Xiaohan Yang

Xiaohan Yang

Xiaohan Yang

Senior Staff Scientist

Bio

Dr. Xiaohan Yang is a Senior Research and Development Staff Member in the Plant Systems Biology Group in the Biosciences Division at Oak Ridge National Laboratory (ORNL). His education covers a wide range of subjects including Forest Science (B.S.; Huazhong Agricultural University, China), Ornamental Botany (M.S.; Huazhong Agricultural University, China) and Horticulture/Plant Molecular Biology/Plant Breeding (Ph.D.; Cornell University, Ithaca, NY). He has five years of postdoc training in the areas of molecular genetics and plant genomics at Cornell University, University of Tennessee and ORNL.

Crassulacean acid metabolism (CAM) is a biological innovation that allows plants to thrive in water-limited environments such as arid deserts and areas with a pronounced seasonal drought. The water-use efficiency of CAM plants is much higher than that of C3 and C4 plants. Transferring CAM machinery into existing crops holds tremendous potential for sustainable production of food and biomass on semi-arid, marginal, or degraded agricultural lands. Dr. Yang leads a research team at ORNL to engineer CAM using Synthetic Biology approach for the purpose of improving water-use efficiency of bioenergy feedstocks. Dr. Yang’s team develops new tools for synthetic biology research, such as high-throughput assembly of various DNA parts into genetic circuits, precise temporal control of plant gene expression using optogenetics approaches, and in-planta stacking of a large number of genes into a single genomic locus. Also, Dr. Yang has extensive experience in plant genomics research. He leads the effort to sequence the genomes of two important CAM models (Agave and Kalanchoe) and performs studies on the plant small proteins and non-coding RNAs involved in the interactions with microbes.

Awards

2008    Distinguished Achievement Award for Post-Graduate Research in Environmental Science (In recognition of outstanding early career productivity, ability to collaborate effectively in a team setting, and ability to integrate bioinformatics and molecular biology to gain novel insights into evolutionary genomics).

2000    Liu Memorial Award in recognition of his excellent progress and high potential for a successful academic career.

Projects

  • Engineering CAM photosynthetic machinery into bioenergy crops for biofuels production in marginal environments
  • Gene atlas for Kalanchoë laxiflora, an obligate crassulacean acid metabolism (CAM) model for genetic improvement of water-use efficiency in bioenergy feedstocks
  • High quality genome sequencing of Agave tequilana, a bioenergy crop with high drought tolerance and low biomass recalcitrance
  • Leveraging the TNT-cloning system potential
  • Establishment of optogenetics capabilities for manipulation of gene expression in plants
  • Plant–Microbe Interfaces
  • The Center for Bioenergy Innovation (CBI)

Publications

Selected from a total of 79

Liu D, Palla KJ, Hu R, Moseley RC, Mendoza C, Chen M, Abraham PE, Labbé JL, Kalluri UC, Tschaplinski TJ, Cushman JC, Borland AM, Tuskan GA, Yang X. 2018. Perspectives on the basic and applied aspects of crassulacean acid metabolism (CAM) research. Plant Science 274: 394-401

Biswal AK, Atmodjo MA, Li M, Baxter HL, Yoo CG, Pu Y, Lee Y-C, Mazarei M, Black IM, Zhang J-Y, Ramanna H, Bray AL, King ZR, LaFayette PR, Pattathil S, Donohoe BS, Mohanty SS, Ryno D, Yee K, Thompson OA, Rodriguez Jr M, Dumitrache A, Natzke J, Winkeler K, Collins C, Yang X, Tan L, Sykes RW, Gjersing EL, Ziebell A, Turner GB, Decker SR, Hahn MG, Davison BH, Udvardi MK, Mielenz JR, Davis MF, Nelson RS, Parrott WA, Ragauskas AJ, Neal Stewart Jr C, Mohnen D. 2018. Sugar release and growth of biofuel crops are improved by downregulation of pectin biosynthesis. Nature Biotechnology doi:10.1038/nbt.4067.

Plett JM, Yin H, Mewalal R, Hu R, Li T, Ranjan P, Jawdy S, De Paoli HC, Butler G, Burch-Smith TM, Guo H-B, Ju Chen C, Kohler A, Anderson IC, Labbé JL, Martin F, Tuskan GA, Yang X. 2017. Populus trichocarpa encodes small, effector-like secreted proteins that are highly induced during mutualistic symbiosis. Scientific Reports 7: 382.

Yang X, Hu R, Yin H, Jenkins J, Shu S, Tang H, Liu D, Weighill DA, Cheol Yim W, Ha J, Heyduk K, Goodstein DM, Guo H-B, Moseley RC, Fitzek E, Jawdy S, Zhang Z, Xie M, Hartwell J, Grimwood J, Abraham PE, Mewalal R, Beltrán JD, Boxall SF, Dever LV, Palla KJ, Albion R, Garcia T, Mayer JA, Don Lim S, Man Wai C, Peluso P, Van Buren R, De Paoli HC, Borland AM, Guo H, Chen J-G, Muchero W, Yin Y, Jacobson DA, Tschaplinski TJ, Hettich RL, Ming R, Winter K, Leebens-Mack JH, Smith JAC, Cushman JC, Schmutz J, Tuskan GA. 2017. The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism. Nature Communications 8: 1899.

Abraham PE, Yin H, Borland AM, Weighill D, Lim SD, De Paoli HC, Engle N, Jones PC, Agh R, Weston DJ, Wullschleger SD, Tschaplinski T, Jacobson D, Cushman JC, Hettich RL, Tuskan GA, Yang X. 2016. Transcript, protein and metabolite temporal dynamics in the CAM plant Agave. Nature Plants 2: 16178.

