Manyuan Long

A fundamental problem in evolutionary biology is how genes with novel functions originate. My research focuses on this problem, although I am also interested in other issues of molecular evolution. Molecular and evolutionary studies have provided powerful analytical tools for the detection of the processes and mechanisms that underlie the origin of new genes. We started from the following problems for research. 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? 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? Finally, what are functions and phenotyoes of new genes? An efficient approach to these questions is 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. 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 that control new gene origination. By evolutionary genetic analysis, we observed a significant role of the adaptive evolution in the determination of the fate of those new genes. New genes provide an excellent opportunity to study systems biology. By using experimental and computational genes-genes interaction analysis, we are investigating how new gene function links are added into gene networks thereby causing cellular functional systems to evolve globally. Using gene silencing analysis, we recently investigated behavioral evolution by new genes in Drosophila.

A fundamental problem in evolutionary biology is how genes with novel functions originate. My research focuses on this problem, although I am also interested in other issues of molecular evolution. Molecular and evolutionary studies have provided powerful analytical tools for the detection of the processes and mechanisms that underlie the origin of new genes. We started from the following problems for research. 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? 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? Finally, what are functions and phenotyoes of new genes? An efficient approach to these questions is 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. 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...

Betrán, E., K. Thornton, and M. Long 2002. Retroposed new genes out of the X in Drosophila Genome Res. 12: 1854-1859.  

Wang W, Thornton K, Berry A, Long M, 2002. Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science 295:134-137.   Evolution: Feel the fourth

Long M, Betran E, Thornton K, Wang W, 2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4: 865-875.   Young Genes

International Chicken Genome Sequencing Consortium. 2004, Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716. 

Emerson JJ, Kaessmann H, Betrán E, Long M, 2004. Extensive gene traffic on the human X chromosome. Science 303: 537-540.   Genome evolution: Escape Planet X

Zhang, J., A. M. Dean, F. Brunet and M. Long 2004. Evolving functional diversity in new genes of Drosophila. Proc Natl Acad Sci USA. 101: 16246 -16250 

Wang, W., H. Yu and M. Long 2004. Duplication-degeneration as a mechanism of gene fission and the origin of Drosophila new genes. Nature Genetics 36: 523 527.  

Arguello JR, Chen Y, Yang S, Wang W, and Long M, 2006. An X-linked Testes Chimeric Gene by Illegitimate Recombination in Drosophila. PLoS Genetics 2: 0745-0754. e77. 

Long M., 2007. Journal Club: Mystery Genes. Nature 449: 511.   De Novo Origination

Drosophila 12 Genomes Consortium, 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218. 

Yang S., Arguello R, Li X, Ding Y, Zhou Q, Chen Y, Zhang Y, Zhao R, Brunet F, Peng L, Long M, Wang W., 2008. Repetitive Elements-mediated Recombination as a Mechanism for New Gene Origination in Drosophila. PLoS Genetics 4: e3. 0001-0010.  Gene evolution: History repeats itself

Dai H, Chen Y, Chen S, Mao Q, Kennedy D, Landback P, Eyre-Walker A, Du D, Long M, 2008. The evolution of courtship behaviors through the origination of a new gene in Drosophila. Proc Natl Acad Sci USA. 105:7478-83. Epub 2008 May 27. 

Emerson JJ, Cardoso-Moreira M, Borevitz JO, Long M, 2008. Natural selection shapes genome wide patterns of copy number polymorphism in D. melanogaster. Science 2008 June 5. [Epub ahead of print].320:1629-1631.  GenomeWeb

Kaessmann H, Vinckenbosch1 N, & Long M, 2009. RNA-based gene duplication: mechanistic and evolutionary insights. Nature Reviews Genetics. 10, 19-31.   RNA-based duplication

Vibranovski MD, Zhang Y, Long M. 2009. General gene movement off the X chromosome in the Drosophila genus. Genome Res. 9:897-903.  

Betrán, E., K. Thornton, and M. Long 2002. Retroposed new genes out of the X in Drosophila Genome Res. 12: 1854-1859.  

Wang W, Thornton K, Berry A, Long M, 2002. Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science 295:134-137.   Evolution: Feel the fourth

Long M, Betran E, Thornton K, Wang W, 2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4: 865-875.   Young Genes

International Chicken Genome Sequencing Consortium. 2004, Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716. 

Emerson JJ, Kaessmann H, Betrán E, Long M, 2004. Extensive gene traffic on the human X chromosome. Science 303: 537-540.   Genome evolution: Escape Planet X