The Phylogeny of Rosoideae (Rosaceae) Based on Sequences of the Internal Transcribed Spacers (ITS) of Nuclear Ribosomal DNA and the trnL/F Region of Chloroplast DNA

2003 ◽  
Vol 164 (2) ◽  
pp. 197-211 ◽  
Author(s):  
Torsten Eriksson ◽  
Malin S. Hibbs ◽  
Anne D. Yoder ◽  
Charles F. Delwiche ◽  
Michael J. Donoghue
Keyword(s):  
Chloroplast Dna ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
F Region

Characterization of Trichuris trichiura from humans and T. suis from pigs in China using internal transcribed spacers of nuclear ribosomal DNA

2012 ◽  
Vol 88 (1) ◽  
pp. 64-68 ◽  
Author(s):  
G.H. Liu ◽  
W. Zhou ◽  
A.J. Nisbet ◽  
M.J. Xu ◽  
D.H. Zhou ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Sequence Variation ◽  
Animal Health ◽  
Trichuris Trichiura ◽  
Its Rdna ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Economic Losses ◽  
Molecular Characteristics ◽  
Rdna Sequences

AbstractTrichuris trichiura and Trichuris suis parasitize (at the adult stage) the caeca of humans and pigs, respectively, causing trichuriasis. Despite these parasites being of human and animal health significance, causing considerable socio-economic losses globally, little is known of the molecular characteristics of T. trichiura and T. suis from China. In the present study, the entire first and second internal transcribed spacer (ITS-1 and ITS-2) regions of nuclear ribosomal DNA (rDNA) of T. trichiura and T. suis from China were amplified by polymerase chain reaction (PCR), the representative amplicons were cloned and sequenced, and sequence variation in the ITS rDNA was examined. The ITS rDNA sequences for the T. trichiura and T. suis samples were 1222–1267 bp and 1339–1353 bp in length, respectively. Sequence analysis revealed that the ITS-1, 5.8S and ITS-2 rDNAs of both whipworms were 600–627 bp and 655–661 bp, 154 bp, and 468–486 bp and 530–538 bp in size, respectively. Sequence variation in ITS rDNA within and among T. trichiura and T. suis was examined. Excluding nucleotide variations in the simple sequence repeats, the intra-species sequence variation in the ITS-1 was 0.2–1.7% within T. trichiura, and 0–1.5% within T. suis. For ITS-2 rDNA, the intra-species sequence variation was 0–1.3% within T. trichiura and 0.2–1.7% within T. suis. The inter-species sequence differences between the two whipworms were 60.7–65.3% for ITS-1 and 59.3–61.5% for ITS-2. These results demonstrated that the ITS rDNA sequences provide additional genetic markers for the characterization and differentiation of the two whipworms. These data should be useful for studying the epidemiology and population genetics of T. trichiura and T. suis, as well as for the diagnosis of trichuriasis in humans and pigs.

Molecular Systematics of the Asteriscus Alliance (Asteraceae: Inuleae) I: Evidence from the Internal Transcribed Spacers of Nuclear Ribosomal DNA

1999 ◽  
Vol 24 (2) ◽  
pp. 249 ◽  
Author(s):  
Javier Francisco-Ortega ◽  
Leslie R. Goertzen ◽  
Arnoldo Santos-Guerra ◽  
Abdelmalek Benabid ◽  
Robert K. Jansen
Keyword(s):  
Molecular Systematics ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna

scholarly journals Phylogenetic analysis of the genus Conringia Heist. Ex Fabr. (Brassicaceae) in Turkey based on nuclear (nrITS) and chloroplast (trnL-F) DNA sequences

2021 ◽  
Vol 13 (3) ◽  
pp. 11034
Author(s):  
Emre SEVINDIK ◽  
Melike AYDOGAN ◽  
Mehmet Y. PAKSOY
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Nuclear Ribosomal Dna ◽  
Neighbor Joining ◽  
F Region ◽  
Brassicaceae Species ◽  
Nj Tree ◽  
Brassicaceae Family

In this study, phylogenetic analysis of Turkish Conringia (Brassicaceae) species was conducted based on nuclear ribosomal DNA (nrITS) and chloroplast DNA (trnL-F) sequences. In addition, the relationships between the sequences of some Brassicaceae family species retrieved from NCBI, and Conringia species were documented. All of the plant specimens were collected at their flowering and vegetation periods from different regions of Turkey, and brought to the laboratory. Total genomic DNA was extracted using the GeneMark kit. In PCR analyses, ITS4 and ITS5A primers were used for the amplification of the nrITS region, while the trnLe and trnLf primers were used for the cpDNA trnL-F region. The DNA sequences obtained were then edited using BioEdit and FinchTV, and analyzed using MEGA 6.0 software. Neighbor joining (NJ) and bootstrap trees were constructed in order to identify the relationships among Conringia taxa. The nrITS sequences ranged between 573 and 672 nucleotides, while the trnL-F sequences ranged between 346 and 764 nucleotides. The divergence values of nrITS sequences differed between 0.177 and 0.00 and divergence values of trnL-F sequences differed between 0.902 and 0.00. NJ tree generated using nrITS and trnL-F sequences consisted of two clades. In trees generated with both the nrITS and trnL-F sequences, C. orientalis, C. grandiflora and C. austriaca appeared within the same group. In addition, according to the phylogenetic analysis results obtained with other Brassicaceae species, it is revealed that the Conringia genus is polyphyletic.

scholarly journals The comparison between nuclear ribosomal DNA and chloroplast DNA in molecular systematic study of four sections of genus Dendrobium sw. (orchidaceae)

2016 ◽  
Vol 5 (03) ◽  
pp. 4944 ◽  
Author(s):  
Maryam Moudi* ◽  
Rusea Go
Keyword(s):  
Chloroplast Dna ◽  
Ribosomal Dna ◽  
Morphological Characters ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Study ◽  
Data Sets ◽  
Molecular Systematic ◽  
Resolution Level ◽  
Reliable Marker

Phylogenetic study of the four sections (Aporum, Crumenata, Strongyle, and Bolbidium) of genus Dendrobium (family Orchidaceae) was conducted using molecular data. Classifications based on morphological characters have not being able to clearly divide these four sections neither do they supported their monophyly origin. Therefore, deeper and detailed analysis especially using molecular data is required to ascertain their status. Molecular evidences were used to clarify their relations either to lump them into one section or reduce them into two. The study has been carried out for the 34 species of Dendrobium using Maximum Parsimony (MP). Three nucleotide sequences data sets from two distinct genomes chloroplast DNA genes (rbcL and matK) and nuclear ribosomal DNA (ITS) were used to construct cladograms. The results that obtained from the Internal Transcribed Spacer (ITS) gene showed that the nuclear genes are reliable marker for the phylogenetic study of Dendrobium compared to chloroplast DNA with low resolution level among sections. 

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