Monophyly of the order Rodentia inferred from mitochondrial DNA sequences of the genes for 12S rRNA, 16S rRNA, and tRNA-valine.

The slow loris (Nycticebus) is a prosimian that is popular among exotic pet lovers. In Japan, many slow lorises have been imported illegally. Prosimians that have been confiscated in raids are protected in Japanese zoos, and the number of such animals has increased. In most cases, the country of origin remains unknown and even the species can be difficult to identify from the animal’s physical appearance alone. We have attempted to resolve this problem by using DNA analysis. DNA samples of five species, consisting of the Pygmy slow loris (Nycticebus pygmaeus), Bengal slow loris (Nycticebus bengalensis), Sunda slow loris (Nycticebus coucang), Javan slow loris (Nycticebus javanicus), and Bornean slow loris (Nycticebus menagensis), were extracted, amplified, and the nucleotide sequences of mitochondrial 12S rRNA, 16S rRNA, and the cytochrome oxidase subunit 1(COI) regions were compared. Differences of nucleic acid sequences of representative individuals were demonstrated.

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Molecular phylogeny of the nasuta subgroup of Drosophila based on 12S rRNA, 16S rRNA and CoI mitochondrial genes, RAPD and ISSR polymorphisms

Genes & Genetic Systems ◽

10.1266/ggs.79.293 ◽

2004 ◽

Vol 79 (5) ◽

pp. 293-299 ◽

Cited By ~ 14

Author(s):

Nagaraja ◽

J. Nagaraju ◽

H. A. Ranganath

Keyword(s):

16S Rrna ◽

Molecular Phylogeny ◽

Mitochondrial Genes ◽

12S Rrna ◽

Rapd And Issr ◽

Rrna 16S

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The mitochondrial DNA haplotypes of snails of the estuarine hydrobiid genus Tatea cross species and biogeographic boundaries

Marine and Freshwater Research ◽

10.1071/mf08200 ◽

2009 ◽

Vol 60 (8) ◽

pp. 861 ◽

Cited By ~ 12

Author(s):

D. J. Colgan ◽

P. da Costa

Keyword(s):

Mitochondrial Dna ◽

Dna Sequences ◽

Marine Species ◽

Habitat Diversity ◽

12S Rrna ◽

Genetic Structuring ◽

Dna Variation ◽

Eastern Australia ◽

Mitochondrial 12S Rrna ◽

Marine Littoral

Investigations of estuarine taxa can provide a perspective on phylogeography that complements studies of marine littoral organisms. For example, reductions in gene flow between populations and increased genetic structuring would be expected in estuarine species. The substantial amount of information about marine species and the habitat diversity along long latitudinal spans makes south-eastern Australia an excellent potential location for comparing marine and estuarine taxa. To investigate this potential, we studied the phylogeography of the two species in the estuarine gastropod genus Tatea. These have extensive and broadly overlapping distributions that encompass known marine phylogeographic boundaries. Against expectation, both Tatea species showed a remarkable lack of geographic and inter-specific variability in mitochondrial 12S rRNA (107 specimens) and cytochrome c oxidase subunit I (39) DNA sequences. No major phylogeographic discontinuities were revealed in either species and there was minimal haplotype divergence between them for either 12S rRNA or COI. The patterns of mitochondrial DNA variation discovered in Tatea may be due to a recent selective sweep or range expansion from a population in which there was little variability. Both possibilities are complicated by having to explain the similarity of the patterns in the two species.

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Copro-PCR based detection of bovine schistosome infection in India

Journal of Helminthology ◽

10.1017/s0022149x1400090x ◽

2015 ◽

Vol 90 (1) ◽

pp. 102-107 ◽

Cited By ~ 1

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.

