Document Detail

Low frequency of microsatellites in the avian genome.
MedLine Citation:
PMID:  9149943     Owner:  NLM     Status:  MEDLINE    
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.
C R Primmer; T Raudsepp; B P Chowdhary; A P Møller; H Ellegren
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Publication Detail:
Type:  Comparative Study; Journal Article    
Journal Detail:
Title:  Genome research     Volume:  7     ISSN:  1088-9051     ISO Abbreviation:  Genome Res.     Publication Date:  1997 May 
Date Detail:
Created Date:  1997-08-04     Completed Date:  1997-08-04     Revised Date:  2006-11-15    
Medline Journal Info:
Nlm Unique ID:  9518021     Medline TA:  Genome Res     Country:  UNITED STATES    
Other Details:
Languages:  eng     Pagination:  471-82     Citation Subset:  IM    
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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MeSH Terms
Base Sequence
Birds / genetics*
Chickens / genetics
Databases, Factual
Gene Frequency*
Genome, Human
In Situ Hybridization / methods
Mammals / genetics
Microsatellite Repeats*
Repetitive Sequences, Nucleic Acid
Swine / genetics
Vertebrates / genetics

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine

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