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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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PTHR12629 phylogenetic tree.
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Figure 6: PTHR12629 phylogenetic tree.

Mentions: Referred to as the ‘Diphosphoinositol polyphosphate phosphohydrolase’ family, genes belonging to this family create phosphotase and are involved in phospholipid metabolism. NUDT10 and NUDT11 are phosphohydrolases that preferentially attack diphosphoinositol polyphosphates (20) and are strongly expressed in testis and brain (21). These two genes are highly similar having 6 nt differences in humans (21). Due to this high similarity and their close proximity, it has been assumed that they are the result of a recent gene duplication . However, as can be seen in Figure 6, we identified orthologs in mouse and rat, leading us to speculate that this duplication occurred before the speciation event between primates and rodents, and that this high similarity is maintained between these genes by gene conversion.Figure 6.


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

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

PTHR12629 phylogenetic tree.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 6: PTHR12629 phylogenetic tree.
Mentions: Referred to as the ‘Diphosphoinositol polyphosphate phosphohydrolase’ family, genes belonging to this family create phosphotase and are involved in phospholipid metabolism. NUDT10 and NUDT11 are phosphohydrolases that preferentially attack diphosphoinositol polyphosphates (20) and are strongly expressed in testis and brain (21). These two genes are highly similar having 6 nt differences in humans (21). Due to this high similarity and their close proximity, it has been assumed that they are the result of a recent gene duplication . However, as can be seen in Figure 6, we identified orthologs in mouse and rat, leading us to speculate that this duplication occurred before the speciation event between primates and rodents, and that this high similarity is maintained between these genes by gene conversion.Figure 6.

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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