Publications

Acknowledgment and Co-authorship

Please refer to our Acknowledgment page for more information.

Please email Elizabeth Ashworth at eashwort@uga.edu to let her know when an article that acknowledges GGBC is published, as we would like to add it to our growing list of publications. Thank you.

Publications 2018 - 2019

Bera, G., S.M. Doyle, U. Passow, M. Kamalanathan, T.L. Wade, J.B. Sylvan, J.L. Serciano, G. Gold, A. Quigg, and A.H. Knap. Biological response to dissolved versus dispersed oil. Marine Pollution Bulletin. In Press.

Kealoha, A., S.M. Doyle, K.E.F. Shamberger, J.B. Sylvan, R.D. Hetland, and S.F. DiMarco.  Localized hypoxia drives coral reef mortality at the Flower Garden Banks. Coral Reefs. In Press.

Sheik, M. L., K. L. LaBounty, E. Mitchell, and E. Gillespie. 2019. Fourteen polymorphic microsatellite markers for the widespread Labrador Tea (Rhododendron groenlandicum, Ericaceae). Applications in Plant Sciences. In press.

Cieslak, M.C., A.M. Castelfranco, V. Roncalli, P.H. Lenz, and D.K. Hartline. 2019.  t-distributed stochastic neighbor embedding (t-SNE): A tool for eco-physiological transcriptomic analysis.  Marine Genomics. In press.

Sateriale, A., J. Slapeta, R. Baptista, J.B. Engiles, J.A. Gullicksrud, G.T. Herbert, C.F. Brooks, E.M. Kugler, J.C. Kissinger, C.A. Hunter, and B. Striepen. 2019. Protective immunity in a genetically tractable natural mouse model of cryptosporidiosis. Cell Host & Microbe, https://doi.org/10.1016/j.chom.2019.05.006.

Oppler, Z.J., M.E. Parrish, and H.A. Murphy. 2019. Variation at an adhesin locus suggests sociality in natural populations of the yeast Saccharomyces cerevisiae. Proc. R. Soc. B  286:20191948.

Lenhart, B.A., B. Meeks, and H.A. Murphy. 2019. Variation in filamentous growth and response to quorum-sensing compounds in environmental isolates of Saccharomyces cerevisiae. G3 9(5):1533-1544

Glenn, T.C., R.A. Nilsen, T.J. Kieran, J.G. Sanders, N.J. Bayona-Vásquez, J.W. Finger, T.W. Pierson, K.E. Bentley, S.L. Hoffberg, S. Louha, F.J. Garcia-De-Leon, M.A. del Rio Portilla, K.D. Reed, J.L. Anderson, J.K. Meece, S.E. Aggery, R. Rekaya, M. Alabady, M. Bélanger, K. Winker, B.C. Faircloth.  2019. Adapterama I: Universal stubs and primers for thousands of 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext). PeerJ. Oct 11;7:e7755.

S. Guo , S. Zhao, H. Sun , X. Wang, S. Wu , T. Lin , Y. Ren, L. Gao, Y. Deng, J. Zhang, X. Lu, H. Zhang, J. Shang, G. Gong, C. Wen, N. He, S. Tian, M. Li, J. Liu, Y. Wang, Y. Zhu, R. Jarret, A. Levi, X. Zhang, S. Huang , Z. Fei , W. Liu , and Y. Xu. 2019. Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits. Nature Genetics. 51:1616–1623.

Yadav, L.K., E.V. McAssey, and H.D. Wilde. 2019. Genetic diversity and population structure of Rhododendron canescens, a Native Azalea for urban landscaping. HortScience 54:647-651.

Gillespie, E., T. Madsen-McQueen, T. Eriksson, A. Bailey, and Z. Murrell. 2019. Microsatellite markers for the biogeographically enigmatic Sandmyrtle (Kalmia buxifolia, Phyllodoceae, Ericaceae). Applications in Plant Sciences 7(6) e11267. https://bsapubs.onlinelibrary.wiley.com/doi/abs/10.1002/aps3.11267.

