scholarly journals Cytomolecular Analysis of Ribosomal DNA Evolution in a Natural Allotetraploid Brachypodium hybridum and Its Putative Ancestors—Dissecting Complex Repetitive Structure of Intergenic Spacers

2016 ◽  
Vol 7 ◽  
Author(s):  
Natalia Borowska-Zuchowska ◽  
Miroslaw Kwasniewski ◽  
Robert Hasterok
Keyword(s):  
Ribosomal Dna ◽  
Intergenic Spacers ◽  
Dna Evolution ◽  
Repetitive Structure

scholarly journals Discrimination of Streptomyces albidoflavus Strains Based on the Size and Number of 16S-23S Ribosomal DNA Intergenic Spacers

1997 ◽  
Vol 47 (1) ◽  
pp. 202-206 ◽  
Author(s):  
T. HAIN ◽  
N. WARD-RAINEY ◽  
R. M. KROPPENSTEDT ◽  
E. STACKEBRANDT ◽  
F. A. RAINEY
Keyword(s):  
Ribosomal Dna ◽  
Intergenic Spacers ◽  
Streptomyces Albidoflavus

scholarly journals Ribosomal DNA evolution and gene conversion in Nicotiana rustica

Heredity ◽  
2003 ◽  
Vol 91 (3) ◽  
pp. 268-275 ◽  
Author(s):  
R Matyasek ◽  
K Y Lim ◽  
A Kovarik ◽  
A R Leitch
Keyword(s):  
Gene Conversion ◽  
Ribosomal Dna ◽  
Nicotiana Rustica ◽  
Dna Evolution

scholarly journals Ribosomal DNA evolution and phylogeny inAloe(Asphodelaceae)

2000 ◽  
Vol 87 (11) ◽  
pp. 1578-1583 ◽  
Author(s):  
Stuart P. Adams ◽  
Ilia J. Leitch ◽  
Michael D. Bennett ◽  
Mark W. Chase ◽  
Andrew R. Leitch
Keyword(s):  
Ribosomal Dna ◽  
Dna Evolution

Variation in Ribosomal DNA Intergenic Spacers Among Populations of Anopheles albimanus in South and Central America

1995 ◽  
Vol 53 (5) ◽  
pp. 469-477 ◽  
Author(s):  
Ana Maria P. de Merida ◽  
Charles H. Porter ◽  
Eduviges Molina ◽  
Margarita P. de Mata ◽  
William C. Black
Keyword(s):  
Central America ◽  
Ribosomal Dna ◽  
Anopheles Albimanus ◽  
Intergenic Spacers

scholarly journals Structure of the intergenic spacers in chicken ribosomal DNA

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
Alexander Dyomin ◽  
Svetlana Galkina ◽  
Valerie Fillon ◽  
Stephane Cauet ◽  
Celine Lopez-Roques ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Ribosomal Dna ◽  
Regulatory Elements ◽  
Molecular Organization ◽  
Whole Genome Sequence ◽  
Likelihood Method ◽  
Rrna Gene ◽  
Intergenic Spacers ◽  
Rdna Sequences ◽  
Long Read

Abstract Background Ribosomal DNA (rDNA) repeats are situated in the nucleolus organizer regions (NOR) of chromosomes and transcribed into rRNA for ribosome biogenesis. Thus, they are an essential component of eukaryotic genomes. rDNA repeat units consist of rRNA gene clusters that are transcribed into single pre-rRNA molecules, each separated by intergenic spacers (IGS) that contain regulatory elements for rRNA gene cluster transcription. Because of their high repeat content, rDNA sequences are usually absent from genome assemblies. In this work, we used the long-read sequencing technology to describe the chicken IGS and fill the knowledge gap on rDNA sequences of one of the key domesticated animals. Methods We used the long-read PacBio RSII technique to sequence the BAC clone WAG137G04 (Wageningen BAC library) known to contain chicken NOR elements and the HGAP workflow software suit to assemble the PacBio RSII reads. Whole-genome sequence contigs homologous to the chicken rDNA repetitive unit were identified based on the Gallus_gallus-5.0 assembly with BLAST. We used the Geneious 9.0.5 and Mega software, maximum likelihood method and Chickspress project for sequence evolution analysis, phylogenetic tree construction and analysis of the raw transcriptome data. Results Three complete IGS sequences in the White Leghorn chicken genome and one IGS sequence in the red junglefowl contig AADN04001305.1 (Gallus_gallus-5.0) were detected. They had various lengths and contained three groups of tandem repeats (some of them being very GC rich) that form highly organized arrays. Initiation and termination sites of rDNA transcription were located within small and large unique regions (SUR and LUR), respectively. No functionally significant sites were detected within the tandem repeat sequences. Conclusions Due to the highly organized GC-rich repeats, the structure of the chicken IGS differs from that of IGS in human, apes, Xenopus or fish rDNA. However, the chicken IGS shares some molecular organization features with that of the turtles, which are other representatives of the Sauropsida clade that includes birds and reptiles. Our current results on the structure of chicken IGS together with the previously reported ribosomal gene cluster sequence provide sufficient data to consider that the complete chicken rDNA sequence is assembled with confidence in terms of molecular DNA organization.

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