Won Cheol Yim


Photo of Won Cheol Yim
Won Yim at the University of Nevada, Reno

Assistant Professor

Department of Biochemistry and Molecular Biology
University of Nevada/Mail Stop 330
1664 N. Virginia Street
Reno,  Nevada   89557

Office: (775) 682-9447
Lab: 682-9448

Cell: 775-229-0453

Email: wyim@unr.edu
Building: Howard Medical Science,  Office 216
Personal Web: https://www.plantbioinformatics.org/
 
 
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EDUCATION
B.S. Dongguk University, Seoul, Korea, 2006
M.S. Dongguk University, Seoul, Korea, 2008
Ph.D. Dongguk University, Seoul, Korea, 2012

ACADEMIC & RESEARCH INTEREST

Recent advance in genomics are generating tremendous amounts of data. As a result, the field of bioinformatics confronts an unprecedented need to move towards greater interdisciplinary to better interpret and understand these data. The goal of our research is to understand the molecular underpinnings of various plant adaptations to semi-arid and arid environments through genomics-enabled bioinformatics approaches. Our research focuses broadly on comparative genomics and gene expression from the perspectives of genomics, systems biology, and bioinformatics. We propose to undertake integrative approaches that span multiple levels of biological organization from the genome to the metabolome.

The Yim’s lab is worked on plant genomics, studying how genomes are organized and how genome structure affects gene expression, phenotypes, and genomic plasticity. We use of bioinformatics to address questions in plant diversity, with an emphasis on enabling crop improvement efforts though through diversification mechanisms associated with large scale genome duplications, while at the same time maintaining core functions. The major objectives of our lab include developing strategies for increased plant tolerance to harsh environments and increased biomass productivity through understanding the basis of polyploidy and genome conformation in plants.

Our on-going research projects include de novo assembly and analysis of multiple genomes and transcriptomes. We participate in a variety of open source software development projects and in other efforts to facilitate data sharing and improving adherence to standards among groups involved in information resource management in plant biology.

Lastly, our lab seeks to illuminate the processes regulating development, metabolomics, protein structure, evolution analysis and photosynthesis and will enable future attempts to characterize gene function in plants, insects and vertebrates.

AWARDS, HONORS, & PROFESSIONAL RECOGNITION

  • 2012 Distinguished Ph.D. Student Award, Dongguk University, Seoul, Korea Rep.
  • 2010 Plant bioinformatics course - Hands-on training at the EMBL-EBI, Hinxton, Cambridge, U.K.
  • 2010 Transcriptomics and related tools from the EBI - School of Biological Science, University of Cambridge, U.K.
  • 2009 Distinguished Paper Award & Scholarship, Dongguk University, Seoul, Korea Rep.
  • 2008 Distinguished Paper Award & Scholarship, Dongguk University, Seoul, Korea Rep.
  • 2008 University Scholarship, Dongguk University, Seoul, Korea Rep.
  • 2007 Best Oral Presentation Award, The Korean Society of Breeding Science, Korea Rep.
  • 2007 University Chancellor’s Scholarship, Dongguk University, Seoul, Korea Rep.
  • 2006 University Scholarship, Dongguk University, Seoul, Korea Rep.