Wendte, J.M., Y. Zhang, L. Ji, X. Shi, R.R. Hazarika, Y. Shahryary, F. Johannes, and R.J. Schmitz. 2019. Epimutations are associated with chromomethylase 3-induced de novo DNA methylation. Elife 29:8. https://doi.org/10.7554/eLife.47891.001.

Riley, L.A., L. Ji, R.J. Schmitz, J. Westpheling, and A.M. Guss. 2019. Rational development of transformation in Clostridium thermocellum ATCC 27405 via complete methylome analysis and evasion of native restriction-modification systems. J. Ind. Microbiol. Biotechnol. 46(9-10):1435-1443.

Noshay, J.M., S.N. Anderson, P. Zhou, L. Ji, W. Ricci, Z. Lu, M.C. Stitzer, P.A. Crisp, C.N. Hirsch, X. Zhang, R.J. Schmitz, and N.M. Springer. 2019. Monitoring the interplay between transposable element families and DNA methylation in maize. PLoS Genet. 15:e1008291.

Ji, L., S. Mathioni, S. Johnson, D. Tucker, A.J. Bewick, K.D. Kim, J. Daron, R.K. Slotkin, S.A. Jackson, W.A. Parrott, B.C. Meyers, and R.J. Schmitz. 2019. Genome-wide reinforcement of DNA methylation occurs during somatic embryogenesis in soybean. Plant Cell 31(10):2315-2331

Bewick, A.J., Y. Zhang, J.M. Wendte, X. Zhang, and R.J. Schmitz. 2019. Evolutionary and experimental loss of gene body methylation and its consequence to gene expression. G3 (Bethesda) 8;9(8):2441-2445.

Bewick, A.J., Z. Sanchez, E.C. McKinney, A.J. Moore, P.J. Moore, and R.J. Schmitz. 2019. Dnmt1 is essential for egg production and embryo viability in the large milkweed bug, Oncopeltus fasciatus. Epigenetics Chromatin 12:6.

Bewick, A.J., B.T. Hofmeister, R.A. Powers, S.J. Mondo, I.V. Grigoriev, T.Y. James, J.E. Stajich, and R.J. Schmitz. 2019. Diversity of cytosine methylation across the fungal tree of life. Nat. Ecol. Evol.  3:479-490.

Hamlin, J.A.P., G. Dias, C.M. Bergman, and D. Bensasson. 2019. Phased diploid assemblies for three strains of Candida albicans isolated from oak trees. G3. 9:3547-3554.

Roncalli, V., M.C. Cieslak, M. Germano, R.R. Hopcroft, and P.H. Lenz.  2019. Regional heterogeneity impacts gene expression in the subarctic zooplankter Neocalanus flemingeri in the northern Gulf of Alaska. Communications Biology 2(1), pp.1-13.

Lenz, P.H. and V. Roncalli. 2019. Diapause within the context of life-history strategies in calanid copepods (Calanoida: Crustacea). The Biological Bulletin 237(2), pp.000-000.

Damashek J., C.F. Edwardson, B.B. Tolar, S.M. Gifford, M.A. Moran, and J.T. Hollibaugh. 2019. Coastal ocean metagenomes and curated metagenome-assembled genomes from marsh landing, Sapelo Island (Georgia, USA). Microbiol. Resour. Announc.  Oct 3;8(40). pii: e00934-19.

Landa M., A.S. Burns, B.P. Durham, K. Esson, B. Nowinski, S. Sharma, A. Vorobev, T. Nielsen, R.P. Kiene, and M.A. Moran. 2019. Sulfur metabolites that facilitate oceanic phytoplankton- bacteria carbon flux. ISME J. Oct;13(10):2536-2550.

