Ning Jiang

Ning Jiang

Contact Me

Professor
Department of Horticulture

Phone:
517-353-0381

Email:

Degrees:
PhD

Quick links: Education    Publications    Research

Joined Department

August 2004

Appointment

90% Research 
10% Teaching

Education

Ph.D., Plant Biology, University of Georgia, 2002
M.S., Plant Physiology, Yangzhou University, China, 1986
B.S., Plant Physiology and Biochemistry, Nanjing University, China, 1983

Research Interest 

My primary research objective is to explore the function of transposable elements (TEs) in order to understand the forces underlying eukaryotic genome diversification. It now seems clear that each genome possesses a unique spectrum of transposable elements and a varying proportion of these are active. An open question is how this diversity of TEs influences the evolutionary trajectory of the genomes in which they reside. I use both computational and molecular biology-based approaches to address this question and to analyze the ever-increasing database of genomic sequence from multiple plant species.

Selected Publications

  • Cerbin S, Ou S, Li Y, Sun Y, Jiang N (2022): Distinct composition and amplification dynamics of transposable elements in sacred lotus (Nelumbo nucifera Gaertn.). Plant J 112:172-92.

  • Li Y, Jiang N, Sun Y (2022): AnnoSINE: a short interspersed nuclear elements annotation tool for plant genomes. Plant Physiol 2022, 188:955-70.

  • Planta J, Liang YY, Xin H, Chansler MT, Prather LA, Jiang N, Jiang J, Childs KL(2022): Chromosome-scale genome assemblies and annotations for Poales species Carex cristatella, Carex scoparia, Juncus effusus, and Juncus inflexus. G3 2022, 12.

  • Cerbin, S., Wai, C. M., VanBuren, R., Jiang, N. (2019) GingerRoot: A Novel DNA Transposon Encoding Integrase-Related Transposase in Plants and Animals. Genome Biol Evol 11 (11):3181-3193.

  • Ou, S., Jiang, N. (2019) LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons. Mob DNA 10:48.

  • Ou, S., Su W, Liao Y, Chougule K, Agda JRA, Hellinga AJ, Lugo CSB, Elliott TA, Ware D, Peterson T, Jiang N, Hirsch CN, Hufford MB (2019) Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol 20 (1):275.

  • Ou, S., Chen, J. and Jiang, N. (2018). Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Research. 46(21):e126.

  • Cerbin, S. and Jiang, N. (2018). Duplication of host genes by transposable elements. Current Opinion in Genetics & Development, 49:63–69.

  • Zhao, D., Hamilton, J. P., Vaillancourt, B., Zhang, W., Eizenga, G. C., Cui, Y., Jiang, J., Buell, C. R., and Jiang, N. (2018). The unique epigenetic features of Pack-MULEs and their impact on chromosomal base composition and expression spectrum. Nucleic Acids Research, 46(5):2380-2397.

  • Ou, S., and Jiang, N. (2018). LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. Plant Physiology, 176(2), 1410-1422.

  • Zhao, D., Hamilton, J. P., Hardigan, M., Yin, D., He, T., Vaillancourt, B., Reynoso, M, Pauluzzi, G.D., Funkhouser, S.,Cui, Y., Bailey-Serres, J., Jiang, J. C., Buell, C.R.,and Jiang, N. 2017. Analysis of ribosome-associated mRNAs in rice reveals the importance of transcript size and GC content in translation. G3, 7:203-219.

  • Kang, H., Zhu, D., Lin, R., Opiyo, S.O., Jiang, N., Shiu, S.H., and Wang, G.L. 2016. A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads. DNA Research, 23(3), 241–251.

  • Zhao, D., Ferguson, A. A., & Jiang, N. 2016. What makes up plant genomes: The vanishing line between transposable elements and genes. Biochimica et biophysica acta (BBA)- Gene Regulatory Mechanisms, 1859(2), 366-380.

  • Zhao, D., Ferguson, A. E., & Jiang, N. 2015. Transposition of a Rice Mutator-Like Element in the Yeast Saccharomyces cerevisiae. Plant cell. 27(1), 132-48.

