Low Frequency of Microsatellites in the Avian Genome
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TLDR
The low microsatellite density in the genome in general and on the microchromosomes in particular imposes an obstacle for the development of marker-rich genetic maps of chicken and other birds, and for the localization of quantitative trait genes.Abstract:
A better insight into the occurrence of microsatellites in a range of taxa may help to understand the evolution of simple repeats. Previous studies have found the relative abundance of several repeat motifs to differ among mammals, invertebrates, and plants. Absolute numbers of microsatellites also tend to correlate positively with genome size. We analyzed the occurrence, frequency, and distribution of microsatellites in birds, a taxon with one of the smallest known genome sizes among vertebrates. Dot-blot hybridization revealed that about half of 22 different di-, tri-, and tetranucleotide repeat motifs were clearly more common in human than in three species of birds: chicken, woodpecker, and swallow. For the remaining motifs no clear difference was found. From searching avian database sequences we estimated there to be 30,000-70,000 microsatellites longer than 20 bp in the avian genome. The number of (CA) > or = 10 would be around 7000-9000 and the number of (CA) > or = 14 about 3000. The calculated density of avian microsatellites (total, one every 20-39 kb; (CA) > or = 10, one every 136-150 kb) is much lower than that estimated for the human genome (one every 6 and 30 kb, respectively). This may be explained by the fact that the avian genome contains relatively less noncoding DNA than most mammals and that avian SINE/LINE elements do not terminate in poly(A) tails, which are known to provide a resource for the evolution of simple repeats in mammals. We found no association between microsatellites and SINEs in birds. Primed in situ labeling suggested fairly even distribution of (CA)n repeats over chicken macrochromosomes and intermediate chromosomes, whereas the microchromosomes, a large part of the Z and W chromosomes, and most telomeres and centromeres had very low concentrations of (CA)n microsatellites. The scarcity of microsatellites on the microchromosomes is compatible to these regions likely being unusually rich in coding sequences. The low microsatellite density in the genome in general and on the microchromosomes in particular imposes an obstacle for the development of marker-rich genetic maps of chicken and other birds, and for the localization of quantitative trait genes.read more
Citations
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References
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Journal ArticleDOI
Microsatellites, from molecules to populations and back
TL;DR: Interspecific studies show that microsatellites are poor markers for phylogenetic inference, however, these studies are fuelling discussions on directional mutation and the role of selection and recombination in their evolution, Nonetheless, it remains true that microSatellites may be considered as good, neutral mendelian markers.
Journal ArticleDOI
Simple sequences are ubiquitous repetitive components of eukaryotic genomes
Diethard Tautz,Manfred Renz +1 more
TL;DR: Many, probably even all possible types of simple sequence are repetitive components of eukaryotic genomes and it is proposed that they arise by common mechanisms namely slippage replication and unequal crossover and that they might have no general function with regards to gene expression.
Journal ArticleDOI
A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes
TL;DR: A huge number of stretches of dT-dG alternating sequence, a sequence that has been shown to adopt the Z-DNA conformation under some conditions, are found in eukaryotic genomes, indicating extraordinary evolutionary conservation.
Journal ArticleDOI
Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox.
TL;DR: Eukaryote DNA can be divided into genic DNA, which codes for proteins (or serves as recognition sites for proteins involved in transcription, replication and recombination), and nucleoskeletal DNA (S-DNA), which exists only because of its nucleoskeleton role in determining the nuclear volume.
Journal ArticleDOI
Survey of human and rat microsatellites.
TL;DR: In this article, summaries of GenBank searches for all possible human and rat microsatellites ranging from mononucleotide to tetranucleotide repeat motifs are presented.
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