NCGR Publications - 2012

Analysis of the transcriptomes downstream of Eyeless and the Hedgehog, Decapentaplegic and Notch signaling pathways in Drosophila melanogaster
Landry E. NfonsamCarlos Cano,  Joann MudgeFaye D. SchilkeyJennifer Curtiss
PLoS ONE (2012) 7(8): e44583.

Next-generation sequencing-based transcriptomic and proteomic analysis of the common reed, Phragmites australis (Poaceae), reveals genes involved in invasiveness and rhizome specificity. 
Ruifeng He, Min-Jeong Kim, William Nelson, Tiago S. Balbuena, Ryan Kim, Robin Kramer, John A. Crow, Greg D. May, Jay J. Thelen, Carol A. Soderlund, and David R. Gang.
American Journal of Botany (2012) 99(2):232-247.

Identification and mapping of conserved ortholog set (COS) II sequences of cacao and their conversion to SNP markers for marker-assisted selection in Theobroma cacao and comparative genomics studies. 
David N. Kuhn, Don Livingstone III, Dorrie Main, Ping Zheng, Chris Saski, F. Alex Feltus, Keithanne Mockaitis, Andrew D. Farmer, Gregory D. May, Raymond J. Schnell, Juan C. Motamayor. 
Tree Genetics & Genomics (2012) 8:97–111.

Analyzing the meiotic transcriptome using isolated meiocytes. 
Changbin Chen and Ernest F. Retzel.
Methods in Molecular Biology, Vol. Plant Meiosis. 

Genome-enabled insights into legume biology
Nevin D. Young and Arvind K. Bharti
Annu Rev Plant Biol 63: x-x. DOI: 10.1146/annurev-arplant-042110-103754. In press, 2012.

Deep Panning: Steps Towards Probing the Complete 
Repertoire of Antibody Specificities in Blood (IgOme) by phage display and Next Generation Sequencing. 
Ryvkin A, Ashkenazy H, Smelyanski L, Kaplan G, Penn O, Weiss-Ottolenghi Y, Privman E, Ngam PB, Woodward JE, May GD, Bell CJ, Pupko T, Gershoni JM. (2012)  
PLoS ONE.  7(8): e41469. Doi:10.1371/journal.pone.0041469.

Next-generation sequencing technologies: Opportunities and obligations in plant genomics.
Varshney R.K. and May G.D.
Briefings in Functional Genomics. 11(1): 1-2 doi:10.1093/bfgp/els001.

Coverage-based consensus calling (CBCC) of short sequence reads and comparison of CBC results to indentify SNPs in chickpea (Cicer arietinum; Fabaceae), A crop species without a reference genome. 
Azam S., Thakur V., Ruperao P., Shah T., Balaji J., Amindala B., Farmer, A.D., Studholme D.J., May G.D., Edwards D., Jones J.D.G. and Varshney R.K.
(2012) Am. J. Bot99:2 186-92.

Identification of candidate genes underlying an iron efficiency QTL in soybean. 
Peiffer G.A., King K., Severin A., May G.D., Cianzio S.R., Lin S.-F., Lauter N.C. and Shoemaker R. (2012)  
Mol. Plant doi: 10.1093/mp/ssr111

Current state-of-art of sequencing technologies for plant genomics research. 
Thudi, M., Li Y., Jackson S.A., May G.D. and Varshney R.K.   
Briefings in Functional Genomics 11(1): 3-11 doi:10.1093/bfgp/elr045.

A Comprehensive Transcriptome Assembly of Pigeonpea (Cajanus cajan L.) using Sanger and Second-Generation Sequencing Platforms
Kudapa H, Bharti AK, Cannon SB, Farmer AD, Mulaosmanovic B, Kramer R, Bohra A, Weeks NT, Crow JA, Tuteja R, Shah T, Dutta S, Gupta DK, Singh A, Gaikwad K, Sharma TR, May GD, Singh NK, Varshney RK.  
Mol Plant. 2012 Jan 18.