  • Law, M., Childs, K. L., Campbell, M. S., Stein, J. C., Olson, A. J., Holt, C., Panchy, N., Lei, J., Jiao, D., Andorf, C. M., Lawrence, C. J., Ware, D., Shiu, S., Sun, Y., Jiang, N., & Yandell, M. 2015. Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes. Plant physiology. 167(1), 25-39.

  • Zhao, D., Jiang, N. 2014. Nested Insertions and Accumulation of Indels are Negatively Correlated with Abundance of Mutator-Like Transposable Elements in Maize and Rice. PLoS ONE 9 (1): e87069.

  • Xu, Y., Jiang, N., Zou, Z., Tu, Z., Chen, A., Zhao, Q., Xiang, Z., and He, N. 2014. Retrotransposon "Qian" mediated segmental duplication in silkworm, Bombyx mori, Insect Biochem Mol Biol 46, 9-16.

  • Campbell, M. S., Law, M., Holt, C., Stein, J. C., Moghe, G. D., Hunagel, D. E., Lei, J., Achawanantakun, R., Jiao, D., Lawrence, C. J., Ware, D., Shiu, S-H., Childs, K. L., Sun, Y., Jiang, N, Yandell, M. 2014. MAKER-P: a tool-kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiology.164 513-524.

  • Ferguson, A., Zhao, D., and Jiang, N. 2013. Selective acquisition and retention of genomic sequences by Pack-MULEs based on GC content and breadth of expression. Plant Physiology. 163, 1419-1432.

  • Ferguson, A. A., Jiang, N. 2012. Mutator-like elements with multiple long terminal inverted repeats (TIR) in plants. Comparative and Functional Genomics. 2012.

  • Ferguson, A. A., Jiang, N. 2011. Pack-MULEs: recycling and reshaping genes through GC-biased acquisition.Mobile Genetic Elements 1:135-138.

  • Jiang, N., Ferguson, A. A., Slotkin, R. K., Lisch, D. 2011. Pack-Mutator-like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition. Proc Natl Acad Sci USA  108:1537-1542.

  • Ammiraju J.S., Fan C., Yu Y., Song X., Cranston K.A., Pontaroli A.C., Lu F., Sanyal A., Jiang N., Rambo T., Currie J., Collura K., Talag J., Bennetzen J.L., Chen M., Jackson S., Wing R.A. 2010. Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza. Plant J. 63:430-442.

  • Zhang, H., Liang, W., Yang, X., Luo, X., Jiang, N., Ma, H., Zhang, D. 2010. Carbon Starved Anther (CSA) Encoding a MYB Domain Protein Regulates Sugar Partitioning Required for Rice Pollen Development. Plant Cell  22(3):672-89.

  • Tsukamoto, T., Hauck, N.R., Tao, R., Jiang, N. and Iezzoni A.F. 2010. Molecular and Genetic Analyses of Four Non-Functional S Haplotype Variants Derived from a Common Ancestral S Haplotype Identified in Sour Cherry (Prunus cerasus L.) Genetics  184 (2):411-27.

  • Gao, D., Gill, N., Kim, H.R., Walling, J.G., Zhang, W., Fan, C., Yu, Y., Ma, J., Sanmiguel, P., Jiang, N., Cheng, Z., Wing, R.A., Jiang, J.and Jackson, S.A. 2009. A lineage-specific centromere retrotransposon in Oryza brachyantha. Plant J. 60 (5):820-831.

  • Jiang, N., Gao, D., Xiao, H. and van der Knaap, E. 2009. Genome organization of the tomato sun locus and characterization of the unusual retrotransposon Rider. Plant J. 60:181-193.

  • Hanada, K., Vallejo, V., Nobuta, K., Slotkin, R.K., Lisch, D., Meyers, B.C., Shiu, S.H. and Jiang, N. 2009. The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression Profile. Plant Cell21:25-38.

  • Lisch, D., and Jiang, N. 2009. Mutator and MULE transposons. In Handbook of Maize: Genetics and Genomics, J.L. Benntzen and S. Hake, eds (New York: Springer), pp.277-306.

