MANYUAN NO LONG

Summary

Affiliation: University of Chicago
Country: USA

Publications

  1. pmc An intronic signal for alternative splicing in the human genome
    Necat Havlioglu
    Department of Pathology, Saint Louis University, St Louis, Missouri, United States of America
    PLoS ONE 2:e1246. 2007
  2. pmc Stage-specific expression profiling of Drosophila spermatogenesis suggests that meiotic sex chromosome inactivation drives genomic relocation of testis-expressed genes
    Maria D Vibranovski
    Department of Ecology, The University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 5:e1000731. 2009
  3. pmc Deficiency of X-linked inverted duplicates with male-biased expression and the underlying evolutionary mechanisms in the Drosophila genome
    Zhen Xia Chen
    Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, PR China
    Mol Biol Evol 28:2823-32. 2011
  4. pmc Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster
    Zheng Li
    Center of Developmental Biology and Genetics, School of Life Sciences, Peking University, Beijing, China
    Nucleic Acids Res 37:4308-14. 2009
  5. ncbi request reprint Origin of new genes: evidence from experimental and computational analyses
    Manyuan Long
    Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    Genetica 118:171-82. 2003
  6. ncbi request reprint Association of intron phases with conservation at splice site sequences and evolution of spliceosomal introns
    M Long
    Department of Ecology and Evolution, University of Chicago, Illinois 60637, USA
    Mol Biol Evol 16:1528-34. 1999
  7. ncbi request reprint Evolution of novel genes
    M Long
    Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago Illinois 60637, USA
    Curr Opin Genet Dev 11:673-80. 2001
  8. ncbi request reprint Testing the "proto-splice sites" model of intron origin: evidence from analysis of intron phase correlations
    M Long
    Department of Ecology and Evolution, University of Chicago, Illinois 60637, USA
    Mol Biol Evol 17:1789-96. 2000
  9. ncbi request reprint A new function evolved from gene fusion
    M Long
    Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 10:1655-7. 2000
  10. ncbi request reprint Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila
    M Long
    Department of Ecology and Evolution, The University of Chicago, IL 60637, USA
    Gene 238:135-41. 1999