Bahulikar*, R., S.R. Chaluvadi,* I. Torres-Jerez, J. Mosali, J.L. Bennetzen, and M. Udvardi. 2019. Nitrogen fertilization reduces diazotroph activity associated with switchgrass roots. Phytobiomes J. In Press. (*Contributed equally)

Dunning, L.T., J.K. Olofsson, C. Parisod, R.R. Choudhury, J.J. Moreno-Villena, Y. Yang, J. Dionora, W.P. Quick, M. Park, and J.L. Bennetzen. 2019. Lateral transfers of large DNA fragments spread functional genes among grasses. PNAS  116(10): 4416-4425. doi.org/10.1073/pnas.1810031116

VanBuren, R., C.M. Wai, J. Pardo, A.E. Yocca, X. Wang, H. Wang, S.R. Chaluvadi, D. Bryant, P.P Edger, J.L. Bennetzen, T.C. Mockler, and T.P. Michael. 2019. Exceptional subgenome stability and functional divergence in allotetraploid teff, the primary cereal crop in Ethiopia. Nature Comm. In Press. BIORXIVdoi.org/10.1101/580720

Chen, Y., K.M. Guo, T. Nagy, and T.L. Guo. 2019. Chronic oral exposure to glycated whey proteins alleviates autoimmune prostatitis by regulating gut microbiome and anti-inflammatory responses. Food Funct., DOI: 10.1039/C9FO01740B.

Glenn, TC, T.W. Pierson, N.J. Bayona-Vásquez, T.J. Kieran, S.L. Hoffberg, J.C. Thomas IV, D.E. Lefever, J.W. Finger, B. Gao, X. Bian, S. Louha, R.T. Kolli, K.E. Bentley, J. Rushmore, K. Wong, T.I. Shaw, M.J. Jr. Rothrock, A.M. McKee, T.L. Guo, R. Mauricio, M. Molina, B.S. Cummings, L.H. Lash, K. Lu, G.S. Gilbert, S.P. Hubbell, and B.C. Faircloth. 2019. Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix). PeerJ 7:e7786 https://doi.org/10.7717/peerj.7786

Xu J., G. Huang, T. Nagy, and T.L. Guo TL. 2019. Bisphenol A alteration of type 1 diabetes in non-obese diabetic (NOD) female mice is dependent on window of exposure. Arch Toxicol.  93:1083-1093.

Xu J., G. Huang, T. Nagy, Q. Teng, and T.L.  Guo.  2019. Sex-dependent effects of bisphenol A on type 1 diabetes development in non-obese diabetic (NOD) mice. Arch Toxicol. 93:997-1008.

Huang, G., J. Xu, D. Cai, S.Y. Chen, T. Nagy, and T.L.  Guo. 2018. Exacerbation of type 1 diabetes in perinatally genistein exposed female non-obese diabetic (NOD) mouse is associated with alterations of gut microbiota and immune homeostasis. Toxicol Sci. 165(2):291-301. (Highlighted by editor).

Chaluvadi, S.R, and J.L. Bennetzen. 2018. Species-associated differences in the below-ground microbiomes of wild and domesticated Setaria. Front. Plant Sci. 9:1183. doi.org/10.3389/fpls.2018.01183

Arthur, R.A. and J.L. Bennetzen. 2018. Discovery of lineage-specific genome change in rice through analysis of resequencing data. Genetics 209(2): 617-626. doi.org/10.1534/genetics.118.300848

Bennetzen, J. L. and M. Park. 2018. Distinguishing friends, foes, and freeloaders in giant genomes. Curr. Opin. Genet. Dev. 49: 49-55. doi.org/10.1016/j.gde.2018.02.013