  • Ammiraju, J.S., Lu, F., Sanyal, A., Yu, Y., Song, X., Jiang, N., Pontaroli, A.C., Rambo, T., Currie, J., Collura, K., Talag, J., Fan, C., Goicoechea, J.L., Zuccolo, A., Chen, J., Bennetzen, J.L., Chen, M., Jackson, S., and Wing, R.A. 2008. Dynamic evolution of Oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell 20:3191-3209.

  • Xiao H., Jiang N., Schaffner E., Stockinger E.J., van der Knaap E. 2008. A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319:1527-1530

  • Ammiraju J.S.S., Zuccolo A., Yu Y., Song X., Piegu B., Chevalier F., Walling J.G., Ma J., Talag J., Brar D.S., SanMiguel P.J., Jiang N., Jackson S.A., Panaud O. and Wing R.A. 2007.  Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant J. 52:342-51

  • Campbell, M.A., Zhu, W., Jiang, N., Haas, B.I., Lin, H., Ouyang, S., Childs, K.L., Hamilton, J.P., and Buell, C.R.. 2007. Identification and characterization of lineage-specific genes within the Poaceae. Plant Physiol.145:1311-22.

  • Zhang, S., Gu, Y.Q., Singh, J., Coleman-Derr, D., Brar, D.S., Jiang, N., Lemaux, P.G. 2007. New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification. Plant Mol Biol.64:589-600.

  • Holligan, D., Zhang, X., Jiang, N., Pritham, E.J. and Wessler, S.R. 2006. The transposable element landscape of the model legume Lotus japonicus. Genetics 174:2215-28.

  • Tsukamoto, T., Hauck, N.R., Tao, R., Jiang, N. and Iezzoni, A.F. 2006 Molecular characterization of three non-functional S-haplotypes in sour cherry (Prunus cerasus) Plant Mol Biol. 62:371-183 .

  • Zhang, S., Chen, C., Li, L., Meng, L., Singh, J, Jiang, N., Deng, X.W., He, Z.H. and Lemaux, P.G.2005. Evolutionary expansion, gene structure, and expression of the rice wall-associated kinase gene family. Plant Physiol. 139:1107-24.

  • Jiang, N., Bao, Z., Zhang, X., Eddy, S.R. and Wessler, S.R. 2004. Pack-MULE transposable elements mediate gene evolution in plants. Nature 431:569-573.

  • Feltus, F.A., Wan, J., Schulze, S.R., Estill, J.C., Jiang, N., and Paterson, A.H. 2004. An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res. 14:1812-9.

  • Jiang, N., Feschotte, C., Zhang, X., and Wessler, S.R. 2004. Using rice to understand the origin and amplification of MITEs. Curr. Opin. Plant Biol. 7:115-119.

  • Zhang, X., Jiang, N., Feschotte, C. and Wessler, S.R. 2004. PIF and Pong-like elements: distribution, evolution and relationship with the Tourist-like miniature inverted-repeat transposable elements. Genetics166:971-986.

  • Jiang, N., Bao, Z., Zhang, X., Hirochika, H., Eddy, S.R., McCouch, S.R. and Wessler, S.R. 2003. An active DNA transposon family in rice. Nature 421:163-167.

  • Jiang, N., Jordan, I.K. and Wessler, S.R. 2002. Dasheng and RIRE2: a non-autonomous LTR element and its putative autonomous partner in the rice genome. Plant Physiol. 130:1697-1705.

  • Jiang, N., Bao, Z., Temnykh, S., Cheng, Z., Jiang, J., Wing, R.A., McCouch, S.R. and Wessler, S.R.  2002.Dasheng: a recently amplified non-autonomous LTR element that is a major component of pericentromeric regions in rice. Genetics 161:1293-1305.

  • Feschotte, C., Jiang, N. and Wessler, S.R. 2002. Plant transposable elements: where genetics meets genomics. Nature Rev. Genet. 3:329-341.

  • Jiang, N. and Wessler, S.R. 2001. Insertion preference of maize and rice MITEs as revealed by the analysis of nested elements.  Plant Cell 13:2553-2564.

  • Zhang, X., Feshotte, C., Zhang, Q., Jiang, N., Eggelston, W.B. and Wessler, S.R. 2001. P Instability Factor: an active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases. Proc. Natl. Acad. Sci. USA. 98:12572-12577.

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