De novo Gene Origination: Evidence, Read and Pattern

[Release time]:2019-04-25  [Hits]:2087

Speaker:Prof. Manyuan LONG

Time:March 17, 2019, 9:30am
Location:Shuhua Multi-functional Hall
Host: Zheng YUAN

Edna K. Paazian Distinguished Service Professor, The University of Chicago Department of Ecology and Evolution 1101 East 57th Street, Chicago, IL 60637(

About speaker:

Manyuan LONG is a tenure professor at the University of Chicago.With many publications in Sciences, Nature and Cell. he is an internationally renowned bioinformatician and the founder of research on Origin of New Genes. Prof. Long is currently a guest reviewer of the National Natural Science Award of the State Council and the key projects of the National Natural Science Foundation of China, member of the project review team of US National Science Foundation (NSF) and US National Institutes of Health (NIH) , and Canadian, Austrian, Irish Evolution and Genome Fundamental Research expert group member and guest reviewer.

Prof. Long also serves as the deputy editor of Journal of Molecular Evolution, editor of Biology Direct and other five international journals. He is a guest reviewer of Nature, Science and PNAS.


An interesting problem in evolutionary biology is how genes with novel functions originate. The research in my laboratory focuses on this problem, although we are also interested in other issues of molecular evolution. Interest in evolutionary novelties can be traced back to the time of Darwin. However, studies of the origin and evolution of genes with new functions have only recently become possible and attracted increasing attention.

Although conceptual revolution is always what we wish to pursue, the available molecular techniques and rapidly expanded genome data from many organisms mean that searching for and characterizing new genes is no longer a formidable technical obstacle. Molecular and evolutionary studies have provided powerful analytical tools for the detection of the processes and mechanisms that underlie the origin of new genes. Two levels of questions about this process can be defined. First, at the level of individual new genes, what are the initial molecular mechanisms that generate new gene structures? Once a new gene arises in an individual genome in a natural population, how does it spread throughout an entire species to become fixed? And, how does the young gene subsequently evolve? Second, at the level of the genome, how often do new genes originate? If new gene formation is not a rare event, are there any patterns that underlie the process? And, what evolutionary and genetic mechanisms govern any such patterns?

I believe that an efficient approach to these questions is to examine young genes because their early processes of origination are directly observable. Pursuit of these problems requires an integrated approach incorporating molecular, genomic and population analyses. My lab applies such an approach to our studies. Using experimental and computational genomic analysis, we identified numerous new genes in Drosophila and mammalian genomes. Using molecular analysis, we revealed some important molecular evolutionary mechanisms responsible for their current gene structures. By evolutionary genetic analysis, we observed a significant role of the adaptive evolution in the determination of the fate of those new genes. Interesting patterns are observed associated with these new genes. We saw, we came, and we found....

Recent publications:

  1. Zhang L, Ren Y, Yang T, Li G, Chen J, Gschwend AR, Yu Y, Hou G, Zi J, Zhou R, Wen B, Zhang J, Chougule K, Wang M, Copetti D, Peng Z, Zhang C, Zhang Y, Ouyang Y, Wing RA, Liu S, Long M (2019) Rapid evolution of protein diversity by de novo origination in Oryza. Nature Ecology & Evolution DOI: 10.1038/s41559-019-0822-5.
  2. VanKuren NW and Long M, 2018. Gene duplicates resolving sexual conflict rapidly evolved essential gametogenesis functions. Nature Ecology & Evolution 2(4):705-712.
  3. Stein JC, Yu Y, Copetti D, ZwicklDJ, Zhang L, Zhang C , Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, Becker C, Kudrna D, Zhang J, Londono CEM, Song X, Lee S, Sanchez P, Zuccolo A, Ammiraju JSS, Talag J, Danowitz A, Rivera LF, Gschwend AR, Noutsos C, Wu CC, Kao SM, Zeng JW, Wei FJ, Zhao Q, Feng Q, El Baidouri M, Carpentier MC, Lasserre E, Cooke R, Rosa Farias DD, da Maia LC, Dos Santos RS, Nyberg KG, McNally KL, Mauleon R, Alexandrov N, Schmutz J, Flowers D, Fan C, Weigel D, Jena KK, Wicker T, Chen M, Han B, Henry R, Hsing YC, Kurata N, de Oliveira AC, Panaud O, Jackson SA, Machado CA, Sanderson MJ, Long M, Ware D and Wing RA, 2018. Sequence of 13 rice-related species unveils the Oryza pan-genome and the origin of genetic innovation. Nature Genetics 50, 285–296.
  4. Lee YCG, Yang Q, Chi W, Turkson SA, Du WA, Kemkemer C, Zeng Z-B, Long M, Zhuang X, 2017. Genetic architecture of natural variation underlying adult foraging behavior that is essential for survival of Drosophila melanogaster. Genome Biol & Evol 9(5):1357-1369
  5. Long M and Emerson JJ, 2017. The Gene Traffic in Evolution: the Compensational Role for the Meiotic Sex Chromosome Inactivation in Mammals. Current Biology 27 (11): R659-R661
  6. Chen Z, Oliver B, Gao G and Long M, 2017. Expressed Structurally Stable Inverted Duplicates in Mammalian Genomes as Functional Noncoding Elements. Genome Biol & Evol 9 (4): 981-992
  7. Zhang W, Landback P, Gschwend AR, Shen B and Long M (2015). New genes drive the evolution of gene interaction networks in the human and mouse genomes. Genome Biology, 16:202.
  8. Zhang C, Gschwend RA, Ouyang Y, Long M (2014). Evolution of gene structural complexity: An alternative-splicing based model accounts for intron-containing retrogenes, Plant Physiology 165(1):412-23.
  9.  Gao G, Vibranovski MD, Zhang L, Li Z, Liu M, Zhang YE, Li X, Zhang W, Fan Q, Vankuren NW, Long M, Wei L, 2014. A long term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster. Genome Res 24(4):629-38.

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