Detail Information

Publications41

  1. pmc An intronic signal for alternative splicing in the human genome
    Necat 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...
  2. pmc Stage-specific expression profiling of Drosophila spermatogenesis suggests that meiotic sex chromosome inactivation drives genomic relocation of testis-expressed genes
    Maria 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...
  3. pmc Deficiency of X-linked inverted duplicates with male-biased expression and the underlying evolutionary mechanisms in the Drosophila genome
    Zhen Xia Chen
    Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, PR China
    Mol Biol Evol 28:2823-32. 2011
    ..These analyses suggest that a selection-driven process, rather than a purely neutral mutation-driven mechanism, contributes to the maintenance of IDs in the Drosophila genome...
  4. pmc Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster
    Zheng Li
    Center of Developmental Biology and Genetics, School of Life Sciences, Peking University, Beijing, China
    Nucleic Acids Res 37:4308-14. 2009
    ..We measured false positive rates for the analyzed genomic approaches including the RT-PCR and tiling array method...
  5. ncbi request reprint Origin of new genes: evidence from experimental and computational analyses
    Manyuan 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...
  6. ncbi request reprint Association of intron phases with conservation at splice site sequences and evolution of spliceosomal introns
    M Long
    Department of Ecology and Evolution, University of Chicago, Illinois 60637, USA
    Mol Biol Evol 16:1528-34. 1999
    ....
  7. ncbi request reprint Evolution of novel genes
    M Long
    Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago Illinois 60637, USA
    Curr Opin Genet Dev 11:673-80. 2001
    ..New genes in humans and our primate relatives add a new component to the understanding of genetic divergence between humans and non-humans...
  8. ncbi request reprint Testing the "proto-splice sites" model of intron origin: evidence from analysis of intron phase correlations
    M Long
    Department of Ecology and Evolution, University of Chicago, Illinois 60637, USA
    Mol Biol Evol 17:1789-96. 2000
    ..Thus, these results reject the null hypothesis that introns are randomly inserted into preexisting proto-splice sites, as suggested by the insertional theory of introns...
  9. ncbi request reprint A new function evolved from gene fusion
    M Long
    Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 10:1655-7. 2000
  10. ncbi request reprint Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila
    M Long
    Department of Ecology and Evolution, The University of Chicago, IL 60637, USA
    Gene 238:135-41. 1999
    ..Thus, the 5' exons/introns originated from a previously existing gene that provided new modules with specific sub-function to create jgw...
  11. pmc Evolving protein functional diversity in new genes of Drosophila
    Jianming 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...
  12. pmc Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selection
    Ana 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...
  13. ncbi request reprint Nucleotide variation along the Drosophila melanogaster fourth chromosome
    Wen 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...
  14. ncbi request reprint Excess of amino acid substitutions relative to polymorphism between X-linked duplications in Drosophila melanogaster
    Kevin 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...
  15. pmc Recurrent tandem gene duplication gave rise to functionally divergent genes in Drosophila
    Chuanzhu 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...
  16. ncbi request reprint Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster
    J 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...
  17. ncbi request reprint Translational effects of differential codon usage among intragenic domains of new genes in Drosophila
    Jianming 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...
  18. ncbi request reprint Extensive gene traffic on the mammalian X chromosome
    J 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...
  19. ncbi request reprint Expansion of genome coding regions by acquisition of new genes
    ESTHER 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...
  20. ncbi request reprint The origin of new genes: glimpses from the young and old
    Manyuan 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
    ....
  21. ncbi request reprint A new retroposed gene in Drosophila heterochromatin detected by microarray-based comparative genomic hybridization
    Chuanzhu 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...
  22. pmc Mutational bias shaping fly copy number variation: implications for genome evolution
    Margarida M Cardoso-Moreira
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Trends Genet 26:243-7. 2010
    ....
  23. pmc Retroposed new genes out of the X in Drosophila
    ESTHER 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...
  24. pmc Origination of an X-linked testes chimeric gene by illegitimate recombination in Drosophila
    J 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...
  25. pmc General gene movement off the X chromosome in the Drosophila genus
    Maria 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...
  26. ncbi request reprint Origins of new male germ-line functions from X-derived autosomal retrogenes in the mouse
    Meng Shin Shiao
    Department of Ecology and Evolution, University of Chicago, USA
    Mol Biol Evol 24:2242-53. 2007
    ....
  27. ncbi request reprint Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene
    ESTHER 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...
  28. pmc Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection
    ESTHER 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...
  29. ncbi request reprint Retrogene movement within- and between-chromosomes in the evolution of Drosophila genomes
    Hongzheng 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...
  30. pmc Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster
    Wen 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
    ....
  31. pmc Recombination yet inefficient selection along the Drosophila melanogaster subgroup's fourth chromosome
    J 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...
  32. pmc Nucleotide variation and recombination along the fourth chromosome in Drosophila simulans
    Wen 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...
  33. pmc The evolution of courtship behaviors through the origination of a new gene in Drosophila
    Hongzheng 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...
  34. pmc Adaptive evolution of the insulin two-gene system in mouse
    Meng 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...
  35. ncbi request reprint Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome
    Kevin 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...
  36. ncbi request reprint 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...
  37. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew 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...
  38. ncbi request reprint Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species
    Wen 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...
  39. pmc Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila
    Shuang 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...
  40. pmc High rate of chimeric gene origination by retroposition in plant genomes
    Wen 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...

Research Grants10

  1. Variation of D. melanogaster chromosome 4
    Manyuan Long; Fiscal Year: 2003
    ..These studies should add significantly to the understanding of the evolutionary genetics of the Drosophila fourth chromosome. ..
  2. Detection of Distribution of New Genes in Drosophila Phylogeny
    MANYUAN NO LONG; Fiscal Year: 2010
    ..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. ..
  3. Detection of Distribution of New Genes in Drosophila Phylogeny
    Manyuan Long; Fiscal Year: 2009
    ..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. ..
  4. Detection of Distribution of New Genes in Drosophila Phylogeny
    Manyuan Long; Fiscal Year: 2007
    ..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. ..
  5. Variation of D. melanogaster chromosome 4
    Manyuan Long; Fiscal Year: 2006
    ..These studies should add significantly to the understanding of the evolutionary genetics of the Drosophila fourth chromosome. ..
  6. Variation of D. melanogaster chromosome 4
    Manyuan Long; Fiscal Year: 2005
    ..These studies should add significantly to the understanding of the evolutionary genetics of the Drosophila fourth chromosome. ..
  7. Variation of D. melanogaster chromosome 4
    Manyuan Long; Fiscal Year: 2005
    ..These studies should add significantly to the understanding of the evolutionary genetics of the Drosophila fourth chromosome. ..
  8. Variation of D. melanogaster chromosome 4
    Manyuan Long; Fiscal Year: 2004
    ..These studies should add significantly to the understanding of the evolutionary genetics of the Drosophila fourth chromosome. ..
  9. Detection of Distribution of New Genes in Drosophila Phylogeny
    Manyuan Long; Fiscal Year: 2009
    ..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. ..