Manyuan Long

Summary

Affiliation: University of Chicago
Country: USA

Publications

  1. 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
  2. pmc Accelerated recruitment of new brain development genes into the human genome
    Yong E Zhang
    Department of Ecology and Evolution, The University of Chicago, Illinois, United States of America
    PLoS Biol 9:e1001179. 2011
  3. pmc Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the X chromosome
    Yong E Zhang
    Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
    PLoS Biol 8:. 2010
  4. pmc Evolutionary patterns of RNA-based duplication in non-mammalian chordates
    Ming Chen
    Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People s Republic of China
    PLoS ONE 6:e21466. 2011
  5. doi request reprint New gene evolution: little did we know
    Manyuan Long
    Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637 email
    Annu Rev Genet 47:307-33. 2013
  6. pmc Positive selection for the male functionality of a co-retroposed gene in the hominoids
    Yong 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
  7. 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
  8. pmc Segmental dataset and whole body expression data do not support the hypothesis that non-random movement is an intrinsic property of Drosophila retrogenes
    Maria D Vibranovski
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    BMC Evol Biol 12:169. 2012
  9. doi request reprint Evolution of enzymatic activities of testis-specific short-chain dehydrogenase/reductase in Drosophila
    Jianming Zhang
    Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
    J Mol Evol 71:241-9. 2010
  10. 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

Collaborators

Detail Information

Publications58

  1. 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
    ....
  2. pmc Accelerated recruitment of new brain development genes into the human genome
    Yong 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...
  3. pmc Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the X chromosome
    Yong 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...
  4. pmc Evolutionary patterns of RNA-based duplication in non-mammalian chordates
    Ming Chen
    Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People s Republic of China
    PLoS ONE 6:e21466. 2011
    ..Taken together, our analyses demonstrate that RNA-based duplication generates many functional genes and can make a significant contribution to the evolution of non-mammalian genomes...
  5. doi request reprint New gene evolution: little did we know
    Manyuan Long
    Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637 email
    Annu Rev Genet 47:307-33. 2013
    ..We highlight findings showing that new genes rapidly change existing genetic systems that govern various molecular, cellular, and phenotypic functions. ..
  6. pmc Positive selection for the male functionality of a co-retroposed gene in the hominoids
    Yong 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...
  7. 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...
  8. pmc Segmental dataset and whole body expression data do not support the hypothesis that non-random movement is an intrinsic property of Drosophila retrogenes
    Maria 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...
  9. doi request reprint Evolution of enzymatic activities of testis-specific short-chain dehydrogenase/reductase in Drosophila
    Jianming 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...
  10. 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...
  11. pmc Adaptive evolution and the birth of CTCF binding sites in the Drosophila genome
    Xiaochun 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...
  12. 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...
  13. pmc Highly tissue specific expression of Sphinx supports its male courtship related role in Drosophila melanogaster
    Ying Chen
    Committee on Genetics, University of Chicago, Chicago, Illinois, United States of America
    PLoS ONE 6:e18853. 2011
    ....
  14. doi request reprint New genes in Drosophila quickly become essential
    Sidi 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...
  15. 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...
  16. 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...
  17. 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...
  18. pmc Age-dependent chromosomal distribution of male-biased genes in Drosophila
    Yong E Zhang
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 20:1526-33. 2010
    ....
  19. doi request reprint Frequent recent origination of brain genes shaped the evolution of foraging behavior in Drosophila
    Sidi 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...
  20. 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...
  21. 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...
  22. pmc A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes
    Yong 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...
  23. pmc The rapid generation of chimerical genes expanding protein diversity in zebrafish
    Beide 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...
  24. 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...
  25. pmc Reshaping of global gene expression networks and sex-biased gene expression by integration of a young gene
    Sidi 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...
  26. 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...
  27. doi request reprint New genes as drivers of phenotypic evolution
    Sidi Chen
    1 Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, Illinois 60637, USA 2 Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
    Nat Rev Genet 14:645-60. 2013
    ..The molecular underpinnings of how new genes can develop these roles are starting to be characterized. These recent discoveries yield fresh insights into our broad understanding of biological diversity at refined resolution. ..
  28. doi request reprint Retrogenes moved out of the z chromosome in the silkworm
    Jun 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...
  29. pmc Direct evidence for postmeiotic transcription during Drosophila melanogaster spermatogenesis
    Maria 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...
  30. 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...
  31. 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...
  32. 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
    ....
  33. 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...
  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. 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...
  36. 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...
  37. 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...
  38. 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...
  39. pmc High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences
    Chengjun Zhang
    Department of Ecology and Evolution, University of Chicago, USA
    Genome Biol Evol 5:1038-48. 2013
    ..The high rate of new gene origination and of chimeric gene formation in rice may demonstrate rice's broad diversification, domestication, its environmental adaptation, and the role of new genes in rice speciation...
  40. 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...
  41. 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...
  42. 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...
  43. ncbi request reprint gKaKs: the pipeline for genome-level Ka/Ks calculation
    Chengjun Zhang
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Bioinformatics 29:645-6. 2013
    ..Results from two methods are compatible. Availability and implementation: gKaKs is implemented in Perl and is freely available on http://longlab.uchicago.edu/?q=gKaKs. The detailed user manual is available on the website...
  44. pmc 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
    Maria 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:..
  45. 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
    ....
  46. pmc Tight junction-associated MARVEL proteins marveld3, tricellulin, and occludin have distinct but overlapping functions
    David 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...
  47. 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
    ....
  48. pmc Evolution of gene structural complexity: an alternative-splicing-based model accounts for intron-containing retrogenes
    Chengjun Zhang
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637
    Plant Physiol 165:412-23. 2014
    ..Given the prevalence of intron retention in plants, this new model gives a support that plant genomes have very complex gene structures. ..
  49. 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...
  50. 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...
  51. 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...
  52. 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...
  53. 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...
  54. 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...
  55. 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...
  56. 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...