Caecilian Phylogeny and Biogeography Inferred from Mitochondrial DNA Sequences of the 12S rRNA and 16S rRNA Genes (Amphibia: Gymnophiona)

1993 ◽  
Vol 7 ◽  
pp. 64 ◽  
Author(s):  
S. Blair Hedges ◽  
Ronald A. Nussbaum ◽  
Linda R. Maxson
Keyword(s):  
Mitochondrial Dna ◽  
16S Rrna ◽  
Dna Sequences ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
12S Rrna

Copro-PCR based detection of bovine schistosome infection in India

2015 ◽  
Vol 90 (1) ◽  
pp. 102-107 ◽  
Author(s):  
B. Lakshmanan ◽  
K. Devada ◽  
S. Joseph ◽  
T.V. Aravindakshan ◽  
L. Sabu
Keyword(s):  
Mitochondrial Dna ◽  
Ribosomal Rna ◽  
Dna Sequences ◽  
Rrna Genes ◽  
12S Rrna ◽  
Gene Sequences ◽  
Schistosome Infection ◽  
Faecal Samples ◽  
Polymerase Chain ◽  
Trematode Infections

AbstractSchistosomosis and amphistomosis are the two economically important and widely prevalent snail-borne trematode infections in grazing cattle of southern India. Acute infections are symptomatically similar and difficult to detect by routine microscopy for eggs. The present study was directed towards the development of a copro-polymerase chain reaction (copro-PCR) for detection of bovine schistosome species, using custom-designed primers targeting 18S and 28S ribosomal RNA as well as mitochondrial DNA. The study demonstrated the enhanced diagnostic specificity of mitochondrial DNA markers over ribosomal RNA genes as genus-specific probes to detect schistosomes. We developed a sensitive PCR assay using primers designed from mitochondrial DNA sequences targeting the partialrrnl(16S rRNA), tCys (transfer RNA for cysteine) and partialrrnS(12S rRNA) genes ofSchistosoma spindaleto specifically detect schistosome infection from faecal samples of naturally infected bovines. The salient findings of the work also throw light on to the high similarity of the ribosomal RNA gene sequences of schistosomes with those ofGastrothylax crumeniferandFischoederius elongatus,the most prevalent pouched amphistomes of the region. Further investigation has to be directed towards unravelling the complete gene sequences of 18S and 28S ribosomal RNA as well as mitochondrial DNA sequences of amphistome isolates from India.

scholarly journals The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR

2023 ◽  
Vol 83 ◽  
Author(s):  
A. Belmok ◽  
T. Rodrigues-Oliveira ◽  
F.A.C. Lopes ◽  
R.H. Krüger ◽  
C.M. Kyaw
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Sequences ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Universal Primers ◽  
Rrna Gene ◽  
Natural Habitats ◽  
16S Rdna Pcr ◽  
Archaeal Communities

Abstract Polymerase chain reaction (PCR) assays targeting 16S rRNA genes followed by DNA sequencing are still important tools to characterize microbial communities present in environmental samples. However, despite the crescent number of deposited archaeal DNA sequences in databases, until now we do not have a clear picture of the effectiveness and specificity of the universal primers widely used to describe archaeal communities from different natural habitats. Therefore, in this study, we compared the phylogenetic profile obtained when Cerrado lake sediment DNA samples were submitted to 16S rDNA PCR employing three Archaea-specific primer sets commonly used. Our findings reveal that specificity of primers differed depending on the source of the analyzed DNA. Furthermore, archaeal communities revealed by each primer pair varied greatly, indicating that 16S rRNA gene primer choice affects the community profile obtained, with differences in both taxon detection and operational taxonomic unit (OTU) estimates.

scholarly journals Target enrichment from a DNA mixture by oligoribonucleotide interference-PCR (ORNi-PCR)

2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Toshitsugu Fujita ◽  
Daisuke Motooka ◽  
Hodaka Fujii
Keyword(s):  
16S Rrna ◽  
Genome Editing ◽  
Dna Sequences ◽  
Pcr Amplification ◽  
Dna Amplification ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Detailed Assessment ◽  
Dna Mixture

Abstract Oligoribonucleotide (ORN) interference-PCR (ORNi-PCR) is a method that suppresses PCR amplification of target DNA in an ORN-specific manner. In this study, we examined whether ORNi-PCR can be used to enrich desirable DNA sequences from a DNA mixture by suppressing undesirable DNA amplification. ORNi-PCR enriched edited DNA sequences from a mixture of genomic DNA subjected to genome editing. ORNi-PCR enabled more efficient analysis of the types of insertion/deletion mutations introduced by genome editing. In addition, ORNi-PCR reduced the detection of 16S ribosomal RNA (16S rRNA) genes in 16S rRNA gene-based microbiome profiling, which might permit a more detailed assessment of populations of other 16S rRNA genes. Enrichment of desirable DNA sequences by ORNi-PCR may be useful in molecular biology, medical diagnosis, and other fields.

