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. 2013 Jun 4;8(6):e64884.
doi: 10.1371/journal.pone.0064884. Print 2013.

The role of recombination in the origin and evolution of Alu subfamilies

Ana Teixeira-Silva  1 , Raquel M Silva, João Carneiro, António Amorim, Luísa Azevedo
Affiliations

The role of recombination in the origin and evolution of Alu subfamilies

Ana Teixeira-Silva et al. PLoS One. .

Abstract

Alus are the most abundant and successful short interspersed nuclear elements found in primate genomes. In humans, they represent about 10% of the genome, although few are retrotransposition-competent and are clustered into subfamilies according to the source gene from which they evolved. Recombination between them can lead to genomic rearrangements of clinical and evolutionary significance. In this study, we have addressed the role of recombination in the origin of chimeric Alu source genes by the analysis of all known consensus sequences of human Alus. From the allelic diversity of Alu consensus sequences, validated in extant elements resulting from whole genome searches, distinct events of recombination were detected in the origin of particular subfamilies of AluS and AluY source genes. These results demonstrate that at least two subfamilies are likely to have emerged from ectopic Alu-Alu recombination, which stimulates further research regarding the potential of chimeric active Alus to punctuate the genome.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Alu consensus alignment and position numbering.
Sequence Alignment of at least one representative of each haplotype defined by the 11 indel markers; node 1 is represented by two sequences: AluJo and AluSx. Position numbering was performed according to the reference AluJo. The first base of each indel is also indicated (red). Poly-A linker polymorphisms were disregarded. Dots represent identical bases and hyphens represent gaps (absent or deleted bases). R represents bases A or G according to the IUPAC code for nucleotide ambiguities.
Figure 2
Figure 2. Sequence hits resulting from whole genome search of indel alleles carried by human consensus Alus.
An example of a genomic sequence carrying each indel allele is given and aligned with the counterpart allele (left). The exact position of the indel is delimited. The complete list of results is provided in the Dataset S2.
Figure 3
Figure 3. Clustering of Alu subfamilies using indel markers.
The blue slice of node 1 represents the oldest subfamilies (AluJ). AluS elements are represented in pink and members of the young AluY are shown in green. Sites of mutational events are shown in blue boxes in the network’s branches. Networks A and B are the result of size heterogeneity in positions 65 and 66: (A) assuming that the three combinations resulted consecutively (65–66 ins –65 del –66 del) and (B) assuming that they were independent events (65–66 ins –65 del and 65–66 ins - 65–66 del). Networks A and B differ only in the right reticulation (circled) and the branch that connects it to node 7.
Figure 4
Figure 4. Alternative pathways for the origin of Alu subfamilies clustered in nodes 2, 3, and 4 of Figure 3.
An alignment of at least a representative of each involved node is displayed, plus two representatives of node 7 (AluY and AluSx3). Alternative pathways are named A to F. A and B represent recombination events (green), C and D represent events of back mutation (orange) and E and F represent recurrent mutations (blue).
Figure 5
Figure 5. Alternative pathways for the origin of Alu subfamilies clustered in nodes 13, 14 and 15 of Figure 3.
An alignment of at least one representative of each involved node is displayed. Alternative pathways are named A to C and represent recombination events (green).
Figure 6
Figure 6. Evolution of human Alu subfamilies.
Blue boxes correspond to indel markers, green boxes correspond to SNPs and purple boxes correspond to putative recombination events and recombinant (chimeric) subfamilies.
See this image and copyright information in PMC

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Publication types

Grants and funding

This work was supported by FCT (Portuguese governmental institution) through the program Ciencia2007 (Hiring of PhDs for the SCTN - financed by POPH - QREN - Tipology 4.2 - Promoting Scientific Employment, co-financed by MCTES national funding and The European Social Fund and the research project PTDC/BIA-PRO/099888/2008. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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