The objective of this research is to systematically study new genes in the Drosophila melanogaster subgroup and to investigate the tempo and mode of new gene originations. We will focus on the new chimerical genes created by RNA-involved retroposition that often evolve novel functions associated with the mosaic gene structures. To meet these objectives, the following four-prong integrated approaches will be pursued using the D. melanogaster subgroup as our model taxa. (1) Detection of New Genes by Genomic Analyses: Taking advantage of the known divergence times within the subgroup (0.5-12 million years (mys)), new gene detection will be based upon an interdisciplinary approach that integrates computational and experimental genomic analyses. Our computational analyses will utilize available genome sequences and work in conjunction with Fluorescence In Situ Hybridization with multiple species genomes (MFISH) and Comparative Genomic Hybridization (CGH) using DMA microarrays. These analyses will detect and provide new gene candidates on the genome-wide scale. (2) Inference of the Functionality of the New Genes: To infer functionality for these new genes we will examine the molecular evolutionary and transcriptional constraints of each new gene and their temporal-spatial expression patterns. Molecular evolution and population genetic analyses will be also conducted to detect adaptive evolution of new functional genes. (3) Analysis of phylogenetic Distribution of New Gene Originations: We will map all detected origination events of new genes on the phylogenetic tree of the melanogaster subgroup species. We will estimate the rate of new gene origination and its variation along branches of the phylogeny, using related statistical analyses including maximum likelihood approach. (4) Sex Chromosome-dependence of the Origination of New Genes: Taking advantage of the young ages of the identified new genes (between 0.5 and 12 mys), we will investigate whether or not the male gene traffic that we observed in ancient retrogene samples is an on- going process by analyzing the chromosomal location distribution of new genes and their parental genes. The results from these four categories of studies will generate the first phylogenetic distribution of new genes and provide the fresh-insight into the rates and patterns of new gene originations in genomes.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Genetic Variation and Evolution Study Section (GVE)
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Eckstrand, Irene A
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University of Chicago
Schools of Medicine
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Wang, Jun; Long, Manyuan; Vibranovski, Maria D (2012) Retrogenes moved out of the z chromosome in the silkworm. J Mol Evol 74:113-26
Chen, Sidi; Ni, Xiaochun; Krinsky, Benjamin H et al. (2012) Reshaping of global gene expression networks and sex-biased gene expression by integration of a young gene. EMBO J 31:2798-809
Chen, Sidi; Spletter, Maria; Ni, Xiaochun et al. (2012) Frequent recent origination of brain genes shaped the evolution of foraging behavior in Drosophila. Cell Rep 1:118-32
Vibranovski, Maria D; Zhang, Yong E; Kemkemer, Claus et al. (2012) Segmental dataset and whole body expression data do not support the hypothesis that non-random movement is an intrinsic property of Drosophila retrogenes. BMC Evol Biol 12:169
Vibranovski, Maria D; Zhang, Yong E; Kemkemer, Claus et al. (2012) Re-analysis of the larval testis data on meiotic sex chromosome inactivation revealed evidence for tissue-specific gene expression related to the drosophila X chromosome. BMC Biol 10:49; author reply 50
Chen, Sidi; Yang, Haiwang; Krinsky, Benjamin H et al. (2011) Roles of young serine-endopeptidase genes in survival and reproduction revealed rapid evolution of phenotypic effects at adult stages. Fly (Austin) 5:345-51
Zhang, Yong E; Vibranovski, Maria D; Krinsky, Benjamin H et al. (2011) A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes. Bioinformatics 27:1749-53
Zhang, Yong E; Landback, Patrick; Vibranovski, Maria D et al. (2011) Accelerated recruitment of new brain development genes into the human genome. PLoS Biol 9:e1001179
Chen, Zhen-Xia; Zhang, Yong E; Vibranovski, Maria et al. (2011) Deficiency of X-linked inverted duplicates with male-biased expression and the underlying evolutionary mechanisms in the Drosophila genome. Mol Biol Evol 28:2823-32
Chen, Ying; Dai, Hongzheng; Chen, Sidi et al. (2011) Highly tissue specific expression of Sphinx supports its male courtship related role in Drosophila melanogaster. PLoS One 6:e18853

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