Postdoctoral Fellow

Gene evolution in genomic context: Integrating genomic location into gene evolution models

PI(s): Mira Han
Start Date: 1-Sep-2011
End Date: 24-Jul-2013
Keywords: genomics, comparative methods, computational modeling

One of the surprising discoveries we learned from the whole genome sequencing of multiple species was the extent of structural rearrangements between the genomes. Different evolutionary forces can shape the non-random organization of genes within a genome, and the physical location can in turn affect the fate of a gene. But even with the completion of several closely related genomes, the statistical modeling of genome rearrangements still appears to be a formidable task. I propose that a feasible approach to the problem is to start from the genes and study how homologous genes are created, clustered, and dispersed in the genome. By learning how each gene family is distributed in the genome, we can learn how whole genomes have come into shape. I plan to model the gene duplication, loss, and transpositions using the birth- death-migration (BDM) process developed in demography. By integrating the BDM process into existing models of gene family evolution, we will be able to infer the sequence substitutions, the duplications and losses, and the transpositions of genes simultaneously. The integrated model can infer correct reconciliations in cases where the sequence and gene tree alone is not informative, and it will also improve the identification of gene transpositions by utilizing the genetic distance between genes. More importantly, genome-wide identification of gene transpositions will offer insight into the non-random organization of genes within a genome.

Related products

Publications
  • Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3 Han, MV., GWC Thomas, J Lugo-Martinez, MW Hahn. 2013. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Molecular biology and evolution
  • Characterizing gene movements between chromosomes in Drosophila Mira V. Han. 2012, Characterizing gene movements between chromosomes in Drosophila, Fly, volume 6, issue 2, pp. 121-125
  • Genome sequence of the model medicinal mushroom Ganoderma lucidum Shilin Chen, Jiang Xu, Chang Liu, Yingjie Zhu, David R. Nelson, Shiguo Zhou, Chunfang Li, Lizhi Wang, Xu Guo, Yongzhen Sun, Hongmei Luo, Ying Li, Jingyuan Song, Bernard Henrissat, Anthony Levasseur, Jun Qian, Jianqin Li, Xiang Luo, Linchun Shi, Liu He, Li Xiang, Xiaolan Xu, Yunyun Niu, Qiushi Li, Mira V. Han, Haixia Yan, Jin Zhang, Haimei Chen, Aiping Lv, Zhen Wang, Mingzhu Liu, David C. Schwartz and Chao Sun. 2012, Genome sequence of the model medicinal mushroom Ganoderma lucidum, Nature Communications, volume 3, pp. 913
  • Inferring the History of Interchromosomal Gene Transposition in Drosophila Using n-Dimensional Parsimony M. V. Han and M. W. Hahn Inferring the History of Interchromosomal Gene Transposition in Drosophila Using n-Dimensional Parsimony, Genetics, volume 190, issue 2, pp. 813-825
Presentations
  • M. V. Han and M. W. Hahn, 1/23/2012, Gene transpositions in the Drosophila genome, Biology Department, College of Charleston