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A New Retroposed Gene in Drosophila Heterochromatin Detected by Microarray-Based Comparative Genomic Hybridization

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Abstract

A genomic pattern of new gene origination is often dependent on a genomic method that can efficiently identify a statistically adequate number of recently originated genes. The heterochromatic regions have often been viewed as genomic deserts with low coding potential and thus a low flux of new genes. However, increasing reports revealed unexpected roles of heterochromatic regions in the evolution of genes and genomes. We identified recently retroposed genes that originated in heterochromatic regions in Drosophila, by developing microarray-based comparative genomic hybridization (CGH) with multiple species. This new gene family, named Ifc-2h, originated in the common ancestor of the clade of D. simulans, D. mauritiana, and D. sechellia. The sequence features and phylogenetic distribution indicated that Ifc-2h resulted from the retroposition from its parental gene, Infertile crescent (Ifc), and integrated into heterochromatic region of common ancester of the three sibling species 2 million years ago. Expression analysis revealed that Ifc-2h had developed a new expression pattern by recruiting a putative regulatory element from its target sequence. The distribution of indel variation in Ifc-2h of D. simulans and D. mauritiana revealed a significant sequence constraint, suggesting that the Ifc-2h gene may be functional. These analyses cast fresh insight into the evolution of heterochromatin and the origin of its coding regions.

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Acknowledgments

The authors thank a number of people (Chung-I Wu, Jerry Coyne, Peter Andolfatto, and Eviatar Nevo) for provision of fly strains; Xinmin Li for performance of the microarray hybridization; members of the Long laboratory for valuable discussions and inputs, particularly, J. J. Emerson and Ying Chen for data analyses and Janice Spofford and Roman Arguello for critical reading of the manuscript; Gerald Wyckoff for discussion about the evolution of the fibronectin gene; and two anonymous reviewers for their suggestions, especially for the interpretation of the detected biased spectrum of polymorphisms. This work was supported by NIH and NSF grants to M.L.

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  1. Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL, 60637, USA

    Chuanzhu Fan & Manyuan Long

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  1. Chuanzhu Fan
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  2. Manyuan Long
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Correspondence to Manyuan Long.

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[Reviewing Editor: Dr. Martin Kreitman]

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Fan, C., Long, M. A New Retroposed Gene in Drosophila Heterochromatin Detected by Microarray-Based Comparative Genomic Hybridization. J Mol Evol 64, 272–283 (2007). https://doi.org/10.1007/s00239-006-0169-9

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