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Ecological Genomics Institute

2013 Publications

Carlson, AL, H Gong, C Toomajian, RJ Swanson. 2013. Parental genetic distance and patterns in nonrandom mating and seed yield in predominantly selfing Arabidopsis thaliana. Plant Reproduction 26:317-328. (doi:10.1007/s00497-013-0228-5).

Coolon, JD, Jones, KL, Todd, TC, Blair, JM, Herman, MA. 2013. Long-term nitrogen amendment alters soil bacterial diversity and assemblage in tallgrass prairiePLoS One, Jun 28;8(6):e67884

Darby, BJ, Todd, TC, Herman, MA. 2013. High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structureMolecular Ecology, 22:5456-54-71, DOI:10.1111/mec.12480.

De Hoff, PL, Ferris, P, Olson, BJSC, Miyagi, A, Geng, S, Umen, JG. 2013. Species and population level molecular profiling reveals cryptic recombination and emergent asymmetry in the dimorphic mating locus of C. reinhardtiiPLoS genetics 9(8), e1003724.

DiRienzo, N. and J.L. Marshall. 2013. Function of the hemolymph nuptial gift in the ground cricket, Allonemobius socius. Ethology 119:104-109. (KAES contribution #:12-178-J).

Elbeaino, T., Whitfield, A.E., Sharma, M., Digiaro, M. 2013. Emaravirus-specific degenerate PCR primers allowed the identification of partial RNA-dependent RNA polymerase sequences of Maize red stripe virusand Pigeonpea sterility mosaic virusJournal of Virological Methods 188: 37-40.

Gomez-Montano, L, Jumpponen, A, Gonzales, MA, Cusicanqui, J, Valdivia, C, Motavelli, PP, Herman, M, Garrett, KA. 2013. Do bacterial and fungal communities in soils of the Bolivian Altiplano change under shorter fallow periods? Soil Biology and Biochemistry 65:50-59. 

Hamaji, T, Smith, DR, Noguchi, H, Toyoda, A, Suzuki, M, Kawai-Toyooka, Fujiyama, A, Nishii, I, Marriage, T, Olson, BJSC, Nozaki, H. 2013. Mitochondrial and Plastid Genomes of the Colonial Green Alga Gonium pectorals Gives Insights into the Origins of Organelle DNA Architecture within the VolvocalesPLoS One 8 (2), e57177.

Jacobson, A.L., Johnston, S., Rotenberg, D., Whitfield, A.E., Booth, W., Vargo, E.L., Kennedy, G.G. 2013. Genome size and ploidy of Thysanoptera. Insect Molecular Biology 22:12-17.

Lounsberry ZT, Ungerer MC, Snyder BA. 2013. Identification of 12 EST-derived SSR markers in Lubricus rubellus Pedobiologia 56:191-193.

Nachappa, P., Margolies, D.C., Nechols, J.R., Whitfield, A.E., and Rotenberg, D. 2013. Tomato spotted wilt virus benefits a non-vector arthropod,Tetranychus urticae, by modulating different plant responses in tomato. PLoS ONE 8 (9):e75909.

Smith, DR, Hamaji, T, Olson, BJSC, Durand, PM, Ferris, P, Michod, RE, et al. 2013. Organelle genome complexity scales positively with organism size in volvocine green algae. Molecular Biology and Evolution 30 (4), 793-797.

Ungerer MC and Kawakami T. 2013. Transcriptional dynamics of LTR retrotransposons in early generation and ancient sunflower hybrids. Genome Biol. Evol. 5:329-337

Ungerer MC, Weitekamp CA, Joern A, Towne EG, Briggs JM. 2013. Genetic variation and mating success in managed American plains bison. Journal of Heredity 104:182-191.

Yao, J., Rotenberg, D., Afsharifar, A., Barandoc-Alviar K., Whitfield, A.E. 2013 Development of RNAi methods for Peregrinus maidis, the corn planthopper. PLoS ONE 8 (8): e70243.

Bengtsson-Palme, J., Ryberg, M., Hartmann, M., Branco, S., Wang, Z., Godhe, A., de Wit, P., Sánchez-García, M., Ebersberger, I., de Sousa, F., Amend, A., Jumpponen, A., Unterseher, M., Kristiansson, E., Abarenkov, K., Bertrand, Y., Sanli, K., Eriksson, M., Vik, U., Veldre, V., Nilsson, R.H. 2013. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods in Ecology and Evolution 4: 914-919. DOI: 10.1111/2041-210X.12073. 

