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PMID: 15590944 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't

Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes.

Genome research ·Vol. 15 ·No. 1 ·2005-01-00 ·Pages 120-5

Axelsson E, Webster MT, Smith NG, Burt DW, Ellegren H

Abstract

A distinctive feature of the avian genome is the large heterogeneity in the size of chromosomes, which are usually classified into a small number of macrochromosomes and numerous microchromosomes. These chromosome classes show characteristic differences in a number of interrelated features that could potentially affect the rate of sequence evolution, such as GC content, gene density, and recombination rate. We studied the effects of these factors by analyzing patterns of nucleotide substitution in two sets of chicken-turkey sequence alignments. First, in a set of 67 orthologous introns, divergence was significantly higher in microchromosomes (chromosomes 11-38; 11.7% divergence) than in both macrochromosomes (chromosomes 1-5; 9.9% divergence; P = 0.016) and intermediate-sized chromosomes (chromosomes 6-10; 9.5% divergence; P = 0.026). At least part of this difference was due to the higher incidence of CpG sites on microchromosomes. Second, using 155 orthologous coding sequences we noted a similar pattern, in which synonymous substitution rates on microchromosomes (13.1%) were significantly higher than were rates on macrochromosomes (10.3%; P = 0.024). Broadly assuming neutrality of introns and synonymous sites, or constraints on such sequences do not differ between chromosomal classes, these observations imply that microchromosomal genes are exposed to more germ line mutations than those on other chromosomes. We also find that dN/dS ratios for genes located on microchromosomes (average, 0.094) are significantly lower than those of macrochromosomes (average, 0.185; P = 0.025), suggesting that the proteins of genes on microchromosomes are under greater evolutionary constraint.

MeSH Terms
Animals Base Composition/genetics Chickens/genetics Chromosomes/genetics Evolution, Molecular Genetic Variation/genetics Genome Molecular Sequence Data Mutagenesis/genetics Nucleotides/genetics Recombination, Genetic/genetics Turkeys/genetics
Chemicals
Nucleotides
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Axelsson Erik
Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden.
Webster Matthew T
Smith Nick G C
Burt David W
Ellegren Hans
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.3021305
Published
2005-01-00
Epub
2004-00-08
Pages
120-5
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC540272
Subset
IM
Databases
GENBANK
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External Links
PubMed source DOI: 10.1101/gr.3021305 PMC Full Text View journal details
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