scholarly journals Phylogenetic Information Content of Copepoda Ribosomal DNA Repeat Units: ITS1 and ITS2 Impact

2014 ◽  
Vol 2014 ◽  
pp. 1-15 ◽  
Author(s):  
Maxim V. Zagoskin ◽  
Valentina I. Lazareva ◽  
Andrey K. Grishanin ◽  
Dmitry V. Mukha
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Trees ◽  
Repeat Unit ◽  
Its2 Rdna ◽  
Minimum Evolution ◽  
Nucleotide Substitutions ◽  
Repeat Units ◽  
Dna Repeat ◽  
Ribosomal Repeat ◽  
Its1 And Its2

The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda (Crustacea). Fragments approximately 2000 bp in length containing the ribosomal DNA (rDNA) 18S and 28S gene fragments, the 5.8S gene, and the internal transcribed spacer regions I and II (ITS1 and ITS2) were amplified and analyzed. The DAMBE (Data Analysis in Molecular Biology and Evolution) software was used to analyze the saturation of nucleotide substitutions; this test revealed the suitability of both the 28S gene fragment and the ITS1/ITS2 rDNA regions for the reconstruction of phylogenetic trees. Distance (minimum evolution) and probabilistic (maximum likelihood, Bayesian) analyses of the data revealed that the 28S rDNA and the ITS1 and ITS2 regions are informative markers for inferring phylogenetic relationships among families of copepods and within the Cyclopidae family and associated genera. Split-graph analysis of concatenated ITS1/ITS2 rDNA regions of cyclopoid copepods suggested that theMesocyclops,Thermocyclops,andMacrocyclopsgenera share complex evolutionary relationships. This study revealed that the ITS1 and ITS2 regions potentially represent different phylogenetic signals.

Polymorphism in ribosomal DNA repeat units of 12 Hordeum species

Genome ◽  
1989 ◽  
Vol 32 (6) ◽  
pp. 1124-1127 ◽  
Author(s):  
Stephen J. Molnar ◽  
George Fedak
Keyword(s):  
Ribosomal Dna ◽  
Repeat Unit ◽  
Unit Length ◽  
Intergenic Spacer ◽  
Rdna Repeat ◽  
Repeat Units ◽  
Dna Repeat ◽  
Rdna Repeat Unit ◽  
Bamhi Restriction Site ◽  
Hordeum Species

Total genomic DNA was isolated from leaves of individual accessions of 12 Hordeum species. SacI, HindIII, and BamHI restriction fragments hybridizing to the wheat rDNA probe pTA71 were compared. Thirteen rDNA repeat unit length variants were recovered, which combined to produce 11 distinct phenotypes. All rDNA repeat units had two SacI sites and no HindIII sites. The rDNA repeat units of H. secalinum, H. hrasdanicum, and H. distichum all had 3 BamHI sites, but in different configurations. The rDNA repeat units of the other species had at least 4 BamHI sites. Ladders of small hybridizing fragments in 8 of 9 of the latter accessions indicated the presence of occasional BamHI sites in some subrepeats within the intergenic spacer regions of the rDNA repeat units. Different distributions of BamHI restriction site maps within the Hordeum sections strengthen the concept of using variation in rDNA restriction sites as a taxonomic character.Key words: Hordeum, ribosomal DNA, polymorphism.

A physical map of the ribosomal DNA repeat unit of Aspergillus nidulans

Gene ◽  
1982 ◽  
Vol 20 (2) ◽  
pp. 135-137 ◽  
Author(s):  
Robin A. Lockington ◽  
Graham G. Taylor ◽  
Michael Winther ◽  
Claudio Scazzocchio ◽  
R.Wayne Davies
Keyword(s):  
Aspergillus Nidulans ◽  
Ribosomal Dna ◽  
Physical Map ◽  
Repeat Unit ◽  
Dna Repeat

Ribosomal DNA repeat unit polymorphism in 49 Vicia species

1995 ◽  
Vol 90 (3-4) ◽  
pp. 477-486 ◽  
Author(s):  
S. N. Raina ◽  
Y. Ogihara
Keyword(s):  
Ribosomal Dna ◽  
Repeat Unit ◽  
Vicia Species ◽  
Dna Repeat

scholarly journals Two distinct intervening sequences in different ribosomal DNA repeat units of Sciara coprophila

1981 ◽  
Vol 9 (15) ◽  
pp. 3747-3764 ◽  
Author(s):  
Renate Renkawitz-Pohl ◽  
Lloyd Matsumoto ◽  
Susan A. Gerbi
Keyword(s):  
Ribosomal Dna ◽  
Repeat Units ◽  
Intervening Sequences ◽  
Dna Repeat

scholarly journals Comparative analysis of the ribosomal DNA repeat unit (rDNA) of Perna viridis (Linnaeus, 1758) and Perna canaliculus (Gmelin, 1791)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7644
Author(s):  
Zhansheng Guo ◽  
Leng Han ◽  
Zhenlin Liang ◽  
Xuguang Hou
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Trees ◽  
Repeat Unit ◽  
Cpg Islands ◽  
Intergenic Spacer ◽  
Initiation Site ◽  
Perna Viridis ◽  
28S Rrna ◽  
Important Species ◽  
Perna Canaliculus

Perna viridis and P. canaliculus are economically and ecologically important species of shellfish. In this study, the complete ribosomal DNA (rDNA) unit sequences of these species were determined for the first time. The gene order, 18S rRNA–internal transcribed spacer (ITS) 1–5.8S rRNA–ITS2–28S rRNA–intergenic spacer (IGS), was similar to that observed in other eukaryotes. The lengths of the P. viridis and P. canaliculus rDNA sequences ranged from 8,432 to 8,616 bp and from 7,597 to 7,610 bp, respectively, this variability was mainly attributable to the IGS region. The putative transcription termination site and initiation site were confirmed. Perna viridis and P. canaliculus rDNA contained two (length: 93 and 40 bp) and one (length: 131 bp) repeat motifs, respectively. Individual intra-species differences mainly involved the copy number of repeat units. In P. viridis, three cytosine-guanine (CpG) sites with sizes of 440, 1,075 and 537 bp were found to cover nearly the entire IGS sequence, whereas in P. canaliculus, two CpG islands with sizes of 361 and 484 bp were identified. The phylogenetic trees constructed with maximum likelihood and neighbour-joining methods and based on ITS sequences were identical and included three major clusters. Species of the same genus were easily clustered together.

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