REPRESENTATIVE PUBLICATIONS

Journals
Crassulacean Acid Metabolism Abiotic Stress-Responsive Transcription Factors: a Potential Genetic Engineering Approach for Improving Crop Tolerance to Abiotic Stress Amin AB, Rathnayake KN, Yim WC, Garcia TM, Wone B, Cushman JC, Wone BWM 2019, Front Plant Sci. 2019; 10: 129.
The bracteatus pineapple genome and domestication of clonally propagated crops. Chen L-Y, VanBuren R, Paris M, Zhou H, Zhang X, Wai CM, Yan H, Chen S, Along M, Ramakrishnan S, Liao Z, Liu J, Lin J, Yue J, Fatima M, Lin Z, Zhang J, Juang L, Wang H, Hwa T-Y, Kao S-M, Choi JY, Sharma A, Song J, Wang H, Yim WC, Cushman JC, Paull RE, Matsumoto T, Qin Y, Wu Q, Wang J, Yu Q, Wu J, Zhang S, Boches P, Tung C-W, Wang M-L, d’Eckenbrugge GC, Sanewski GM, Purrugganan MD, Schatz MC, Bennetzen JL, Lexer C, Ming R. 2019, Nature Genetics. 51: 1549–1558
Biology and chemistry of an Umbravirus-like 2989 bp single-stranded RNA as a possible causal agent for Opuntia stunting disease (engrosamiente de cladidios) – A review Felker P, Bunch R, Russo G, Preston K, Tine JA, Suter B, Mo X, Cushman JC, Yim WC 2019, Journal of the Professional Association for Cactus Development. 21: 1–31.
Evolution of l-DOPA 4,5-dioxygenase activity allows for recurrent specialisation to betalain pigmentation in Caryophyllales
The evolution of l-DOPA 4,5-dioxygenase activity, encoded by the gene DODA, was a key step in the origin of betalain biosynthesis in Caryophyllales. We previously proposed that l-DOPA 4,5-dioxygenase activity evolved via a single Caryophyllales-specific neofunctionalisation event within the DODA gene lineage. However, this neofunctionalisation event has not been confirmed and the DODA gene lineage exhibits numerous gene duplication events, whose evolutionary significance is unclear. To address this, we functionally characterised 23 distinct DODA proteins for l-DOPA 4,5-dioxygenase activity, from four betalain-pigmented and five anthocyanin-pigmented species, representing key evolutionary transitions across Caryophyllales. By mapping these functional data to an updated DODA phylogeny, we then explored the evolution of l-DOPA 4,5-dioxygenase activity. We find that low l-DOPA 4,5-dioxygenase activity is distributed across the DODA gene lineage. In this context, repeated gene duplication events within the DODA gene lineage give rise to polyphyletic occurrences of elevated l-DOPA 4,5-dioxygenase activity, accompanied by convergent shifts in key functional residues and distinct genomic patterns of micro-synteny. In the context of an updated organismal phylogeny and newly inferred pigment reconstructions, we argue that repeated convergent acquisition of elevated l-DOPA 4,5-dioxygenase activity is consistent with recurrent specialisation to betalain synthesis in Caryophyllales.
Sheehan H, Feng T, Walker-Hale N, Lopez-Nieves S, Pucker B, Guo R, Yim WC, Badgami R, Timoneda A, Zhao L, Tiley H, Copetti D, Sanderson MJ, Cushman JC, Moore MJ, Smith SA, Brockington SF 2019, New Phytologist 01 August 2019 https://doi.org/10.1111/nph.16089
Mitochondrial haplotypes are not associated with mice selectively bred for high voluntary wheel running
Mitochondrial haplotypes have been associated with human and rodent phenotypes, including nonshivering thermogenesis capacity, learning capability, and disease risk. Although the mammalian mitochondrial D-loop is highly polymorphic, D-loops in laboratory mice are identical, and variation occurs elsewhere mainly between nucleotides 9820 and 9830. Part of this region codes for the tRNAArg gene and is associated with mitochondrial densities and number of mtDNA copies. We hypothesized that the capacity for high levels of voluntary wheel-running behavior would be associated with mitochondrial haplotype. Here, we analyzed the mtDNA polymorphic region in mice from each of four replicate lines selectively bred for 54 generations for high voluntary wheel running (HR) and from four control lines (Control) randomly bred for 54 generations. Sequencing the polymorphic region revealed a variable number of adenine repeats. Single nucleotide polymorphisms (SNPs) varied from 2 to 3 adenine insertions, resulting in three haplotypes. We found significant genetic differentiations between the HR and Control groups (Fst?=?0.779, p?=?0.0001), as well as among the replicate lines of mice within groups (Fsc?=?0.757, p?=?0.0001). Haplotypes, however, were not strongly associated with voluntary wheel running (revolutions run per day), nor with either body mass or litter size. This system provides a useful experimental model to dissect the physiological processes linking mitochondrial, genomic SNPs, epigenetics, or nuclear-mitochondrial cross-talk to exercise activity.
