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Gene family size conservation is a good indicator of evolutionary rates.

Chen FC, Chen CJ, Li WH, Chuang TJ - Mol. Biol. Evol. (2010)

Bottom Line: In addition, we show that the duplicate genes with family size conservation evolve significantly more slowly than those without family size conservation.Our results thus suggest that the controversy on whether duplicate genes evolve more slowly than singletons can be resolved when family size conservation is taken into consideration.Our results thus point to the importance of family size conservation in the evolution of duplicate genes.

View Article: PubMed Central - PubMed

Affiliation: Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, Taiwan.

ABSTRACT
The evolution of duplicate genes has been a topic of broad interest. Here, we propose that the conservation of gene family size is a good indicator of the rate of sequence evolution and some other biological properties. By comparing the human-chimpanzee-macaque orthologous gene families with and without family size conservation, we demonstrate that genes with family size conservation evolve more slowly than those without family size conservation. Our results further demonstrate that both family expansion and contraction events may accelerate gene evolution, resulting in elevated evolutionary rates in the genes without family size conservation. In addition, we show that the duplicate genes with family size conservation evolve significantly more slowly than those without family size conservation. Interestingly, the median evolutionary rate of singletons falls in between those of the above two types of duplicate gene families. Our results thus suggest that the controversy on whether duplicate genes evolve more slowly than singletons can be resolved when family size conservation is taken into consideration. Furthermore, we also observe that duplicate genes with family size conservation have the highest level of gene expression/expression breadth, the highest proportion of essential genes, and the lowest gene compactness, followed by singletons and then by duplicate genes without family size conservation. Such a trend accords well with our observations of evolutionary rates. Our results thus point to the importance of family size conservation in the evolution of duplicate genes.

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The data collation processes.
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fig1: The data collation processes.

Mentions: In this study, only the families that are present in all the three primate genomes (designated as “H-C-M” homologous families) are considered. To minimize potential errors in family size assignments, we excluded three types of families (also see fig. 1): 1) the families of which all the member genes are located in uncertain genomic regions, 2) the families that include at least one human or chimpanzee member gene that is located on chromosome Y (because the sequences of Y chromosome are unavailable for rhesus macaque), and 3) the families that include potentially uncharacterized protein-coding genes (which will be described in the next paragraph). Consequently, a total of 9,446 H-C-M families were extracted, which contained 17,211 human genes, 16,580 chimpanzee genes, and 17,402 macaque genes (table 1). The H-C-M families were further divided into two types of families: families whose sizes remain the same (i.e., H=C=M families) and those whose sizes vary among the three species (i.e., non-H=C=M families). To eliminate the potential confounding factor of gene copy number variations (CNVs), the families that included at least one human member gene that overlaps with experimentally validated genomic CNVs (downloaded from the Database of Genomic Variants [Iafrate et al. 2004] at http://projects.tcag.ca/variation/) were excluded from the H=C=M families (table 1). Throughout this study, “H=C=M families” indicate the H=C=M families in which the human genes do not overlap with any CNVs. The list of the human, chimpanzee, and macaque genes analyzed in this study is available at http://idv.sinica.edu.tw/trees/Duplication/Duplication.html.


Gene family size conservation is a good indicator of evolutionary rates.

Chen FC, Chen CJ, Li WH, Chuang TJ - Mol. Biol. Evol. (2010)

The data collation processes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2908708&req=5

fig1: The data collation processes.
Mentions: In this study, only the families that are present in all the three primate genomes (designated as “H-C-M” homologous families) are considered. To minimize potential errors in family size assignments, we excluded three types of families (also see fig. 1): 1) the families of which all the member genes are located in uncertain genomic regions, 2) the families that include at least one human or chimpanzee member gene that is located on chromosome Y (because the sequences of Y chromosome are unavailable for rhesus macaque), and 3) the families that include potentially uncharacterized protein-coding genes (which will be described in the next paragraph). Consequently, a total of 9,446 H-C-M families were extracted, which contained 17,211 human genes, 16,580 chimpanzee genes, and 17,402 macaque genes (table 1). The H-C-M families were further divided into two types of families: families whose sizes remain the same (i.e., H=C=M families) and those whose sizes vary among the three species (i.e., non-H=C=M families). To eliminate the potential confounding factor of gene copy number variations (CNVs), the families that included at least one human member gene that overlaps with experimentally validated genomic CNVs (downloaded from the Database of Genomic Variants [Iafrate et al. 2004] at http://projects.tcag.ca/variation/) were excluded from the H=C=M families (table 1). Throughout this study, “H=C=M families” indicate the H=C=M families in which the human genes do not overlap with any CNVs. The list of the human, chimpanzee, and macaque genes analyzed in this study is available at http://idv.sinica.edu.tw/trees/Duplication/Duplication.html.

Bottom Line: In addition, we show that the duplicate genes with family size conservation evolve significantly more slowly than those without family size conservation.Our results thus suggest that the controversy on whether duplicate genes evolve more slowly than singletons can be resolved when family size conservation is taken into consideration.Our results thus point to the importance of family size conservation in the evolution of duplicate genes.

View Article: PubMed Central - PubMed

Affiliation: Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, Taiwan.

ABSTRACT
The evolution of duplicate genes has been a topic of broad interest. Here, we propose that the conservation of gene family size is a good indicator of the rate of sequence evolution and some other biological properties. By comparing the human-chimpanzee-macaque orthologous gene families with and without family size conservation, we demonstrate that genes with family size conservation evolve more slowly than those without family size conservation. Our results further demonstrate that both family expansion and contraction events may accelerate gene evolution, resulting in elevated evolutionary rates in the genes without family size conservation. In addition, we show that the duplicate genes with family size conservation evolve significantly more slowly than those without family size conservation. Interestingly, the median evolutionary rate of singletons falls in between those of the above two types of duplicate gene families. Our results thus suggest that the controversy on whether duplicate genes evolve more slowly than singletons can be resolved when family size conservation is taken into consideration. Furthermore, we also observe that duplicate genes with family size conservation have the highest level of gene expression/expression breadth, the highest proportion of essential genes, and the lowest gene compactness, followed by singletons and then by duplicate genes without family size conservation. Such a trend accords well with our observations of evolutionary rates. Our results thus point to the importance of family size conservation in the evolution of duplicate genes.

Show MeSH
Related in: MedlinePlus