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Sushma Naithani


 Sushma Naithani

Assistant Professor (Senior Research)
Ph.D., 1999, University of Lucknow


Faculty of Center for Genome Research and Biocomputing

Office: Cordley 1078
Phone: 541-737-8022


Research Area

Genomics, Transcriptomics, Plant system biology, Plant metabolic networks, Cell signaling, Self-incompatibility, and Organelle biogenesis.

Description of Research

The current focus of my research program is centered on the following themes:

Functional genomics of S-domain Receptor-like Kinase subfamily in plants

Receptors-like kinases (RLKs) are major players in perceiving and transducing extracellular signals into appropriate cellular responses in plants.  Fully sequenced plant genomes suggest that RLKs form one of the largest gene families in plants.  However, function of majority of RLKs and their interactions with other proteins are unknown.  My laboratory is interested in analyzing the second largest subfamily of RLKs known as “S-Domain” (SD)-RLKs, so named because its members share sequence and structural similarity with the extracellular-ligand binding domain or “S Domain” of the S-locus receptor kinase, SRK.

Development and Curation of Plant Pathways Databases  

As more plant genomes are getting sequenced, complementary system-level metabolic, genetic and signaling networks must be developed to discover spatial, temporal, and developmental changes in plant’s metabolism and how it’s affected by various biotic and abiotic stresses.  Species-specific metabolic pathway databases can provide a framework to score differences among cultivars and across plant species, and thus, can foster discoveries of novel interaction among genes, gene products, and metabolites.  Some of the Plant metabolic pathway databases developed by our group are available here.

Curation of Rice Reactome: Dr. Naithani collaborates with the Gramene database project team on curation of the Plant Reactome and project outreach.

Research Group Members

Undergraduate Students

2014-present Christina M. Partipilo
2014-present Kelsey M. Nadeau
2013-2014 Eli N. Waddell
2013 Kate Threlfall
2009-2011 Alnakhli, Ali
2008-2009 Jimmy Hoang
2008-2009 Tracy Nguyen

Selected Publications

see also PubMed

Vining K.J., E. Romanel, R.C. Jones, A. Klocko, M. Alves-Ferreira, C. A. Hefer,V. Amarasinghe, P. Dharmawardhana, S. Naithani, M. Ranik, J. Wesley-Smith, L. Solomon, P. Jaiswal, A.A. Myburg andS. Strauss(2014).  The floral Transcriptome of Eucalyptus grandisNew Phytol., Epub 2014 Oct 29, doi: 10.1111/nph.13077. Article

Myburg A.A., D. Grattapaglia, G.A. Tuskan, U. Hellsten, R.D. Hayes, G.J.J. Jenkins, E. Lindquist, H. Tice, D. Bauer, D.M. Goodstein, I. Dubchak, A. Poliakov, E. Mizrachi, A.R.K. Kullan, I.V. Jaarsveld, S.G. Hussey, D. Pinard, K.V.D. Merwe, P. Singh, O.B. Silva-Junior, R.C. Togawa, M.R. Pappas, D.A. Faria, C.P. Sansaloni, C.D. Petroli, X. Yang, P. Ranjan,  T.J. Tschaplinski, C.-Y. Ye,  T. Li, L. Sterck, K. Vanneste,  F. Murat, M. Soler, H.S. Clemente, N. Saidi,  H. Cassan-Wang, C. Dunand, C.A. Hefer, E. Bornberg-Bauer,  A.R. Kersting, K. Vining,  V. Amarasinghe, M. Ranik, S. Naithani,  J. Elser,  A.E. Boyd,  A. Liston, J.W. Spatafora, P. Dharmwardhana, R. Raja, C. Sullivan, E. Romanel, M. Alves-Ferreira, C. Külheim, W. Foley, V. Carocha, J. Paiva, D. Kudrna, S.H. Brommonschenke, G. Pasquali, M. Byrne M, P. Rigault, J. Tibbits, A. Spokevicius, R.C. Jones, D.A. Steane, R.E. Vaillancourt, B.M. Potts, F. Joubert, K. Barry, G.J. Pappas Jr., S.H. Strauss, P. Jaiswal, J. Grima-Pettenati, J. Salse, Y. Van de Peer, S. Daniel, D.S. Rokhsar,  and J. Schmutz (2014): The genome of Eucalyptus grandis - a global tree for fiber and energy.  Nature 19;510(7505):356-362. Article.