Wone BWM, Yim WC, Schutz H, Meek TH, Garland T 2019, Mitochondrion Volume 46, May 2019, Pages 134-139
Identification of Genes Encoding Enzymes Catalyzing the Early Steps of Carrot Polyacetylene Biosynthesis Busta L, Yim WC, LaBrant EW, Wang P, Grimes L, Malyszka K, Cushman JC, Santos P, Kosma DK, Cahoon EB 2018, Plant Physiology December 2018
A Vitis vinifera basic helix–loop–helix transcription factor enhances plant cell size, vegetative biomass and reproductive yield Lim SD, Yim WC, Liu D, Hu R, Yang X, Cushman JC 2018, Plant Biotechnology Journal 09 March 2018
Mitochondrial haplotypes are not associated with mice selectively bred for high voluntary wheel running. Wone BWM, Yim WC, Schutz H, Meek TH, Garland Jr T. 2018, Mitochondrion. doi:10.1016/j.mito.2018.04.002
Draft Nuclear Genome Sequence of the Halophilic and Beta-Carotene-Accumulating Green Alga Dunaliella salina Strain CCAP19/1. Polle JEW, Barry K, Cushman JC, Schmutz J, Tran D, Hathwaik LT, Yim WC, Jenkins J, McKie-Krisberg Z, Prochnik S, Lindquist S, Dockter R, Adam C, Molina H, Bunkenborg J, Jin ES, Buchheim M, Magnuson J. 2017, Genome Announcements doi:10.1128/genomeA.01105-17
Expression of Heat Shock Proteins by Heat Stress in Soybean. Song K, Yim WC, Lee B-M. 2017, Plant Breed. Biotech. 5(4):344~353 doi:10.9787/PBB.2017.5.4.344
Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple. Wai CM, VanBuren R, Zhang J, Huang L, Miao W, Edger P, Yim WC, Priest HD, Meyers BC, Mockler T, Smith JAC, Cushman JC, Ming R 2017, The Plant Journal DOI:10.1111/tpj.13630
The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism. Yang X, Hu R. Yin H, Jenkins J, Shu S, Tang H, Liu D, Weighill DA, Yim WC, Ha J, Heyduk K, Goodstein D, Gou HB, Moseley R, Fitzek E, Jawdy S, Zhang Z, Xie M, Hartwell J, Grimwood J, Abraham P, Mewalal R, Beltrán J, Boxall S, Denver L, Palla K, Albion R, Garcia T, Mayer J, Lim SD, Wai CM, Peluso P, VanBuren R, De Paoli H, Borland A, Guo H, Chen JG, Muchero W, Yin Y, Jacobson D, Tschaplinski T, Hettich R, Ming R, Winter K, Leebens-Mack K, Smith JAC, Cushman JC, Schmutz J, Tuskan G. 2017, Nature Communications doi:10.1038/s41467-017-01491-7
An rbcL mRNA binding protein is associated with C3 to C4 evolution and light-induced production of Rubisco in Flaveria. Yerramsetty PK, Agar EM, Yim WC, Cushman JC, Berry JO 2017, Journal of Experimental Botany DOI:10.1093/jxb/erx264
Divide and Conquer (DC) BLAST: Fast and easy BLAST execution within HPC environments. Yim WC, Cushman JC 2017, PeerJ. 5: e3486.
Sporobolus stapfianus: Insights into desiccation tolerance in the resurrection grasses from linking transcriptomics to metabolomics. Yobi A, Schlauch KA, Tillett RL, Yim WC, Espinoza C, Wone BWM, Cushman JC, Oliver MJ 2017, BMC Plant Biol doi: 10.1186/s12870-017-1013-7.
Identification of ice plant (Mesembryanthemum crystallinum L.) microRNAs using RNA-Seq and their putative roles in high salinity responses in seedlings. Chiang C, Yim WC, Sun Y, Ohnishi M, Mimura T, Cushman JC, Yen HE. 2016, Frontiers in Plant ScienceFront Plant Sci. doi: 10.3389/fpls.2016.01143
The pineapple genome and the evolution of CAM photosynthesis. Ming R, Van Buren R, Wai CM, Tang H, Schatz MC, Bowers, JE, Lyons E, Wang M-L, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, Ye Z, Miao C, Lin Z, Wang H, Zhou H, Yim WC, Priest HD, Zheng C, Woodhouse M, Edger PP, Guyot R, Guo H-B, Guo H, Zheng G, Singh R, Sharma A, Min X, Zheng Y, Lee H, Gurtowski J, Sedlazeck F, Harkess A, McKain MR, Liao Z, Fang J, Liu J, Zhang X, Zhang Q, Hu W, Yuan Q, Wang K, Chen L-Y, Shirley N, Lin Y-R, Liu L-Y, Hernandez AG, Wright CL, Bulone V, Tuskan GA 2016, Nature Genetics. 47: 1435–1442