ArticleGenome research2005
Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes.
Article in Genome research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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79 citing papers in PubMed.
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- Managing genomic diversity in conservation programs of Chinese domestic chickens.Genetics, selection, evolution : GSE · 2023Article
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- Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- A chromosome-level reference genome and pangenome for barn swallow population genomics.Cell reports · 2023Article
- Cytogenetic Analysis of the Bimodal Karyotype of the Common European Adder,Animals : an open access journal from MDPI · 2022Article
- Linked-Read Sequencing of Eight Falcons Reveals a Unique Genomic Architecture in Flux.Genome biology and evolution · 2022Article
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- Sequencing refractory regions in bird genomes are hotspots for accelerated protein evolution.BMC ecology and evolution · 2021Article
- A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes.Genetics, selection, evolution : GSE · 2021Article
- Why Do Some Vertebrates Have Microchromosomes?Cells · 2021Review
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- Microchromosomes Exhibit Distinct Features of Vertebrate Chromosome Structure and Function with Underappreciated Ramifications for Genome Evolution.Molecular biology and evolution · 2021Article
- Comparison of Karyotypes in Two Hybridizing Passerine Species: Conserved Chromosomal Structure but Divergence in Centromeric Repeats.Frontiers in genetics · 2021Article
- Runs of Homozygosity in Modern Chicken Revealed by Sequence Data.G3 (Bethesda, Md.) · 2020Article
19 more citing papers are in PubMed but not listed here.
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5 authors.
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No grant is acknowledged in the PubMed record.
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.
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