Effect of DNA Methylation on 18S rRNA Gene Sequences during Culture of Taxus chinensis Cells

Cell suspension culture has rapidly become an alternative source of taxol, an anticancer compound. To investigate the role of DNA methylation in the cultural course of Taxus chinensis cells, analyses of 18S rRNA gene sequences of cultured T. chinensis cells and related species were conducted. The phylogenetic analysis of 18S rRNA gene sequences indicated that HG-1 (the cultured T. chinensis cells), like T. mairei (the natural variety of T. chinensis), should be a new variety of T. chinensis, and cell culture can change the 18S rRNA gene sequence at the level of species despite 18S rRNA is the most conserved gene. The analyses of the CpG and TpG+CpA relative abundance and GC content of the 18S rRNA gene sequences made clear that DNA methylation contributed to changes of the 18S rRNA gene sequence of HG-1 at the level of species, which can make HG-1 to become a new variety of T. chinensis.

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Phylogenetic Analysis of Indian Freshwater Pond Mussels Lamellidens corrianus and L. phenchooganjensis (Bivalvia: Unionidae) from the Upper Brahmaputra Basin of Assam, India

Biosciences Biotechnology Research Asia ◽

10.13005/bbra/2907 ◽

2021 ◽

Vol 18 (1) ◽

pp. 197-206

Author(s):

Jyotish Sonowal ◽

Pankaj Chetia ◽

Devid Kardong

Keyword(s):

Phylogenetic Analysis ◽

18S Rrna ◽

Gene Sequence ◽

18S Rrna Gene ◽

Phylogenetic Study ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Gene Sequences ◽

Freshwater Molluscs ◽

First Time

To update the present knowledge of freshwater molluscs, a phylogenetic analysis of two species of Indian pond mussels was carried out using amplified sequence of 18S rRNA gene. From the phylogenetic study of 18S rRNA gene sequencing, it was found that the Lamellidenscorrianus and L. phenchooganjensis are phylogenetically closely related to 18S rRNA gene sequences of other freshwater bivalve mussels belonging to the family Unionidae of order Unionida. Like other members of the Unionidae family, the two Lamellidensspp. showed monophyletic evolutionary lineage and shared a common ancestor. The result obtained from the phylogenetic analysis of Lamellidensspp. was significant as the 18S rRNA gene sequence of L. phenchooganjensis was submitted for the first time in the global nucleotide database (Genbank, NCBI). Similarly, the 18S rRNA gene sequence of L. corrianuswas also submitted to the database for the first time from this region having unique ecological niche. Therefore, the present study on phylogenetic analysis is a contribution to the global database of 18S rRNA gene sequences of freshwater mollusc, particularly from this part of the region.

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18S rRNA Gene Sequence-Structure Phylogeny of the Trypanosomatida (Kinetoplastea, Euglenozoa) with Special Reference on Trypanosoma

European Journal of Protistology ◽

10.1016/j.ejop.2021.125824 ◽

2021 ◽

pp. 125824

Author(s):

Alyssa R. Borges ◽

Markus Engstler ◽

Matthias Wolf

Keyword(s):

Special Reference ◽

18S Rrna ◽

Gene Sequence ◽

18S Rrna Gene ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Sequence Structure

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Correction to: A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms

BMC Microbiology ◽

10.1186/s12866-019-1628-y ◽

2019 ◽

Vol 19 (1) ◽

Author(s):

Stefanos Banos ◽

Guillaume Lentendu ◽

Anna Kopf ◽

Tesfaye Wubet ◽

Frank Oliver Glöckner ◽

...

Keyword(s):

Fungal Community ◽

18S Rrna ◽

Gene Sequence ◽

18S Rrna Gene ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Community Surveys ◽

Research Issues ◽

Nomenclature System ◽

Sequencing Platforms

Following publication of the original article [1], we have been notified that three of the primer names identified as most promising candidates for fungal community surveys were incorrectly renamed following the primer nomenclature system proposed by Gargas & DePriest [2].

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Phylogeny of Intestinal Ciliates, Including Charonina ventriculi, and Comparison of Microscopy and 18S rRNA Gene Pyrosequencing for Rumen Ciliate Community Structure Analysis

Applied and Environmental Microbiology ◽

10.1128/aem.03697-14 ◽

2015 ◽

Vol 81 (7) ◽

pp. 2433-2444 ◽

Cited By ~ 30

Author(s):

Sandra Kittelmann ◽

Savannah R. Devente ◽

Michelle R. Kirk ◽

Henning Seedorf ◽

Burk A. Dehority ◽

...

