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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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The Phylogenetic Distribution of the 17 New DLR Duplicates Identified in This StudyThe species phylogeny and time scale are from [58]. Different color bars show different gene families. The kep1 gene family has six new duplicates (indicated by red bars).
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pgen-0040003-g002: The Phylogenetic Distribution of the 17 New DLR Duplicates Identified in This StudyThe species phylogeny and time scale are from [58]. Different color bars show different gene families. The kep1 gene family has six new duplicates (indicated by red bars).

Mentions: To exclude false positives from the 266 candidates, we carried out Southern hybridizations and conducted BLAST searches against the available genome sequences of D. simulans (droSim1), D. yakuba (droYak1), D. sechellia (droSec1), D. melanogaster (dm2) and D. erecta (droEre1) (http://genome.ucsc.edu) (Figure 1). The Southern and BLAST analyses confirmed 17 young duplicates generated through DLR (Table 1; Figure 2). The genomic sequences of all 17 dispersed duplicates contain the intron(s) and/or non-coding flanking sequences that exist in their parental copies, suggesting that the new genes originated through DLR. In addition, we also identified ten new copies of retrogenes and 53 young copies of REs including retroelements and other repetitive sequences. In this report, we have focused on the 17 dispersed duplicates and investigate possible DLR mechanisms that generate dispersed duplications.


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)

The Phylogenetic Distribution of the 17 New DLR Duplicates Identified in This StudyThe species phylogeny and time scale are from [58]. Different color bars show different gene families. The kep1 gene family has six new duplicates (indicated by red bars).
© Copyright Policy
Related In: Results  -  Collection

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

pgen-0040003-g002: The Phylogenetic Distribution of the 17 New DLR Duplicates Identified in This StudyThe species phylogeny and time scale are from [58]. Different color bars show different gene families. The kep1 gene family has six new duplicates (indicated by red bars).
Mentions: To exclude false positives from the 266 candidates, we carried out Southern hybridizations and conducted BLAST searches against the available genome sequences of D. simulans (droSim1), D. yakuba (droYak1), D. sechellia (droSec1), D. melanogaster (dm2) and D. erecta (droEre1) (http://genome.ucsc.edu) (Figure 1). The Southern and BLAST analyses confirmed 17 young duplicates generated through DLR (Table 1; Figure 2). The genomic sequences of all 17 dispersed duplicates contain the intron(s) and/or non-coding flanking sequences that exist in their parental copies, suggesting that the new genes originated through DLR. In addition, we also identified ten new copies of retrogenes and 53 young copies of REs including retroelements and other repetitive sequences. In this report, we have focused on the 17 dispersed duplicates and investigate possible DLR mechanisms that generate dispersed duplications.

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