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Birth of three stowaway-like MITE families via microhomology-mediated miniaturization of a Tc1/Mariner element in the yellow fever mosquito.

Yang G, Fattash I, Lee CN, Liu K, Cavinder B - Genome Biol Evol (2013)

Bottom Line: Upon close inspection of the sequence junctions, the internal deletions during the formation of these three MITE families always occurred between two microhomologous sites (6-8 bp).These results suggest that multiple MITE families may originate from a single ancestral autonomous element, and formation of MITEs can be mediated by sequence microhomology.Ozma and its related MITEs are exceptional candidates for the long sought-after endogenous active transposon tool in genetic control of mosquitoes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Toronto Mississauga, Ontario, Canada.

ABSTRACT
Eukaryotic genomes contain numerous DNA transposons that move by a cut-and-paste mechanism. The majority of these elements are self-insufficient and dependent on their autonomous relatives to transpose. Miniature inverted repeat transposable elements (MITEs) are often the most numerous nonautonomous DNA elements in a higher eukaryotic genome. Little is known about the origin of these MITE families as few of them are accompanied by their direct ancestral elements in a genome. Analyses of MITEs in the yellow fever mosquito identified its youngest MITE family, designated as Gnome, that contains at least 116 identical copies. Genome-wide search for direct ancestral autonomous elements of Gnome revealed an elusive single copy Tc1/Mariner-like element, named as Ozma, that encodes a transposase with a DD37E triad motif. Strikingly, Ozma also gave rise to two additional MITE families, designated as Elf and Goblin. These three MITE families were derived at different times during evolution and bear internal sequences originated from different regions of Ozma. Upon close inspection of the sequence junctions, the internal deletions during the formation of these three MITE families always occurred between two microhomologous sites (6-8 bp). These results suggest that multiple MITE families may originate from a single ancestral autonomous element, and formation of MITEs can be mediated by sequence microhomology. Ozma and its related MITEs are exceptional candidates for the long sought-after endogenous active transposon tool in genetic control of mosquitoes.

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Distribution of sequence divergence for Gnome, Elf, and Goblin families. The numbers of elements in a certain range of divergence from the consensus sequences are plotted against the divergence range. Bin size, 0.005. Dashed lines, broken y axis for better view of the three families. x axis, divergence value; y axis, number of elements in a certain range of divergence value.
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evt146-F5: Distribution of sequence divergence for Gnome, Elf, and Goblin families. The numbers of elements in a certain range of divergence from the consensus sequences are plotted against the divergence range. Bin size, 0.005. Dashed lines, broken y axis for better view of the three families. x axis, divergence value; y axis, number of elements in a certain range of divergence value.

Mentions: During the amplification of a TE family, mutations in the elements will accumulate. The degree of divergence of the elements from the consensus sequence of a TE family can be used to estimate the relative age of a family (Kapitonov and Jurka 1996). To understand whether Gnome, Elf, and Goblin were generated at the same time during evolution, consensus sequences were generated for each family and the divergence rate of each copy from the consensus was calculated. The average divergence value for the three families, Gnome, Elf, and Goblin, are 0.6%, 2.42%, and 1.64%, respectively. Numbers of copies of an element at a certain range of divergence rate were plotted against the divergence rate (fig. 5). The number of elements peaked at the divergence value of ∼0.5%, ∼2%, and ∼1.5% for Gnome, Elf, and Goblin, respectively, suggesting that the order of appearance for the three families is Elf, Goblin, and Gnome. The highest divergence rates for the three families are 2.82% (Gnome), 7.11% (Elf), and 3.72% (Goblin), in agreement with the order of their appearance. In addition, Gnome has the largest number of identical elements as described earlier, Goblin has five identical copies, and Elf has no identical elements. This observation further supports the order of their appearance during evolution. Based on the rough estimation of the mutation rate for the mosquito genome at 1 × 10−7/base/year (Haag-Liautard et al. 2007; Struchiner et al. 2009), the average time of appearance for these families are estimated to be 60, 164, and 242 thousand years ago. Even though Elf appears to have formed before the insertion of the two repeat elements into Ozma, it is unclear whether Gnome and Goblin arose before or after the insertion events.Fig. 5.—


Birth of three stowaway-like MITE families via microhomology-mediated miniaturization of a Tc1/Mariner element in the yellow fever mosquito.