A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species. 
Ilut, D.C., Coate, J.E., Luciano, A.K., Owens, T.G., May G.D., Farmer A. and Doyle J.J.
Am. J. Botany.  99:175-185.


Identification of candidate genes in rice for resistance to sheath blight disease by whole genome sequencing. 
Silva J., Scheffler B., Sanabria Y., De Guzman C., Galam D., Farmer A., Woodward J., May
 G. and Oard J. 
Theor Appl Genet. 124:1 63-74. 2011 Sep 7. [Epub ahead of print]


Evolutionary fate of duplicated genes in a polyploid plant genome: a Glycine max model. 
Roulin A., Auer P., Libault M., Schlueter J., Farmer A., May G.D., Stacey G., Doerge R.W. and Jackson S.A. 
The Plant Journal. DOI: 10.1111/tpj.12026.


Prevalence of single nucleotide polymorphisms among 27 divers alfalfa genotypes assessed by transcriptome sequencing.
Li X., Acharya A., Farmer A.D., Crow J.A., Bharti A.K., Kramer R.S., Wei Y., Han Y., Gou J., May G.D., Monteros M.J. and Brummer E.C.
BMC Genomics (In press).


Large-scale development of cost-effective SNP marker assays for genetic mapping in pigeonpea and comparative mapping in legumes. 
Saxena R.K., Penmetsa, R.V., Upadhyaya H.D, Kumar A., Carrasquilla-Garcia N., Schlueter J.A., Farmer A., Whaley A.M., Sarma B.K, May G.D., Cook D.R. and Varshney, R.K.
DNA Research (in press).

Phylogenetic signal variation in the genomes of genus Medicago (Fabaceae).
Yoder J.B., Briskine R., Mudge J., Farmer A., Paape T., Steele K., Weiblen G.D., Bharti A.K., Zhou P., May G.D., Young N., Tiffin P.
Systematic Biology (Under review).


Sequence-based association genetics of the Medicago truncatula - Sinorhizobium symbiosis. 
Stanton-Geddes J., Paape T., Epstein B., Yoder J., Briskine R., Mudge J., Bharti A.K., Farmer A.D., Zhou P., Denny R., May G.D., Erlandson S., Sugawara M., Sadowsky M.J., Young N.D. and Tiffin P.
ature Genetics (Under review).


Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains spanning five genospecies.
Sugawara W., Badgley B., Unno T., Epstein D., Xu L., Reese J., Prasad G., Denny R., Mudge J., Bharti A.K., Farmer A.D., May G.D.,Woodward J.E., Médigue C., Vallenet D., Lajus A., Rouy Z., Martinez-Vaz B., Tiffin P., Young N.D. and Sadowsky M.J.
PNAS. (Under review.)


Genome-wide association genetics of an adaptive trait in lodgepole pine. 
Parchman TL, Gompert Z, Mudge J, Schilkey FD, Benkman CW, Buerkle CA.
Mol Ecol. 2012 Jun;21(12):2991-3005. doi: 10.1111/j.1365-294X.2012.05513.x. Epub 2012 Mar 8.


Differential hippocampal gene expression is associated with climate-related natural variation in memory and the hippocampus in food-caching chickadees. 
V. V. Pravosudov, T. C. Roth II, M. L. Forister, L. D. LaDage, R. Kramer, F. Schilkey, A. M. van der Linden 


Characterization of a set of novel meiotically-active promoters in Arabidopsis
J. Li, A. Farmer, I. Lindquist, S. Dukowic-Schulze, J. Mudge, T. Li, E. Retzel and C. Chen
BMC plant biology. 2012; 12(1):104.


Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici
K. H. Lamour, J. Mudge, D. Gobena, O. P. Hurtado-Gonzales, J. Schmutz, A. Kuo, N. A. Miller, B. J. Rice, S. Raffaele and L. M. Cano
Molecular Plant-Microbe Interactions. 2012; 25(10):1350-1360.