Keyword(s):

Community Structure ◽

High Throughput ◽

18S Rrna ◽

Gene Sequence ◽

18S Rrna Gene ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Content Type ◽

Advantages And Disadvantages ◽

Ciliate Community

ABSTRACTThe development of high-throughput methods, such as the construction of 18S rRNA gene clone or pyrosequencing libraries, has allowed evaluation of ciliate community composition in hundreds of samples from the rumen and other intestinal habitats. However, several genera of mammalian intestinal ciliates have been described based only on morphological features and, to date, have not been identified using molecular methods. Here, we isolated single cells of one of the smallest but widely distributed intestinal ciliates,Charonina ventriculi, and sequenced its 18S rRNA gene. We verified the sequence in a full-cycle rRNA approach using fluorescencein situhybridization and thereby assigned an 18S rRNA gene sequence to this species previously known only by its morphology. Based on its full-length 18S rRNA gene sequence,Charonina ventriculiwas positioned within the phylogeny of intestinal ciliates in the subclass Trichostomatia. The taxonomic framework derived from this phylogeny was used for taxonomic assignment of trichostome ciliate 18S rRNA gene sequence data stemming from high-throughput amplicon pyrosequencing of rumen-derived DNA samples. The 18S rRNA gene-based ciliate community structure was compared to that obtained from microscopic counts using the same samples. Both methods allowed identification of dominant members of the ciliate communities and classification of the rumen ciliate community into one of the types first described by Eadie in 1962. Notably, each method is associated with advantages and disadvantages. Microscopy is a highly accurate method for evaluation of total numbers or relative abundances of different ciliate genera in a sample, while 18S rRNA gene pyrosequencing represents a valuable alternative for comparison of ciliate community structure in a large number of samples from different animals or treatment groups.

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Reassessment of the classification of the Order Haplosclerida (Class Demospongiae, Phylum Porifera) using 18S rRNA gene sequence data

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2006.10.021 ◽

2007 ◽

Vol 43 (1) ◽

pp. 344-352 ◽

Cited By ~ 45

Author(s):

N.E. Redmond ◽

R.W.M. van Soest ◽

M. Kelly ◽

J. Raleigh ◽

S.A.A. Travers ◽

...

Keyword(s):

18S Rrna ◽

Gene Sequence ◽

Sequence Data ◽

18S Rrna Gene ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Gene Sequence Data

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Identification of Theileria parva and Theileria sp. (buffalo) 18S rRNA gene sequence variants in the African Buffalo (Syncerus caffer) in southern Africa

Veterinary Parasitology ◽

10.1016/j.vetpar.2011.05.041 ◽

2011 ◽

Vol 182 (2-4) ◽

pp. 150-162 ◽

Cited By ~ 27

Author(s):

Mamohale E. Chaisi ◽

Kgomotso P. Sibeko ◽

Nicola E. Collins ◽

Fred T. Potgieter ◽

Marinda C. Oosthuizen

Keyword(s):

Southern Africa ◽

18S Rrna ◽

Gene Sequence ◽

18S Rrna Gene ◽

Rrna Gene ◽

Sequence Variants ◽

Theileria Parva ◽

African Buffalo ◽

Syncerus Caffer ◽

Rrna Gene Sequence

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Characterization of two novel yeast strains used in mediated biosensors for wastewater

Canadian Journal of Microbiology ◽

10.1139/w02-035 ◽

2002 ◽

Vol 48 (5) ◽

pp. 418-426 ◽

Cited By ~ 3

Author(s):

Steve P Trosok ◽

John H.T Luong ◽

David F Juck ◽

Brian T Driscoll

Keyword(s):

18S Rrna ◽

Gene Sequence ◽

Phylogenetic Analyses ◽

Pulp Mill ◽

18S Rrna Gene ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Candida Spp ◽

Yeast Strains ◽

Physiological Tests

After isolation from a pulp mill wastewater treatment facility, two yeast strains, designated SPT1 and SPT2, were characterized and used in the development of mediated biochemical oxygen demand (BOD) biosensors for wastewater. 18S rRNA gene sequence analysis revealed a one nucleotide difference between the sequence of SPT1 and those of Candida sojae and Candida viswanthii. While SPT2 had the highest overall homology to Pichia norvegensis, at only 73.5%, it is clearly an ascomycete, based on BLAST comparisons and phylogenetic analyses. Neighbor-joining dendrograms indicated that SPT1 clustered with several Candida spp., and that SPT2 clustered with Starmera spp., albeit as a very deep branch. Physiological tests, microscopic observations, and fatty acid analysis confirmed that SPT1 and SPT2 are novel yeast strains. Physiological tests also indicated that both strains had potential for use in mediated biosensors for estimation of BOD in wastewater. The lower detection limits of SPT1- and SPT2-based K3Fe(CN)6-mediated biosensors for a pulp-mill effluent were 2 and 1 mg BOD/L, respectively. Biosensor-response times for effluents from eight different pulp mills were in the range of 5 min. Reliability and sensitivity of the SPT1- and SPT2-based biosensors were good, but varied with the wastewater.Key words: yeast characterization, 18S rRNA gene sequence, pulp-mill wastewater, BOD5, mediated BOD biosensor.

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