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Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila.

Yang S, Arguello JR, Li X, Ding Y, Zhou Q, Chen Y, Zhang Y, Zhao R, Brunet F, Peng L, Long M, Wang W - PLoS Genet. (2007)

Bottom Line: Lack of a dataset comprising experimentally verified young duplicates has hampered an effective examination of these models as well as an investigation of sequence features that mediate the rearrangements.Examination of their flanking sequences revealed an excess of repetitive sequences, with the majority belonging to the transposable element DNAREP1 family, associated with the new genes.Our dataset strongly suggests an important role for REs in the generation of chimeric genes within these species.

View Article: PubMed Central - PubMed

Affiliation: Chinese Academy of Sciences-Max Planck Junior Research Group, Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.

ABSTRACT
Previous studies of repetitive elements (REs) have implicated a mechanistic role in generating new chimerical genes. Such examples are consistent with the classic model for exon shuffling, which relies on non-homologous recombination. However, recent data for chromosomal aberrations in model organisms suggest that ectopic homology-dependent recombination may also be important. Lack of a dataset comprising experimentally verified young duplicates has hampered an effective examination of these models as well as an investigation of sequence features that mediate the rearrangements. Here we use approximately 7,000 cDNA probes (approximately 112,000 primary images) to screen eight species within the Drosophila melanogaster subgroup and identify 17 duplicates that were generated through ectopic recombination within the last 12 mys. Most of these are functional and have evolved divergent expression patterns and novel chimeric structures. Examination of their flanking sequences revealed an excess of repetitive sequences, with the majority belonging to the transposable element DNAREP1 family, associated with the new genes. Our dataset strongly suggests an important role for REs in the generation of chimeric genes within these species.

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Two Examples of New Genes with Repetitive Sequences at the Breakpoints(A) Shows a satellite DNA sequence (SAR) located at the 5′ breakpoints of mkg-r2 and its parental gene mkg-r.(B) Shows the existence of a transposon (DNAREP1-DM) at all the four breakpoints of a CR9337 duplicate pair.
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pgen-0040003-g004: Two Examples of New Genes with Repetitive Sequences at the Breakpoints(A) Shows a satellite DNA sequence (SAR) located at the 5′ breakpoints of mkg-r2 and its parental gene mkg-r.(B) Shows the existence of a transposon (DNAREP1-DM) at all the four breakpoints of a CR9337 duplicate pair.

Mentions: Among these 10 pairs associated with REs, 5 have shared repeats at or near the breakpoints of both the parental and the new duplicate copies (Table 2). For these 5 paralog pairs, 4 (CG3875-CG3927, mkgr-mkgr2, CG3101-CG3101-r and CR9337-CR9337-r) maintain very high sequence identity over the flanking elements; the remaining CR9337-CR33318 pair, though both harboring DNAREP1 sequence at their 5′ ends, provides a weak alignment. The other five paralog pairs contain a repetitive element at the breakpoint of one copy (Table 2; 2 examples with highly similar TEs shown in Figure 4). In addition, klg-r, CG7635-r and CG8490-r (not included in the ten above) were found next to sequencing gaps in the genomic databases (Table 2), and resequencing these regions resulted in sequence profiles characteristic of repetitive sequences (data not shown). If these are included, the majority of new duplicates (13/17, 76.5%) are associated with repetitive elements.


Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila.

Yang S, Arguello JR, Li X, Ding Y, Zhou Q, Chen Y, Zhang Y, Zhao R, Brunet F, Peng L, Long M, Wang W - PLoS Genet. (2007)

Two Examples of New Genes with Repetitive Sequences at the Breakpoints(A) Shows a satellite DNA sequence (SAR) located at the 5′ breakpoints of mkg-r2 and its parental gene mkg-r.(B) Shows the existence of a transposon (DNAREP1-DM) at all the four breakpoints of a CR9337 duplicate pair.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2211543&req=5

pgen-0040003-g004: Two Examples of New Genes with Repetitive Sequences at the Breakpoints(A) Shows a satellite DNA sequence (SAR) located at the 5′ breakpoints of mkg-r2 and its parental gene mkg-r.(B) Shows the existence of a transposon (DNAREP1-DM) at all the four breakpoints of a CR9337 duplicate pair.
Mentions: Among these 10 pairs associated with REs, 5 have shared repeats at or near the breakpoints of both the parental and the new duplicate copies (Table 2). For these 5 paralog pairs, 4 (CG3875-CG3927, mkgr-mkgr2, CG3101-CG3101-r and CR9337-CR9337-r) maintain very high sequence identity over the flanking elements; the remaining CR9337-CR33318 pair, though both harboring DNAREP1 sequence at their 5′ ends, provides a weak alignment. The other five paralog pairs contain a repetitive element at the breakpoint of one copy (Table 2; 2 examples with highly similar TEs shown in Figure 4). In addition, klg-r, CG7635-r and CG8490-r (not included in the ten above) were found next to sequencing gaps in the genomic databases (Table 2), and resequencing these regions resulted in sequence profiles characteristic of repetitive sequences (data not shown). If these are included, the majority of new duplicates (13/17, 76.5%) are associated with repetitive elements.

Bottom Line: Lack of a dataset comprising experimentally verified young duplicates has hampered an effective examination of these models as well as an investigation of sequence features that mediate the rearrangements.Examination of their flanking sequences revealed an excess of repetitive sequences, with the majority belonging to the transposable element DNAREP1 family, associated with the new genes.Our dataset strongly suggests an important role for REs in the generation of chimeric genes within these species.

View Article: PubMed Central - PubMed

Affiliation: Chinese Academy of Sciences-Max Planck Junior Research Group, Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.

ABSTRACT
Previous studies of repetitive elements (REs) have implicated a mechanistic role in generating new chimerical genes. Such examples are consistent with the classic model for exon shuffling, which relies on non-homologous recombination. However, recent data for chromosomal aberrations in model organisms suggest that ectopic homology-dependent recombination may also be important. Lack of a dataset comprising experimentally verified young duplicates has hampered an effective examination of these models as well as an investigation of sequence features that mediate the rearrangements. Here we use approximately 7,000 cDNA probes (approximately 112,000 primary images) to screen eight species within the Drosophila melanogaster subgroup and identify 17 duplicates that were generated through ectopic recombination within the last 12 mys. Most of these are functional and have evolved divergent expression patterns and novel chimeric structures. Examination of their flanking sequences revealed an excess of repetitive sequences, with the majority belonging to the transposable element DNAREP1 family, associated with the new genes. Our dataset strongly suggests an important role for REs in the generation of chimeric genes within these species.

Show MeSH
Related in: MedlinePlus