 This site needs to be updated, but the email address is still valid. Please see http://www.biology.washington.edu/users/yaowu-yuan for the time being Yao-Wu Yuan I am a postdoc in Dr. Sue Wessler's lab at the University of Georgia (Athens, 2009-present), studying transposable elements of plants. Before that I was studying plant molecular systematics with Dr. Richard Olmstead at the University of Washington (Seattle, 2004-2008) as a graduate student. And before that I was studying everything (or nothing) towards a Bachelor degree at Sichuan University (Chengdu, China, 2000-2004). Even before that I was playing in the muddy rice paddies and vegetable gardens in a remote agricultural area in central China for 17 years, without a single clue that I was going to study science. It was the numerous field trips in the magnificent mountains of Southwestern China (Sichuan and Yunnan) during the early undergraduate years that stimulated my unflagging love for nature and deep curiosity for the great diversity of plant forms, especially flower color and shape. This curiosity has been gradually transformed into a long-term professional interest over the past several years: Diversity of flower color and shape –– Patterns, Processes, and Consequences.
Brief overview of my past and ongoing work
Plant systematics/phylogenetics: My past work focused on plant molecular systematics. While mainly working in Dr. Richard Olmstead's lab at the University of Washington, I have improved or established phylogenetic frameworks for a few plant groups, including the tribe Hyoscyameae of Solanaceae (Yuan et al., 2006, in collaboration with Drs. Zhiyun Zhang and Zhiduan Chen in China), the Verbena complex and the family Verbenaceae (Yuan and Olmstead, 2008a; 2008b; Yuan et al., 2010a), and the genus Clerodendrum and allies of Lamiaceae (Yuan et al., 2010b, in collaboration with Dr. David Mabberley). Based on these phylogenetic frameworks, we were able to make inferences on various historical events, including an ancient hybrid origin of belladonna (Atropa belladonna), independent intergeneric chloroplast transfers in the Verbena complex, and shift of floral presentation and mating system in Clerodendrum and its relatives. Perhaps more significantly, with an undergraduate student and other folks in the Olmstead lab, I have developed a useful toolkit (over 120 PPR gene loci, Yuan et al., 2009; 2010a) that can be utilized to help resolve phylogenetic relationships of almost all angiosperm groups at various taxonomic levels. Relevant to my long-term interest, this toolkit will be of great value in studying evolutionary patterns of natural variation in flower color and shape found in innumerable plant groups.
Transposable elements and dynamics of plant genomes: With a strong side interest in transposable elements (TEs) and the realization that skills in utilizing the burgeoning resources in OMICS (e.g., genome, proteome, transcriptome, etc.) will be extremely helpful to address questions in essentially all biological disciplines, I decided to take a short detour to study TEs and the dynamics of plant genomes in Dr. Sue Wessler's lab (2009-present). In the past year, I have annotated all the transposable elements in the genome of Mimulus guttatus, as part of the Mimulus genome project led by Dr. John Willis (Duke University). I am interested in studying Mimulus TEs for two major reasons –– (1) The contribution of TEs to gene and genome evolution is interesting in its own right. With a complete set of representative sequences of all TE families from the sequenced M. guttatus IM62 inbred line, we will be able to conduct an extensive comparative genomic analysis on the 10 more inbred lines that have been or are being re-sequenced by next-generation sequencing platforms. The comparison of TE diversity, abundance, and distribution on such a scale will generate a colorful picture of dynamics of TEs as well as their host genomes on a population level, which may provide initial evidence for the potential role of TEs in diversification of genomes and phenotypes. (2) Identifying active TEs (particular "cut and paste" DNA TEs) will facilitate gene isolation by transposon tagging. Active TEs have played an important role in gene isolation from various model plants (e.g., maize, snapdragon, etc.). I have been hoping to find an active TE system in the M. guttatus genome that is suitable for transposon tagging, and consequently to move the genetics of Mimulus forward. This is of great relevance to my long-term interest, because Mimulus, with its myriad diversity in flower color and shape, is a superb system to study the processes (i.e., genetics or/and epigenetic basis and developmental process) that generate flower color and shape variations and the consequences of these variations (e.g., reproductive isolation between M. lewisii and M. cardinalis).
Resequencing the rice HEG4 strain: More recently, I have been analyzing ultra-high throughput sequence data (generated by the Illumina platform) of the rice HEG4 strain, where a particular miniature inverted transposable element (MITE), mPing, has been amplified from ~50 to ~1, 000 copies in the past ~100 years (Naito et al., 2006 PNAS 103:17620-17625; Naito et al., 2009 Nature 461:1130-1134). Using both reference-based and de novo assembly, I am hoping to produce a relatively well assembled HEG4 genome. Through genome alignment of HEG4 and the publicly available Nipponbare genome, we will be able to detect essentially all structural variation (variation caused by the mPing activity, in particular) between the two genomes that have diverged for only ~100 years. In so doing, we can watch for the first time how a particular TE is altering genome structure in a largely selfing species in real-time.  Selected Publications (for a complete list see my CV) Yuan, Y. W., S. R. Wessler. 2011. The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies. Proceedings of the National Academy of Sciences, U.S.A. doi/10.1073/pnas.1104208108. Yuan, Y. W., D. J. Mabberley, D. A. Steane, R. G. Olmstead. 2010. Further disintegration and redefinition of Clerodendrum (Lamiaceae): Implications for the understanding of the evolution of an intriguing breeding strategy. Taxon. 59 (1): 125-133. Yuan, Y. W., C. Liu, H. E. Marx, R. G. Olmstead. 2010. An empirical demonstration of using pentatricopeptide repeat (PPR) genes as plant phylogenetics tools: Phylogeny of Verbenaceae and the Verbena complex. Molecular Phylogenetics and Evolution. 54: 23-35. Yuan, Y. W. , C. Liu, H. E. Marx, R. G. Olmstead. 2009. The pentatricopeptide repeat (PPR) gene family, a tremendous resource for plant phylogenetic studies. New Phytologist. 182: 272-283. Yuan, Y. W., R. G. Olmstead. 2008. Evolution and phylogenetic utility of the PHOT gene duplicates in the Verbena complex (Verbenaceae): dramatic intron size variation and footprint of ancestral recombination. American Journal of Botany. 95:1166-1176. Yuan, Y. W., R. G. Olmstead. 2008. A species-level phylogenetic study of the Verbena complex (Verbenaceae) indicates two independent Intergeneric chloroplast transfers. Molecular Phylogenetics and Evolution. 48:23-33. Yuan, Y. W., Z. Y. Zhang, Z. D. Chen, R. G. Olmstead. 2006. Tracking ancient polyploids: A retroposon insertion reveals an extinct diploid ancestor in the polyploid origin of Belladonna. Molecular Biology and Evolution. 23:2263-2267. |