Yang G, Fattash I, Lee CN, Liu K, Cavinder B - Genome Biol Evol (2013)

Distribution of sequence divergence for Gnome, Elf, and Goblin families. The numbers of elements in a certain range of divergence from the consensus sequences are plotted against the divergence range. Bin size, 0.005. Dashed lines, broken y axis for better view of the three families. x axis, divergence value; y axis, number of elements in a certain range of divergence value.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814204&req=5

evt146-F5: Distribution of sequence divergence for Gnome, Elf, and Goblin families. The numbers of elements in a certain range of divergence from the consensus sequences are plotted against the divergence range. Bin size, 0.005. Dashed lines, broken y axis for better view of the three families. x axis, divergence value; y axis, number of elements in a certain range of divergence value.
Mentions: During the amplification of a TE family, mutations in the elements will accumulate. The degree of divergence of the elements from the consensus sequence of a TE family can be used to estimate the relative age of a family (Kapitonov and Jurka 1996). To understand whether Gnome, Elf, and Goblin were generated at the same time during evolution, consensus sequences were generated for each family and the divergence rate of each copy from the consensus was calculated. The average divergence value for the three families, Gnome, Elf, and Goblin, are 0.6%, 2.42%, and 1.64%, respectively. Numbers of copies of an element at a certain range of divergence rate were plotted against the divergence rate (fig. 5). The number of elements peaked at the divergence value of ∼0.5%, ∼2%, and ∼1.5% for Gnome, Elf, and Goblin, respectively, suggesting that the order of appearance for the three families is Elf, Goblin, and Gnome. The highest divergence rates for the three families are 2.82% (Gnome), 7.11% (Elf), and 3.72% (Goblin), in agreement with the order of their appearance. In addition, Gnome has the largest number of identical elements as described earlier, Goblin has five identical copies, and Elf has no identical elements. This observation further supports the order of their appearance during evolution. Based on the rough estimation of the mutation rate for the mosquito genome at 1 × 10−7/base/year (Haag-Liautard et al. 2007; Struchiner et al. 2009), the average time of appearance for these families are estimated to be 60, 164, and 242 thousand years ago. Even though Elf appears to have formed before the insertion of the two repeat elements into Ozma, it is unclear whether Gnome and Goblin arose before or after the insertion events.Fig. 5.—

Bottom Line: Upon close inspection of the sequence junctions, the internal deletions during the formation of these three MITE families always occurred between two microhomologous sites (6-8 bp).These results suggest that multiple MITE families may originate from a single ancestral autonomous element, and formation of MITEs can be mediated by sequence microhomology.Ozma and its related MITEs are exceptional candidates for the long sought-after endogenous active transposon tool in genetic control of mosquitoes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Toronto Mississauga, Ontario, Canada.

ABSTRACT
Eukaryotic genomes contain numerous DNA transposons that move by a cut-and-paste mechanism. The majority of these elements are self-insufficient and dependent on their autonomous relatives to transpose. Miniature inverted repeat transposable elements (MITEs) are often the most numerous nonautonomous DNA elements in a higher eukaryotic genome. Little is known about the origin of these MITE families as few of them are accompanied by their direct ancestral elements in a genome. Analyses of MITEs in the yellow fever mosquito identified its youngest MITE family, designated as Gnome, that contains at least 116 identical copies. Genome-wide search for direct ancestral autonomous elements of Gnome revealed an elusive single copy Tc1/Mariner-like element, named as Ozma, that encodes a transposase with a DD37E triad motif. Strikingly, Ozma also gave rise to two additional MITE families, designated as Elf and Goblin. These three MITE families were derived at different times during evolution and bear internal sequences originated from different regions of Ozma. Upon close inspection of the sequence junctions, the internal deletions during the formation of these three MITE families always occurred between two microhomologous sites (6-8 bp). These results suggest that multiple MITE families may originate from a single ancestral autonomous element, and formation of MITEs can be mediated by sequence microhomology. Ozma and its related MITEs are exceptional candidates for the long sought-after endogenous active transposon tool in genetic control of mosquitoes.

Show MeSH
Related in: MedlinePlus