Brown, S.P., Oliver, A.K., Callaham, M.A., and Jumpponen, A. 2013. Deep Ion Torrent sequencing identifies soil fungal community shifts after frequent prescribed fires in a southeastern US forest ecosystem. FEMS Microbiology Ecology 86: 557-566. DOI: 10.1111/1574-6941.12181

Mandyam, K., Roe, J., and Jumpponen, A. 2013. Arabidopsis thaliana model system reveals a continuum of responses to root endophyte colonization. Fungal Biology 117: 250-260 DOI: 10.1016/j.funbio.2013.02.001

Rigdon, A.R., Jumpponen, A.M., Vadlani, P. and Maier, D.E. 2013. Impact of various storage conditions on enzymatic activity, biomass components and conversion to ethanol yields form sorghum biomass used as a bioenergy crop. Bioresource Technology 132: 269-275. DOI: 10.1016/j.biortech.2013.01.055

Zeglin, L.H., Bottomley, P.J., Jumpponen, A., Rice, C.W., Arango, M., Lindsey, A., McGowan, A., Mfombep, P., Myrold, D.D. 2013. Altered precipitation regime affects the function and composition of soil microbial communities on multiple time scales. Ecology 94: 2334-2345. DOI: 10.1890/12-2018.1

Jumpponen, A., Mandyam, K. 2013. Adoption and utility of an Arabidopsis model to dissect endophyte symbioses. In: Endophytes in plant protection: the state of the art. Ed. Schneider, C., Leifert, C., Feldman, F. Deuthche Phytomedizinische Gesellschaft. Braunscweig, Germany. p. 244-247.  

Fournier‐Level A, Wilczek AM, Cooper MD, Roe JL, Anderson J, Eaton D, Moyers BT, Petipas RH, Schaeffer RN, Pieper B, Reymond M, Koornneef M, Welch SM, Remington DL, Schmitt J. 2013. Paths to selection on life history loci in different natural environments across the native range of Arabidopsis thaliana. Molecular Ecology, 22:3552-3566.

Bulatewicz, T., A. Allen, J.M. Peterson, S. Staggenborg, S.M. Welch, and D.R. Steward. 2013. The Simple Script Wrapper for OpenMI: Enabling interdisciplinary modeling studies, Environmental Modelling & Software, 39, 283-294.

Leong W.F., S. Das, S. M. Welch, C. Weinig, SHARP: Shade-Avoidance Response in Plants: An Evolutionary Simulation Software Package. Proceedings of the 3rd International Conference on Simulation and Modeling Methodologies,Technologies & Applications (SIMULTECH), Reykjavik, Iceland, July 2013.

Weinig C, BE Ewers, SM Welch. 2013. Ecological genomics and process modeling of local adaptation to climate. Current Opinion in Plant Biology 18: 66-72. 

i5k Consortium. 2013. The i5k Initiative: Advancing Arthropod Genomics for knowledge human healther agriculture and the Environment. Journal of Heredity, 104: 595-600.  Sue Brown is the second author of this multi -author paper.

Morris GP, Rhodes DH, Brenton Z, Ramu P, Thayil VM, Deshpande S, Hash CT, Acharya C, Mitchell SE, Buckler ES, Yu J, Kresovich S. 2013. Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits.G3:Genes|Genomes|Genetics 3(11):2085-2094.

Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE, Harriman J, Glaubitz JC, Buckler ES, Kresovich S. 2013. Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proceedings of the National Academy of Sciences 110: 453–458.

BJSC Olson. 2013. Multicellularity: From brief encounters, to lifelong unions. eLife 2:e01893

Y Arakaki, H Kawai-Toyooka, Y Hamamura, T Higashiyama, A Noga, M Hirono, BJSC Olson, H Nozakiø. 2013. The simplest integrated multicellular organism unveiled. PLoS One 8 (12), e81641.

PL De Hoff, P Ferris, BJSC Olson, A Miyahi, S Geng and JG Umenø. Species and Population Level Molecular Profiling Reveals Cryptic Recombination and Emergent Asymmetry in the Dimorphic Mating Locus of C. reinhardtii. PLoS Genetics 9 (8), e1003724.

Zhiyong Yang, Zhengxing Shen, Hannah Tetreault, Loretta Johnson, Bernd Friebe, Taylor Frazier, Lin-kai Huang, Bin Xu, Caitlin Burklew, Xin-Quan  Zhang, Bingyu Zhao, 2013. Production of autopolyploid lowland switchgrass lines through in vitro chromosome doublingBioenergy Research 7(1):232-242.

