Research Topics
Genomes and Genes | Manyuan LongSummaryAffiliation: University of Chicago Country: USA Publications
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Publications
The rapid generation of chimerical genes expanding protein diversity in zebrafishBeide Fu
Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P R China
BMC Genomics 11:657. 2010..Retroposition, as a special type of gene duplication- the RNA-based duplication, has been found to play an important role in new gene evolution in mammals and plants, but little is known about the process in the teleostei genome...- Positive selection for the male functionality of a co-retroposed gene in the hominoidsYong Zhang
Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, 100871, PR China
BMC Evol Biol 9:252. 2009..However, understanding of the origination and biological function of PIPSL requires determination of the coding potential of this gene as well as the evolutionary forces acting on its hominoid copies... 
The origin of new genes: glimpses from the young and oldManyuan Long
Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, Illinois 60637, USA
Nat Rev Genet 4:865-75. 2003....- Nucleotide variation and recombination along the fourth chromosome in Drosophila simulansWen Wang
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
Genetics 166:1783-94. 2004..melanogaster. Finally, estimates of the recombination parameters are shown to support a crossover-plus-conversion model... 
Evolution of enzymatic activities of testis-specific short-chain dehydrogenase/reductase in DrosophilaJianming Zhang
Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
J Mol Evol 71:241-9. 2010..Our results lend support to a general mechanism for the evolution of a new enzyme, in which catalytic chemistry evolves first followed by diversification of substrate utilization...- Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogasterJ J Emerson
Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
Science 320:1629-31. 2008..Among duplications, those overlapping exons or introns, as well as those falling on the X chromosome, seem to be subject to stronger purifying selection... - New genes in Drosophila quickly become essentialSidi Chen
Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
Science 330:1682-5. 2010..Lethality was attributed to diverse cellular and developmental defects, such as organ formation and patterning defects. These data suggest that new genes frequently and rapidly evolve essential functions and participate in development... - Origin of new genes: evidence from experimental and computational analysesManyuan Long
Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
Genetica 118:171-82. 2003..Both findings are consistent with the requirements for the molecular process of exon shuffling. Thus, these non-vertebrate genomes may have also been strongly impacted by exon shuffling in general... - Evolving protein functional diversity in new genes of DrosophilaJianming Zhang
Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
Proc Natl Acad Sci U S A 101:16246-50. 2004..These data suggest that protein functional diversity can expand rapidly under the joint forces of exon shuffling, gene duplication, and natural selection... - Extensive gene traffic on the mammalian X chromosomeJ J Emerson
Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
Science 303:537-40. 2004..Such export is incompatible with mutational bias and is likely driven by natural selection to attain male germline function. However, the excess recruitment is consistent with a combination of both natural selection and mutational bias... - Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the X chromosomeYong E Zhang
Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
PLoS Biol 8:. 2010..These two findings cast new light on the evolutionary history of the mammalian X chromosome in terms of gene gain, sequence, and expressional evolution... - A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genesYong E Zhang
Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA
Bioinformatics 27:1749-53. 2011..Here, we examined the alternative possibility that intronless genes could be generated by partial DNA-based duplication of intron-containing genes in the fruitfly genome... - Recurrent tandem gene duplication gave rise to functionally divergent genes in DrosophilaChuanzhu Fan
Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA
Mol Biol Evol 25:1451-8. 2008..Biased polymorphism frequency spectrum, linkage disequilibrium, nucleotide substitution, and McDonald-Kreitman analyses suggested that the evolution of CG6999 and CG32706 were driven by positive Darwinian selection... - Adaptive evolution of the insulin two-gene system in mouseMeng Shin Shiao
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
Genetics 178:1683-91. 2008..Our data suggest an adaptive divergence in the mouse insulin two-gene system, which may result from the response to environmental change caused by the rise of agricultural civilization, as proposed by the thrifty-genotype hypothesis... - Origination of an X-linked testes chimeric gene by illegitimate recombination in DrosophilaJ Roman Arguello
Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA
PLoS Genet 2:e77. 2006..Following speciation of the D. simulans complex, this novel gene evolved lineage-specifically with evidence for positive selection acting along the D. simulans branch... - Retrogenes moved out of the z chromosome in the silkwormJun Wang
Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
J Mol Evol 74:113-26. 2012..These properties of gene traffic in the ZW system suggest a general role for the heterogamety of sex chromosomes in determining the chromosomal locations and the evolution of sex-biased genes... - Recombination yet inefficient selection along the Drosophila melanogaster subgroup's fourth chromosomeJ Roman Arguello
