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Sexy gene conversions: locating gene conversions on the X-chromosome.

Lawson MJ, Zhang L - Nucleic Acids Res. (2009)

Bottom Line: Gene conversion can have a profound impact on both the short- and long-term evolution of genes and genomes.Comparing the results with those of two gene conversion prediction programs (GENECONV and Partimatrix), we found that both GENECONV and Partimatrix have very high false negative rates (i.e. failed to predict gene conversions), which leads to many undetected gene conversions.The combination of phylogenetic analyses with physical synteny evidence exhibits high resolution in the detection of gene conversions.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Virginia Tech, USA.

ABSTRACT
Gene conversion can have a profound impact on both the short- and long-term evolution of genes and genomes. Here, we examined the gene families that are located on the X-chromosomes of human (Homo sapiens), chimpanzee (Pan troglodytes), mouse (Mus musculus) and rat (Rattus norvegicus) for evidence of gene conversion. We identified seven gene families (WD repeat protein family, Ferritin Heavy Chain family, RAS-related Protein RAB-40 family, Diphosphoinositol polyphosphate phosphohydrolase family, Transcription Elongation Factor A family, LDOC1-related family, Zinc Finger Protein ZIC, and GLI family) that show evidence of gene conversion. Through phylogenetic analyses and synteny evidence, we show that gene conversion has played an important role in the evolution of these gene families and that gene conversion has occurred independently in both primates and rodents. Comparing the results with those of two gene conversion prediction programs (GENECONV and Partimatrix), we found that both GENECONV and Partimatrix have very high false negative rates (i.e. failed to predict gene conversions), which leads to many undetected gene conversions. The combination of phylogenetic analyses with physical synteny evidence exhibits high resolution in the detection of gene conversions.

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PTHR14754 phylogenetic tree.
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Figure 1: PTHR14754 phylogenetic tree.

Mentions: Figure 1 shows the phylogeny of the human TCEAL3, TCEAL5 and TCEAL6 genes and their orthologs across the other four species. Again, we have an example of gene conversions occurring within biological order (primates and rodents), as the mouse and rat genes are more similar to each other, and the human/chimpanzee/rhesus genes show a similar pattern. Within mouse there may even be a stronger level of gene conversion between TCEAL3 and TCEAL6; however, we were unable to identify TCEAL6 in the rat genome.Figure 1.


Sexy gene conversions: locating gene conversions on the X-chromosome.

Lawson MJ, Zhang L - Nucleic Acids Res. (2009)

PTHR14754 phylogenetic tree.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2724270&req=5

Figure 1: PTHR14754 phylogenetic tree.
Mentions: Figure 1 shows the phylogeny of the human TCEAL3, TCEAL5 and TCEAL6 genes and their orthologs across the other four species. Again, we have an example of gene conversions occurring within biological order (primates and rodents), as the mouse and rat genes are more similar to each other, and the human/chimpanzee/rhesus genes show a similar pattern. Within mouse there may even be a stronger level of gene conversion between TCEAL3 and TCEAL6; however, we were unable to identify TCEAL6 in the rat genome.Figure 1.

Bottom Line: Gene conversion can have a profound impact on both the short- and long-term evolution of genes and genomes.Comparing the results with those of two gene conversion prediction programs (GENECONV and Partimatrix), we found that both GENECONV and Partimatrix have very high false negative rates (i.e. failed to predict gene conversions), which leads to many undetected gene conversions.The combination of phylogenetic analyses with physical synteny evidence exhibits high resolution in the detection of gene conversions.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Virginia Tech, USA.

ABSTRACT
Gene conversion can have a profound impact on both the short- and long-term evolution of genes and genomes. Here, we examined the gene families that are located on the X-chromosomes of human (Homo sapiens), chimpanzee (Pan troglodytes), mouse (Mus musculus) and rat (Rattus norvegicus) for evidence of gene conversion. We identified seven gene families (WD repeat protein family, Ferritin Heavy Chain family, RAS-related Protein RAB-40 family, Diphosphoinositol polyphosphate phosphohydrolase family, Transcription Elongation Factor A family, LDOC1-related family, Zinc Finger Protein ZIC, and GLI family) that show evidence of gene conversion. Through phylogenetic analyses and synteny evidence, we show that gene conversion has played an important role in the evolution of these gene families and that gene conversion has occurred independently in both primates and rodents. Comparing the results with those of two gene conversion prediction programs (GENECONV and Partimatrix), we found that both GENECONV and Partimatrix have very high false negative rates (i.e. failed to predict gene conversions), which leads to many undetected gene conversions. The combination of phylogenetic analyses with physical synteny evidence exhibits high resolution in the detection of gene conversions.

Show MeSH