiased ◽  
Nuclear Group

This paper investigates the morphology and infraciliature of three karyorelictean ciliates, Trachelocerca chinensis sp. n., Tracheloraphis dragescoi sp. n. and a rarely known form, Geleia acuta (Dragesco, 1960) Foissner, 1998, which were isolated from the intertidal zone of sandy beaches at Zhanjiang and Qingdao, China. Trachelocerca chinensis sp. n. is distinguished from related forms by having 26–30 somatic kineties, a narrow glabrous stripe and a single nuclear group composed of approximately four to six macronuclei and two micronuclei. Tracheloraphis dragescoi sp. n. can be recognized through its 14–22 somatic kineties, wide glabrous stripe and a single nuclear group composed of about four macronuclei. Phylogenetic analyses based on small-subunit (SSU) rRNA gene sequences indicated that the genera Trachelocerca and Tracheloraphis are closely related but that neither of them appears to be a clearly monophyletic group. Nonetheless, the monophyly of Trachelocerca is not rejected by the approximately unbiased (AU) test (P = 0.143, >0.05), although that of Tracheloraphis is rejected (P = 0.011, <0.05). Geleia acuta, meanwhile, branched with Geleia fossata and falls in the Geleia clade.

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 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.

scholarly journals Nuclear small-subunit ribosomal RNA gene sequences from representative Ceramiaceae (Ceramiales, Rhodophyta)

1996 ◽  
Vol 31 (1) ◽  
pp. 23-29 ◽  
Author(s):  
Gary W. Saunders ◽  
Isabelle M. Strachan ◽  
John A. West ◽  
Gerald T. Kraft
Keyword(s):  
Ribosomal Rna ◽  
Small Subunit ◽  
Gene Sequences ◽  
Ribosomal Rna Gene ◽  
Small Subunit Ribosomal Rna

Redescription and SSU rRNA gene-based phylogeny of an anaerobic ciliate, Plagiopyla ovata Kahl, 1931 (Ciliophora, Plagiopylea)

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Ran Li ◽  
Wenbao Zhuang ◽  
Congcong Wang ◽  
Hamed El-Serehy ◽  
Saleh A. Al-Farraj ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Gene Trees ◽  
Ssu Rrna Gene ◽  
Anaerobic Ciliate ◽  
Pr China

The morphology and molecular phylogeny of Plagiopyla ovata Kahl, 1931, a poorly known anaerobic ciliate, were investigated based on a population isolated from sand samples collected from the Yellow Sea coast at Qingdao, PR China. Details of the oral ciliature are documented for the first time to our knowledge and an improved species diagnosis is given. The small subunit ribosomal RNA (SSU rRNA) gene was newly sequenced and phylogenetic analyses revealed that P. ovata clusters within the monophyletic family Plagiopylidae. However, evolutionary relationships within both the family Plagiopylidae and the genus Plagiopyla remain obscure owing to undersampling, the lack of sequence data from known species and low nodal support or unstable topologies in gene trees. A key to the identification of the species of the genus Plagiopyla with validly published names is also supplied.

scholarly journals Three redescriptions in Tintinnopsis (Protista: Ciliophora: Tintinnina) from coastal waters of China, with cytology and phylogenetic analyses based on ribosomal RNA genes

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Yang Bai ◽  
Rui Wang ◽  
Wen Song ◽  
Lifang Li ◽  
Luciana F. Santoferrara ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Coastal Waters ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Middle Portion ◽  
Closely Related Species ◽  
Molecular Information ◽  
Ciliary Tuft ◽  
Rna Genes ◽  
Rrna Sequences

Abstract Background The taxonomy of tintinnine ciliates is vastly unresolved because it has traditionally been based on the lorica (a secreted shell) and it has only recently incorporated cytological and molecular information. Tintinnopsis, the most speciose tintinnine genus, is also the most problematic: it is known to be non-monophyletic, but it cannot be revised until more of its species are studied with modern methods. Results Here, T. hemispiralis Yin, 1956, T. kiaochowensis Yin, 1956, and T. uruguayensis Balech, 1948, from coastal waters of China, were studied. Lorica and cell features were morphometrically investigated in living and protargol-stained specimens, and sequences of three ribosomal RNA (rRNA) loci were phylogenetically analyzed. The three species show a complex ciliary pattern (with ventral, dorsal, and posterior kineties and right, left, and lateral ciliary fields), but differ in lorica morphology, details of the somatic ciliature and rRNA gene sequences. Tintinnopsis hemispiralis is further distinguished by a ciliary tuft (a ribbon of very long cilia originated from the middle portion of the ventral kinety and extending out of the lorica) and multiple macronuclear nodules. Both T. kiaochowensis and T. uruguayensis have two macronuclear nodules, but differ in the number of somatic kineties and the position of the posterior kinety. Two neotypes are fixed for T. hemispiralis and T. kiaochowensis to stabilize the species names objectively, mainly because of the previous unavailability of type materials. By phylogenetic analysis and comparison with closely-related species, we infer that the ciliary tuft and details such as the commencement of the rightmost kinety in the lateral ciliary field are synapomorphies that may help clarify the systematics of Tintinnopsis-like taxa. Conclusion The redescriptions of three poorly known Tintinnopsis species, namely T. hemispiralis, T. kiaochowensis, and T. uruguayensis firstly revealed their ciliary patterns and rRNA sequences. This study expands knowledge and database of tintinnines and helps in identifying potential synapomorphies for future taxonomic rearrangements.

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