De Paoli HC, Tuskan GA, Yang X. 2016. An innovative platform for quick and flexible joining of assorted DNA fragments. Scientific Reports 6: 19278.

Liu D, Hu R, Palla KJ, Tuskan GA, Yang X. 2016. Advances and perspectives on the use of CRISPR/Cas9 systems in plant genomics research. Current Opinion in Plant Biology 30: 70-77.

Mielenz JR, Rodriguez M, Thompson OA, Yang X, Yin H. 2015. Development of Agave as a dedicated biomass source: production of biofuels from whole plants. Biotechnology for Biofuels 8: 79.

Ming R, VanBuren 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 FJ, Harkess A, McKain MR, Liao Z, Fang J, Liu J, Zhang X, Zhang Q, Hu W, Qin Y, Wang K, Chen L-Y, Shirley N, Lin Y-R, Liu L-Y, Hernandez AG, Wright CL, Bulone V, Tuskan GA, Heath K, Zee F, Moore PH, Sunkar R, Leebens-Mack JH, Mockler T, Bennetzen JL, Freeling M, Sankoff D, Paterson AH, Zhu X, Yang X, Smith JAC, Cushman JC, Paull RE, Yu Q. 2015. The pineapple genome and the evolution of CAM photosynthesis. Nature Genetics 47: 1435.

Yang X, Cushman JC, Borland AM, Edwards EJ, Wullschleger SD, Tuskan GA, Owen NA, Griffiths H, Smith JAC, De Paoli HC, Weston DJ, Cottingham R, Hartwell J, Davis SC, Silvera K, Ming R, Schlauch K, Abraham P, Stewart JR, Guo H-B, Albion R, Ha J, Lim SD, Wone BWM, Yim WC, Garcia T, Mayer JA, Petereit J, Nair SS, Casey E, Hettich RL, Ceusters J, Ranjan P, Palla KJ, Yin H, Reyes-García C, Andrade JL, Freschi L, Beltrán JD, Dever LV, Boxall SF, Waller J, Davies J, Bupphada P, Kadu N, Winter K, Sage RF, Aguilar CN, Schmutz J, Jenkins J, Holtum JAM. 2015. A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter, drier world. New Phytologist 207: 491-504.

De Paoli HC, Borland AM, Tuskan GA, Cushman JC, Yang X. 2014. Synthetic biology as it relates to CAM photosynthesis: challenges and opportunities. Journal of Experimental Botany 65: 3381-3393.

Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, Jenkins J, Lindquist E, Tice H, Bauer D, Goodstein DM, Dubchak I, Poliakov A, Mizrachi E, Kullan ARK, Hussey SG, Pinard D, van der Merwe K, Singh P, van Jaarsveld I, Silva-Junior OB, Togawa RC, Pappas MR, Faria DA, Sansaloni CP, Petroli CD, Yang X, Ranjan P, Tschaplinski TJ, Ye C-Y, Li T, Sterck L, Vanneste K, Murat F, Soler M, Clemente HS, Saidi N, Cassan-Wang H, Dunand C, Hefer CA, Bornberg-Bauer E, Kersting AR, Vining K, Amarasinghe V, Ranik M, Naithani S, Elser J, Boyd AE, Liston A, Spatafora JW, Dharmwardhana P, Raja R, Sullivan C, Romanel E, Alves-Ferreira M, Külheim C, Foley W, Carocha V, Paiva J, Kudrna D, Brommonschenkel SH, Pasquali G, Byrne M, Rigault P, Tibbits J, Spokevicius A, Jones RC, Steane DA, Vaillancourt RE, Potts BM, Joubert F, Barry K, Pappas GJ, Strauss SH, Jaiswal P, Grima-Pettenati J, Salse J, Van de Peer Y, Rokhsar DS, Schmutz J. 2014. The genome of Eucalyptus grandis. Nature 510: 356.

Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J, Jenkins J, Barry K, Lindquist E, Hellsten U, Deshpande S, Wang X, Wu X, Mitros T, Triplett J, Yang X, Ye C-Y, Mauro-Herrera M, Wang L, Li P, Sharma M, Sharma R, Ronald PC, Panaud O, Kellogg EA, Brutnell TP, Doust AN, Tuskan GA, Rokhsar D, Devos KM. 2012. Reference genome sequence of the model plant Setaria. Nature Biotechnology 30: 555.

Yang X, Tschaplinski TJ, Hurst GB, Jawdy S, Abraham PE, Lankford PK, Adams RM, Shah MB, Hettich RL, Lindquist E, Kalluri UC, Gunter LE, Pennacchio C, Tuskan GA. 2011. Discovery and annotation of small proteins using genomics, proteomics, and computational approaches. Genome Research 21: 634-641.

The International Brachypodium Initiative. 2010. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763.

 

Patents

Patent

Tuskan GA, Yang X, De Paoli HC. “TNT Cloning System”. (US Patent No.: 10,017,770 B2; Date of patent: July 10, 2018)

Pending patent

Chen J-G, Gunter LE, Jawdy SS, Yang X, Tuskan GA, Bryan AC, “Modulating laccase enzyme to regulate cell wall biosynthesis and recalcitrance in plants”. US Patent App. 15/647,819, 2018.

Chen J-G, Jawdy S, Yang X, Tuskan GA, Yang Y, Gunter LE. “PtDUF266 gene regulating cell wall biosynthesis and recalcitrance in Populus”. US Patent App. 15/687,818, 2018