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Phylogeny of Meloidogyne spp. based on 18S rDNA and the intergenic region of mitochondrial DNA sequences

Nematology ◽

10.1163/156854105776186325 ◽

2005 ◽

Vol 7 (6) ◽

pp. 851-862 ◽

Cited By ~ 58

Author(s):

Regina Carneiro ◽

Don Dickson ◽

Ayyamperumal Jeyaprakash ◽

Byron Adams ◽

Myrian Tigano

Keyword(s):

Mitochondrial Dna ◽

16S Rrna ◽

Dna Sequences ◽

18S Rdna ◽

Phylogenetic Trees ◽

Optimality Criteria ◽

Cytochrome Oxidase Subunit ◽

Meloidogyne Spp ◽

Rdna Analysis ◽

Cytochrome Oxidase Subunit Ii

AbstractThe 18S rDNA of 19 populations of Meloidogyne spp. was amplified and directly sequenced. The region of mitochondrial DNA, located in the 3′ portion of the gene that codes for cytochrome oxidase subunit II (COII) through a portion of the 16S rRNA (lRNA) gene, from 16 of these populations was cloned and sequenced. Heteroplasmic sequences were identified from both rDNA and mtDNA regions for several taxa. Several sequences sampled from nominal taxa differed from previously published accounts. Phylogenetic trees based on alignments of these sequences were constructed using distance, parsimony and likelihood optimality criteria. For 18S rDNA data, three main clades were identified. One well supported clade (86–91% bootstrap) included the most common and widely disseminated species, e.g.,M. arenaria, M. javanica and M. incognita, some recently described or redescribed species (M. floridensis, M. paranaensis, and M. ethiopica) plus numerous unidentified isolates. All mitotic parthenogenetic species, except for M. oryzae, were included in this clade. Other, less well supported clades included the amphimictic and facultative meiotic species M. hapla, M. microtyla, M. maritima and M. duytsi. One such clade comprised three meiotic parthenogens (M. exigua, M. graminicola and M. chitwoodi) and M. oryzae. This clade was moderately supported (77% bootstrap) but the relationships within this clade were poor. For mitochondrial DNA data, only the species in clade I from rDNA analysis, and M. hapla were analysed. These species formed a well supported clade (100% bootstrap) to the exclusion of M. mayaguensis and M. hapla. The addition of taxa and mtDNA data to publicly available records improved the discrimination sensitivity of species and atypical, non-identified, isolates.

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Phylogeny of the Genera Anastrepha and Toxotrypana (Trypetinae: Toxotrypanini) Based upon 16S rRNA Mitochondrial DNA Sequences

Fruit Flies (Tephritidae) ◽

10.1201/9781420074468-21 ◽

1999 ◽

pp. 361-380

Keyword(s):

Mitochondrial Dna ◽

16S Rrna ◽

Dna Sequences

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A novel PCR-clamping assay reducing plant host DNA amplification significantly improves prokaryotic endo-microbiome community characterization

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa110 ◽

2020 ◽

Vol 96 (7) ◽

Cited By ~ 2

Author(s):

Emilie Lefèvre ◽

Courtney M Gardner ◽

Claudia K Gunsch

Keyword(s):

Mitochondrial Dna ◽

16S Rrna ◽

16S Rrna Gene ◽

Dna Sequences ◽

High Throughput Sequencing ◽

Dna Amplification ◽

Rrna Gene ◽

Plant Host ◽

Plant Chloroplast

ABSTRACT Due to the sequence homology between the bacterial 16S rRNA gene and plant chloroplast and mitochondrial DNA, the taxonomic characterization of plant microbiome using amplicon-based high throughput sequencing often results in the overwhelming presence of plant-affiliated reads, preventing the thorough description of plant-associated microbial communities. In this work we developed a PCR blocking primer assay targeting the taxonomically informative V5-V6 region of the 16S rRNA gene in order to reduce plant DNA co-amplification, and increase diversity coverage of associated prokaryotic communities. Evaluation of our assay on the characterization of the prokaryotic endophytic communities of Zea mays, Pinus taeda and Spartina alternifora leaves led to significantly reducing the proportion of plant reads, yielded 20 times more prokaryotic reads and tripled the number of detected OTUs compared to a commonly used V5-V6 PCR protocol. To expand the application of our PCR-clamping assay across a wider taxonomic spectrum of plant hosts, we additionally provide an alignment of chloroplast and mitochondrial DNA sequences encompassing more than 200 terrestrial plant families as a supporting tool for customizing our blocking primers.

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