Fox S.E., M. Geniza, M. Hanumappa, S. Naithani, C. Sullivan, J. Preece, V.K. Tiwari, J. Elser, J.M. Leonard, A. Sage, C. Gresham, A. Kerhornou, D. Bolser, F. McCarthy, P. Kersey, G.R. Lazo and P. Jaiswal (2014): De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcumPLoS One 12;9(5):e96855. Article

Monaco MK, J. Stein, S. Naithani, S. Wei, P. Dharmawardhana, S. Kumari, V. Amarasinghe, K. Youens-Clark, J. Thomason, J. Preece, S. Pasternak, A. Olson, Y. Jiao, Z. Lu, D. Bolser, A. Kerhornou, D. Staines, B. Walts, G. Wu, P. D'Eustachio, R. Haw, D. Croft, P.J. Kersey, L. Stein, P. Jaiswal, and D. Ware (2014): Gramene 2013: comparative plant genomics resources.  Nucleic Acids Res. 42(Database issue): D1193-9. doi: 10.1093/nar/gkt1110.: article , Epub 2013 Nov 11.

Monaco M.K., Z. T.Sen, P. Dharmawardhana, L.Ren, M. Schaeffer, S. Naithani, V. Amarasinghe, J. Thomason, L. Harper, J. Gardiner, E. K.S. Cannon, C. J. Lawrence, D. Ware, and P. Jaiswal (2013): Maize Metabolic Network Construction and Transcriptome Analysis.  Plant Genome, 6: 1-12.  Article (doi: 10.3835/plantgenome2012.09.0025).

Naithani S., P. Dharmawardhana and J. B. Nasrallah (2013).  SCR, in “Handbook of Biologically Active Peptides, 2nd edition, Abba J. Kastin ed., Elsevier Publication, pp. 58-66, ISBN: 978-0-12-385095-9.

Shulaev V., D.J. Sargent, R.N. Crowhurst, T. Mockler, R.E. Veilleux, O. Folkerts, A.L. Delcher, P. Jaiswal, A. Liston, S.P.Mane, P.Burns, K. Mockaitis, T. M. Davis, J. P. Slovin, N. Bassil, R.P. Hellens, C. Evans , R.V. Jensen, A.C. Allan, T.P. Michael, J.C. Setubal, J-M Celton, D.J.G. Rees, K.P. Williams, S.H. Holt, A. Dickerman, J.J.R. Rojas, M. Chatterjee, B. Liu, H. Silva, L. Meisel, A. Adavo, S. Filichkin, R. Velasco, M. Troggio, R. Viola, M. Borodovsky, T-L Ashman, A. Aharoni, J. Bennetzen, P. Dharmawardhana, J. Elser, R. Raja, H.D. Priest, D.W. Bryant Jr., S. E. Fox, A. Scott, S.A. Givan, S. Naithani, A. Christoffels, D.Y. Salama, J. Carter, E.L. Girona, A. Zdepski, W.Wang, R.A. Kerstetter, S.L. Salzberg, W. Schwab, S.S. Korban, J. Davik, A. Monfort, B. Denoyes-Rothan, P. Arus, R. Mittler, B. Flinn and K.M. Folta (2011). The genome of woodland strawberry (Fragaria vesca). Nat Genet., 43:109-116.Article

Naithani S., T. Chookajorn, D. R. Ripoll and J. B. Nasrallah (2007). Structural modules for receptor dimerization in the S-locus receptor kinase extracellular domain. Proc. Natl. Acad. Sci. USA, 104:12211-12216.  [Selected by faculty of 1000 Biology]. Article

S. Naithani, S.A. Saracco, C. Butler and T.D. Fox (2003): Interactions among COX1, COX2 and COX3 mRNA-specific translational activator proteins on inner surface of mitochondrial inner membrane in S. cerevisiae, Mol. Biol. Cell, 14:324-333.  Article.

T.W. Johnson, S. Naithani, B. Zybailov, A. D. Jones, J.H. Golbeck and P.R. Chitnis (2003): The menD and MenE homologues code for 2-succinyl-6-hydroxyl-2, 4-cyclohexadiene-1-carboxylate synthase and O-succinylbenzoic acid-CoA ligase in the phylloquinone biosynthetic pathway of Synechocystis sp. PCC 6803, Biochim. Biophys. Acta, (Bioenergetics), 1557:67-76.  Article.