My overall research interest is to understand how the biodiversity on earth has evolved and the molecular mechanisms creating biological traits that are important in evolution, medicine, agriculture, biofuel production, and environmental protection. I take a holistic approach to address these questions, combining data at molecular, genomic, cellular, developmental, and ecological/environmental levels. And I employ both experimental and computational methods in my research.
Microbial Genomics for the Study of Evolution, Biofuel, and Environmental Protection
The origin of eukaryotes is a major evolutionary event in the history of life. It is commonly assumed that all eukaryotes (including all plants) have the same origin through endosymbiosis. However, evidences are still needed to test this hypothesis. I use a comparative genomic approach to address this question. In particular, I focus on the great diversity of microscopic prokaryotes and eukaryotes that have not been extensively studied or are yet to be discovered. They may elucidate the origin and early evolution of eukaryotes, particularly on the evolution of multicellularity, sexual reproduction, and important genetic, biochemical, and developmental pathways.
Many microbes play fundamental roles in ecosystems by decomposing biomacromolecules found for example in plant tissues or petroleum, which in turn could be used for biofuel production and bioremediation. I am studying microbes that can be used for such purposes, particularly in order to identify the biochemical pathways and the underlying genetic elements for degrading cellulose, lignin, and other macromolecules through genomic analysis.
Speciation & Plant and Animal Domestication
How new species evolved has been a major question in evolutionary biology. I have used DNA sequence data from multiple loci across the nuclear genome, as well as mitochondrial gene, to examine the evolutionary relationship among the sibling taxa within the maggot fly Rhagoletis pomonella species complex, a textbook model for sympatric speciation. Surprisingly, my study revealed that allopatric speciation (with geographic isolation), together with ecological differentiation and chromosomal rearrangements, have played very important roles in the divergence of this species complex (see publications below). In a separate study with yeasts, I found sexual adhesins, i.e., proteins localized on the cell surface and used to "hook up" different mating types of yeast cells, have evolved much more rapidly than other types of proteins, thus promoting reproductive isolation between previously closely related organisms. Interestingly, some of the reproductive proteins in yeasts is similar to those proteins involved in fertilization process in animals, including humans. Even more surprisingly, these reproductive proteins across yeasts and animals even have similar structures. I continue to be interested in studying the genetic mechanisms of reproductive isolation across different organisms, with its medical implication to human infertility in mind.
Plant and animal domestication is a special case of speciation with the intervention of humans. It gave rise to agriculture and set in motion human civilization. It has also been used by Charles Darwin as an analogous example to show how natural selection could shape species in nature. Asian domesticated rice feeds about half of the world's population and is one of the most important crop plants for humans. I use population genetics methods to study how natural selection shapes genomic evolution during rice domestication, in which we have elucidated the evolutionary history of Asian domesticated rice and identified genomic regions that have been shaped by selection during the domestication process (see publication below). I am interested in further studying the genetic differentiation between the two major varieties of cultivated rice and the history and mechanism of plant and animal domestication in general.
Integrated -Omics and Systems Biology for the Study of Biology, Medicine, and Evolution
To fully understand the mechanism producing new phenotypes in evolution and new traits important for agriculture and diseases, we have to integrate the genomic, epigenomic, transcriptomic, proteomic, metabolic, and environmental data with a systems biological approach. In collaboration with others, I have been studying how the differentiation at various molecular levels between domesticated and wild rice has contributed to the phenotypic divergence between them (see publication below). I am interested in extending this integrated -omic approach to study human diseases like cancers. From an evolutionary systems biological perspective, another ongoing project of mine examines how the genes/proteins across the yeast genome have evolved and what genomic factors or biological processes determine the different evolutionary rates found in different genes/proteins.
Protein Evolution and Structural Biology: Get to the Bottom
Most biological functions that produce traits important for evolution, diseases, agriculture, or environment at the end depend on how proteins interact with each other or with small molecules, which in turn depend on the structure of the proteins and other molecules. From an evolutionary perspective, I am very interested in how all the different types of proteins have originated and evolved. At structural biological level, I am interested in how the particular structure of a certain protein serves its function and affects its evolution. One of my ongoing projects is to look at what proteins in human can form amyloid, which causes Parkinson's, Alzheimer's, and other neurodegenerative diseases, and how exactly this occurs at structural level.
Bioinformatics: Indispensable Tools
None of the above research could be done without appropriate bioinformatic tools. I am interested in developing statistical and computational methods used for population genetics, phylogenetics, comparative genomics, and systems biology analysis.
If you are interested in joining my research group or developing research collaborations, or have any question or comment, please feel free to contact me!
Li, X., J. Zhu, F. Hu, S. Ge, M. Ye, H. Xiang, G. Zhang, X. Zheng, H. Zhang, S. Zhang, Q. Li, R. Luo, C. Yu, J. Yu, J. Sun, X. Zou, X. Cao, X. Xie*, J. Wang*, W. Wang*. 2012. Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. BMC Genomics13, 300. [read the paper]
Xie, X.*, J. Molina, R. Hernandez, A. Reynolds, A.R. Boyko, C.D. Bustamante, and M. Purugganan. 2011. Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection. PLoS One 6, e20670. [read the paper]
Xie, X.*, W. Qiu, and P. Lipke. 2011. Accelerated and adaptive evolution of yeast sexual adhesins. Molecular Biology and Evolution 28, 3127-3137. [read the paper]
Xie, X.* and P. Lipke. 2010. The evolution of fungal and yeast cell walls. Yeast 27, 479-488. [read the paper]
Xie, X., A. P. Michel, D. Schwarz, J. Rull, S. Velez, A. A. Forbes, M. Aluja, and J. Feder*. 2008. Radiation and divergence in the Rhagoletis pomonella species complex: Inferences from DNA sequence data. Journal of Evolutionary Biology 21, 900-913. [read the paper]
Xie, X., J. Rull, S. Velez, A. Forbes, A. P. Michel, S. Velez, A. A. Forbes, N. Lobo, M. Aluja, and J. Feder*. 2007. Hawthorn-infesting populations of Rhagoletis pomonella in Mexico and speciation mode plurality. Evolution 61, 1091-1105. [read the paper]
Feder, J.L.*, X. Xie, J. Rull, S. Velez, A. Forbes, B. Leung, H. Dambroski, K. Filchak, and M. Aluja. 2005. Mayr, Dobzhansky and Bush: A golden braid of biogeography, inversions, differential introgression, clines, and sympatric speciation? Proceedings of the National Academy of Sciences USA 102, 6573-6580. [read the paper]
* Corresponding author