Jacob T. Olsen, Keri L. Caudle, Loretta C. Johnson, Sara G. Baer, Brian R. Maricle  2013. Variation in leaf anatomy among populations of Andropogon gerardii along a precipitation gradient. American Journal of Botany 100(10):1957. 

Gibson, D.J., Sandor, G., Donatelli, J., Baer, S.G., Johnson, L. 2013. Reproductive effort of Andropogon gerardii ecotypes in an Illinois common garden. Torrey Botanical Club Journal. 140(3):269 

Scott J. G., Michel K., Bartholomay L., Siegfried B. D., Hunter W. B., Smagghe G., Zhu K. Y., Douglas A. E. 2013. Towards the elements of successful insect RNAi. Journal of Insect Physiology. 59: 1212-1221 (No. 3 Most Downloaded Paper from ScienceDirect in the Last 90 Days of 04/25/2014).

Mascher M, Richmond TA, Gerhardt DJ, Himmelbach A, Clissold L, Sampath D, Ayling S, Steuernagel B, Pfeifer M, D'Ascenzo M, Akhunov ED, Hedley PE, Gonzales AM, Morrell PL, Kilian B, Blattner FR, Scholz U, Mayer KF, Flavell AJ, Muehlbauer GJ, Waugh R, Jeddeloh JA, Stein N. 2013. Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. Plant Journal, 76:494-505.

Krasileva KV, Buffalo V, Bailey P, Pearce S, Ayling S, Tabbita F, Soria M, Wang S, Consortium I, Akhunov E, Uauy C, Dubcovsky J. 2013. Separating homeologs by phasing in the tetraploid wheat transcriptome. Genome Biology 14:R66.

Saintenac C, Jiang D, Wang S, Akhunov E. 2013. Sequence-based mapping of the polyploid wheat genome. G3 (Bethesda). 3:1105-1114.

Cavanagh CR, Chao S, Wang S, Huang BE, Stephen S, Kiani S, Forrest K, Saintenac C, Brown-Guedira GL, Akhunova A, See D, Bai G, Pumphrey M, Tomar L, Wong D, Kong S, Reynolds M, da Silva ML, Bockelman H, Talbert L, Anderson JA, Dreisigacker S, Baenziger S, Carter A, Korzun V, Morrell PL, Dubcovsky J, Morell MK, Sorrells ME, Hayden MJ, Akhunov E. 2013. Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proceedings of the National Academy of Science U S A. 110:8057-8062.

Würschum T, Langer SM, Longin CF, Korzun V, Akhunov E, Ebmeyer E, Schachschneider R, Schacht J, Kazman E, Reif JC. 2013. Population structure, genetic diversity and linkage disequilibrium in elite winter wheat assessed with SNP and SSR markers. Theoretical Applied Genetics 126:1477-1486.

Akhunov E, Sehgal S, Liang H, Wang S. Akhunova A, Kaur G, Li W, Forrest K, See D, Simkova H, Hayden M, Luo M, Farris JD, Dolezel J, Gill BS. 2013. Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat. Plant Physiology. 161:252-265.

Cox, C. M., W. W. Bockus, R. D. Holt, L. Fang, and K. A. Garrett. 2013. The spatial connectedness of plant species: Potential links for apparent competition via plant diseases. Plant Pathology 62(6): 1195-1204.

Garrett, K. A., G. A. Forbes, L. Gomez, M. A. Gonzales, M. Gray, P. Skelsey, and A. H. Sparks. 2013. Cambio climático, enfermedades de las plantas e insectos plaga. In Cambio climático en los Andes. Edition: First, Chapter: Cambio climatico, enfermedades de last plantas e insectos plaga, Publisher: cides-umsa, Editors: Jimenez, E., pp. 71-98.

Garrett, K. A., S. Thomas, G. A. Forbes, and J. Hernandez Nopsa. 2013. Climate change and plant pathogen invasions. In Invasive Species and Climate Change. Editors: Ziska, L.H.; Dukes, J.S. CABI Publishing. ISBN 978-1-78064-164-5. pp. 22-44. 

Skelsey, P., K. A. With, and K. A. Garrett. 2013. Why dispersal should be maximized at intermediate scales of heterogeneity. Theoretical Ecology 6:203-211.