My overall research interest is to understand the mechanisms creating biodiversity and specific 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.
Comparative Study of Genomic Evolution
Horizontal (lateral) gene transfer has been suggested to be a very important process in the early evolution of all three domains of life. However, how prevalent HGT has been and what genes have been transferred laterally remain unclear. Furthermore, how HGT has contributed to the functional evolution of various lineages remain largely unanswered. I use a comparative genomic approach to address these questions, particularly by focusing on the great diversity of microscopic prokaryotes and eukaryotes that have not been extensively studied or are yet to be discovered.
Different genes within the same genome often evolve at different rates. Using an evolutionary systems biological approach, I am studying 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.
Metagenomics Study of Microbiomes In Relation to Human Health and Biofuel Production
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.
Similary, the microbial communities in/on human body also plays very important roles in human health. Using comparative metagenomic analyses, I am interested in studying the effects of diet, living environment, and genetic heritage on the microbiomic composition in human digestive system and how it in turn affect human health.
Cancer research has long been focused on genetic mutations. However, epigenetic changes caused by environmental factors are more likely to be under the occurence of cancers. Using an integrated genomic approach, we are currently studying how environmental pollutants could cause epigenetic changes leading to cancer.
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.
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.
To fully understand the mechanism producing new phenotypes in evolution and new traits important for agriculture and diseases, we need 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 other crop plants.
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.
Project Director, Establish Next-Generation Sequencing Facility at VSU, DoD Instrumentation Grant ($486K)
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 2, 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
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