Evolution & Comparative Genomics
Team leader: Jun Li, Guojie Zhang, Xun Xu
We are interested on different topics in phylogenetics, molecular evolution and comparative genomics, including:
1.Phylogeography and intraspecific phylogenetics
2.Detection of signature of selection from comparative or population data
4.Development of relative bioinformatics tools and website
5.Relative algorithms design and improvement
1) Artificial selection during rice domestication project.
Domestication involves a series of profound genetic changes resulting from selection that make a wild species more amenable for cultivation and consumption by humans. There are lots of traits such as grain size, shape, color, fragrance and amylase content which distinguish modern rice varieties from their wild ancestor. Our rice domestication project will make effort to identify and catalog genes and functional regions which may result in these traits among different rice populations. To achieve these, we need to identify the regions with low SNP incidence (which we call SNP desert) and regions with high SNP incidence (which we can call SNP forest), and then map these regions to the traits data such as gene linkage-disequilibrium. In addition to some cultivation traits association loci which have lots of benefits for breeding, we can also get the clear answer for the history of the rice domestication from the project.
2) Searching functional element from recent selection signal
Natural selection has strongly influenced recent human evolution; by scanning the entire human genome in search of genetic variations we may detect the genome regions that have been targets of natural selection. The functions of these regions may help us to understand the recent evolution of human.
3) Adaptive evolution on phylogenetic branches
The project has three primary goals: (1) determine the best method for detecting adaptive evolution by testing against previously characterized biochemical pathways, (2) design improved methods of adaptive evolution detection, and (3) create a comprehensive database of these results.
4) De novo sequencing of D. albomicans.
We wish to find the evidence chromosomes fusion and illustrated the pattern of stepwise chromosome evolution.
5) Detecting genome structure variation
There are many forms of variation, including insertion, deletion, tandem duplication, reversion and segmental duplication, forming and altering the structure of chromosomes. We are developing a tool to detect these variations without any prior knowledge.