scholarly journals Characterization of Burkholderia pseudomallei and Burkholderia pseudomallei-like strains

1997 ◽  
Vol 118 (2) ◽  
pp. 137-148 ◽  
Author(s):  
P. J. BRETT ◽  
D. DESHAZER ◽  
D. E. WOODS
Keyword(s):  
16S Rrna ◽  
Dna Sequences ◽  
Burkholderia Pseudomallei ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Virulent Strains ◽  
Syrian Golden Hamsters ◽  
Highly Virulent

Previous reports in the literature suggest that Burkholderia pseudomallei strains can be differentiated on the basis of animal virulence. Twenty environmentally and clinically derived isolates of Burkholderia pseudomallei were examined for the production of exoenzymes, morphological and biochemical phenotypes and virulence for Syrian golden hamsters. The partial sequence of the 16S ribosomal RNA [rRNA] genes from a number of these strains was also determined. Based upon these observations, it is suggested that highly virulent Burkholderia pseudomallei strains are true Burkholderia pseudomallei strains. The DNA sequences of the 16S rRNA genes of the true Burkholderia pseudomallei strains were identical to the published sequences for Burkholderia pseudomallei while differences were revealed between the published sequences and those of the lowly virulent strains. Thus, these latter strains have been designated as Burkholderia pseudomallei-like organisms since they demonstrate significant differences in exoenzyme production, hamster virulence and 16S rRNA gene sequences.

The systematics of freshwater crayfish of the genus Cherax Erichson (Decapoda : Parastacidae) in eastern Australia re-examined using nucleotide sequences from 12S rRNA and 16S rRNA genes

2004 ◽  
Vol 18 (2) ◽  
pp. 215 ◽  
Author(s):  
D. H. N. Munasinghe ◽  
C. P. Burridge ◽  
C. M. Austin
Keyword(s):  
16S Rrna ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
12S Rrna ◽  
Freshwater Crayfish ◽  
Separate Species ◽  
Nucleotide Sequence Data ◽  
Eastern Australia

Nucleotide sequence data were used to re-examine systematic relationships and species boundaries within the genus Cherax from eastern Australia. Partial sequences were amplified from the 12S (~365 bp) and 16S (~545 bp) rRNA mitochondrial gene regions. Levels of intra- and inter-specific divergence for Cherax species were very similar between the two gene regions and similar to that reported for other freshwater crayfish for 16S rRNA. Phylogenetic analyses using the combined data provided strong support for a monophyletic group containing 11�eastern Australian species and comprising three well-defined species-groups: the 'C. destructor' group containing three species, the 'C. cairnsensis' group containing four species and the 'C. cuspidatus' group containing two species. Cherax dispar and C. robustus are distinct from all other species and each other. In addition, two northern Australian and a New Guinean species were placed in the 'Astaconephrops' group, which is the sister-group to the eastern Australian Cherax lineage. Several relationships were clarified, including: the status of northern and southern C. cuspidatus as separate species; a close relationship between C. cairnsensis and C. depressus; the validity of C. rotundus and C. setosus as separate species and their close affinities with C. destructor; and the distinctiveness of the northern forms of Cherax. The analysis of the 12S rRNA and 16S rRNA data is highly concordant with the results of previous allozyme studies.

The genus Neoromicia (Family Vespertilionidae) in Madagascar, with the description of a new species

Zootaxa ◽  
2012 ◽  
Vol 3250 (1) ◽  
pp. 1 ◽  
Author(s):  
STEVEN M. GOODMAN ◽  
PETER J. TAYLOR ◽  
FANJA RATRIMOMANARIVO ◽  
STEVEN R. HOOFER
Keyword(s):  
New Species ◽  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
12S Rrna ◽  
Sexual Organ ◽  
Unknown Species ◽  
Dental Measurements ◽  
Conservation Concern ◽  
A New Species

Using molecular genetics, male sexual organ morphology (baculum), and cranio-dental characters, we describe a new spe-cies of the genus Neoromicia from Madagascar, N. robertsi sp. nov. It is presumed to be endemic to the island and isknown from three specimens taken in montane areas of the eastern central region. The new species shows 1.0 % and 2.8%divergence in the 12S rRNA and 16S rRNA genes, respectively, from its nearest congener and is notably larger in cranio-dental measurements than other members of the genus occurring on Madagascar. This new species was previously iden-tified as N. melckorum, which is considered a junior synonym of southern African N. capensis. Neoromicia malagasyen-sis, an endemic to central western Madagascar, is the sister species to N. robertsi and the two are best considered vicariantspecies. Specimens provisionally assigned to N. malagasyensis, but notably smaller in baculum and skull size, and withdifferent baculum morphology, probably represent another unknown species from the island. Given the apparent rarity ofN. robertsi compared with other Malagasy members of this genus living in the eastern portion of Madagascar, it is considered a taxon of conservation concern.

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