Committee on Evolutionary Biology, University of Chicago, Chicago, IL, USA
Mol Biol Evol 27:848-61. 2010..The signatures of relaxed constraint can be detected at both the level of polymorphism and divergence... - Direct evidence for postmeiotic transcription during Drosophila melanogaster spermatogenesisMaria D Vibranovski
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, 60637, USA
Genetics 186:431-3. 2010..These results strengthen the newly emerging notion that postmeiotic transcription is dynamic and integral to the overall process of spermatogenesis... - Age-dependent chromosomal distribution of male-biased genes in DrosophilaYong E Zhang
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
Genome Res 20:1526-33. 2010.... - Origins of new male germ-line functions from X-derived autosomal retrogenes in the mouseMeng Shin Shiao
Department of Ecology and Evolution, University of Chicago, USA
Mol Biol Evol 24:2242-53. 2007.... - Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selectionESTHER BETRAN
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
Genetics 164:977-88. 2003..We discuss the possibility that the action of positive selection in Dntf-2r is related to its putative male-specific functions... - Reshaping of global gene expression networks and sex-biased gene expression by integration of a young geneSidi Chen
Department of Ecology and Evolution, The University of Chicago, IL, USA
EMBO J 31:2798-809. 2012..These data demonstrate, for the first time, how a new gene quickly evolved novel networks governing essential biological processes at the genomic level... - Retroposed new genes out of the X in DrosophilaESTHER BETRAN
Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637, USA
Genome Res 12:1854-9. 2002..These observations may be explained by natural selection favoring those new retrogenes that moved to autosomes and avoided the spermatogenesis X inactivation, and suggest the important role of genome position for the origin of new genes... - Stage-specific expression profiling of Drosophila spermatogenesis suggests that meiotic sex chromosome inactivation drives genomic relocation of testis-expressed genesMaria D Vibranovski
Department of Ecology, The University of Chicago, Chicago, Illinois, United States of America
PLoS Genet 5:e1000731. 2009..These results suggest MSCI as a general mechanism affecting the evolution of some testis-expressed genes... - The evolution of courtship behaviors through the origination of a new gene in DrosophilaHongzheng Dai
Committee on Genetics, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
Proc Natl Acad Sci U S A 105:7478-83. 2008..melanogaster. D. melanogaster therefore seems to have evolved in its courtship behaviors by the recruitment of a new chimeric gene... - Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selectionAna Llopart
Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
Proc Natl Acad Sci U S A 99:8121-6. 2002..Forward simulations suggest that the intensity of this selection is weak to moderate, roughly equal to the selection intensity on most replacement mutations in Drosophila... - Translational effects of differential codon usage among intragenic domains of new genes in DrosophilaJianming Zhang
Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
Biochim Biophys Acta 1728:135-42. 2005..The in vitro expression of jgw further demonstrated that the heterogeneous distribution of rare codons has played a role in regulating gene expression, particularly, affecting the quality of protein translation... - A new retroposed gene in Drosophila heterochromatin detected by microarray-based comparative genomic hybridizationChuanzhu Fan
Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
J Mol Evol 64:272-83. 2007..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... - Segmental dataset and whole body expression data do not support the hypothesis that non-random movement is an intrinsic property of Drosophila retrogenesMaria D Vibranovski
Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
BMC Evol Biol 12:169. 2012..These observations led the authors to suggest that selective forces (such as meiotic sex chromosome inactivation and sexual antagonism) were not responsible for the observed pattern of retrogene movement out of the X chromosome... - General gene movement off the X chromosome in the Drosophila genusMaria D Vibranovski
Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
Genome Res 19:897-903. 2009..These analyses of both DNA-based and RNA-based gene relocations reveal that the out-of-the-X movement of testis-expressed genes is a general pattern in the Drosophila genus... - Expansion of genome coding regions by acquisition of new genesESTHER BETRAN
Department of Ecology and Evolution, The University of Chicago, IL 60637, USA
Genetica 115:65-80. 2002..Despite this, the correlation between complexity of life and gene number is low and closely related species (with very similar life histories) can have very different number of genes. We call this phenomenon the G-value paradox... - Retrogene movement within- and between-chromosomes in the evolution of Drosophila genomesHongzheng Dai
Committee on Genetics, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA
Gene 385:96-102. 2006..Analyses of a large expression database for D. melanogaster genes revealed that the vast majority of the X-derived autosomal retroposed genes had evolved testis expression functions, consistent with other previous genomic analyses... - Re-analysis of the larval testis data on meiotic sex chromosome inactivation revealed evidence for tissue-specific gene expression related to the drosophila X chromosomeMaria D Vibranovski
Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
BMC Biol 10:49. 2012..abstract:.. - Adaptive evolution and the birth of CTCF binding sites in the Drosophila genomeXiaochun Ni
Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
PLoS Biol 10:e1001420. 2012..Our data indicate that binding of Drosophila CTCF protein has evolved under natural selection, and CTCF binding evolution has shaped both the evolution of gene expression and genome evolution during the birth of new genes... - Tight junction-associated MARVEL proteins marveld3, tricellulin, and occludin have distinct but overlapping functionsDavid R Raleigh
Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
Mol Biol Cell 21:1200-13. 2010..The data further suggest that these proteins are best considered as a group with both redundant and unique contributions to epithelial function and tight junction regulation... - Mutational bias shaping fly copy number variation: implications for genome evolutionMargarida M Cardoso-Moreira
Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
Trends Genet 26:243-7. 2010.... - Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate geneESTHER BETRAN
Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
Mol Biol Evol 19:654-63. 2002..PGAM3 is located in a region of very low recombination; therefore, it is conceivable that the rapid fixation events in this newly arising gene may have contributed to a selective sweep of variation in the region... - Frequent recent origination of brain genes shaped the evolution of foraging behavior in DrosophilaSidi Chen
Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
Cell Rep 1:118-32. 2012..Our data suggest that during adaptive evolution, new genes gain expression in specific brain structures and evolve new functions in neural circuits, which might contribute to the phenotypic evolution of animal behavior... - Accelerated recruitment of new brain development genes into the human genomeYong E Zhang
Department of Ecology and Evolution, The University of Chicago, Illinois, United States of America
PLoS Biol 9:e1001179. 2011..These data demonstrate a striking recruitment of new genes into the early development of the human brain... - Nucleotide variation along the Drosophila melanogaster fourth chromosomeWen Wang
Department of Ecology and Evolution, Committee on Genetics, University of Chicago, 1101 East 57 Street, Chicago, IL 60637, USA
Science 295:134-7. 2002..Finally, contrary to the expectation of no recombination, we identified six recombination events within the chromosome. Thus, positive Darwinian selection and recombination have affected the evolution of this chromosome... - Origin of sphinx, a young chimeric RNA gene in Drosophila melanogasterWen Wang
Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
Proc Natl Acad Sci U S A 99:4448-53. 2002.... - Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosomeKevin Thornton
Committee on Genetics, University of Chicago
Mol Biol Evol 19:918-25. 2002..We also show that there is an excess of X-linked duplicates with low K(s), suggesting a larger proportion of relatively young duplicates on the D. melanogaster X chromosome relative to autosomes... - Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila speciesWen Wang
CAS Max Planck Junior Scientist Group, Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
Nat Genet 36:523-7. 2004..The mechanism underlying this process is gene duplication with subsequent partial degeneration... - Repetitive element-mediated recombination as a mechanism for new gene origination in DrosophilaShuang Yang
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
PLoS Genet 4:e3. 2008..Our dataset strongly suggests an important role for REs in the generation of chimeric genes within these species... - Sex chromosomes and male functions: where do new genes go?ESTHER BETRAN
Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
Cell Cycle 3:873-5. 2004..As a result, future work elucidating sex chromosome differentiation by other mutational mechanisms will shed light on this important process... - Excess of amino acid substitutions relative to polymorphism between X-linked duplications in Drosophila melanogasterKevin Thornton
Department of Ecology and Evolution and the Committee on Genetiecs, University of Chicago, USA
Mol Biol Evol 22:273-84. 2005..In contrast, available data from autosomal duplicates show a deficit of fixations, consistent with gene conversion being a strong homogenizing force... - Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolutionLadeana W Hillier
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Nature 432:695-716. 2004..The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture... - Evolution of genes and genomes on the Drosophila phylogenyAndrew G Clark
Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
Nature 450:203-18. 2007..These may prove to underlie differences in the ecology and behaviour of these diverse species... - An intronic signal for alternative splicing in the human genomeNecat Havlioglu
Department of Pathology, Saint Louis University, St Louis, Missouri, United States of America
PLoS ONE 2:e1246. 2007..Together, these results suggest that the In100-like elements represent a family of intronic signals for alternative splicing in the human genome... - High rate of chimeric gene origination by retroposition in plant genomesWen Wang
CAS Max Plank Junior Research Group, Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
Plant Cell 18:1791-802. 2006..These observations suggest that retroposition is an important mechanism that governs gene evolution in rice and other grass species...