Chaluvadi, S.R., J. Bennetzen, P. Young, K. Thompson, B.A. Barhi, B. Gajera, B., . . . and R. Krueger. 2018. Phoenix phylogeny, genetic diversity, distribution and population structure characterized in a world collection of date palm (Phoenix dactylifera) and its wild relatives. Plant Diversity. DOI:10.1016/j.pld.2018.11.005

de Souza, T.B, S.R. Chaluvadi, L. Johnen, A. Marques, M.S. Gonzalez-Elizondo, J.L. Bennetzen, et al. 2018. Analysis of retrotransposon abundance, diversity and distribution in holocentric Eleocharis (Cyperaceae) genomes. Ann. Bot. 122(2):279-90. doi.org/10.1093/aob/mcy066

Frailey, D.C, S.R. Chaluvadi, J.N. Vaughn, C.G. Coatney, and J.L. Bennetzen. 2018. Gene loss and genome rearrangement in the plastids of five hemiparasites in the family Orobanchaceae. BMC Plant Biol. 18(1):30. 10.1186/s12870-016-0705-8

Malmberg, R. L., W.L. Rogers, and M.S. Alabady. 2018. A carnivorous plant genetic map: pitcher/insect-capture QTL on a genetic linkage map of Sarracenia. Life Science Alliance. 1(6):e201800146.

Dawe, R.K., E.G. Lowry, J.I. Gent, M.C. Stitzer, K.W. Swentowsky, D.M. Higgins, J. Ross-Ibarra, J.G. Wallace, L.B. Kanizay, M. Alabady, W. Qiu, K.F. Tseng, N. Wang, Z. Gao, J.A. Birchler, A.E. Harkess, A.L. Hodges, E.N. Hiatt. 2018. A kinesin-14 motor activates neocentromeres to promote meiotic drive in maize. Cell. 173(4):839-850.e18.

 Findly, R.C., F.D. Niagro, R.P. Sweeney, A.C. Camus, and H.W. Dickerson. 2018. Rearranged T cell receptor sequences in the germline genome of channel catfish are preferentially expressed in response to infection. Frontiers in Immunology  9.2117. https://doi.org/10.3389/fimmu.2018.02117.

Kasireddy, V., E. Mitchell, Z. Murrell, and E. Gillespie. 2018. Fifteen microsatellite markers for the Appalachian Rockcap Fern, Polypodium appalachianum (Polypodiaceae), and its relatives. Applications in Plant Sciences  6(11) e1195. https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.1195.

Lovelace, A.H., A. Smith, and B.H. Kvitko. 2018. Pattern-triggered immunity alters the transcriptional regulation of virulence-associated genes and induces the sulfur starvation response in Pseudomonas syringae pv. tomato DC3000. Mol. Plant Microbe Interact. Jul;31(7):750-765.

Wilmoth, J.L., M.A. Moran, and A. Thompson. 2018. Transient O2 pulses direct Fe crystallinity and Fe(III)-reducer gene expression within a soil microbiome. Microbiome  Oct 23;6(1):189.

Bewg W.P., D. Ci, and C.-J. Tsai. 2018. Genome editing in trees: From multiple repair pathways to long-term stability. Frontiers in Plant Science  9:1732.

Harding S.A., H. Hu, B. Nyamdari, L.-J. Xue, R. Naran, and C.-J. Tsai. 2018. Tubulins, rhythms and cell walls in poplar leaves: it’s all in the timing. Tree Physiology  38:397-408.

Volden, R., T. Palmer, A. Byrne, C. Cole, R.J. Schmitz, R.E. Green, and C. Vollmers. 2018. Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA. Proc. Natl. Acad. Sci. U S A  25;115(39):9726-9731.

Rajshekar, S., J. Yao, P.K. Arnold, S.G. Payne, Y. Zhang, T.V. Bowman, R.J. Schmitz, J.R. Edwards, and G. Goll. 2018. Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome. Elife 28:7.

Lee, B.H., Z.T. Weber, M. Zourelidou, B.T. Hofmeister, R.J. Schmitz, C. Schwechheimer, and A.A. Dobritsa. 2018. Arabidopsis protein kinase D6PKL3 is involved in the formation of distinct plasma membrane aperture domains on the pollen surface. Plant Cell  30:2038-2056.

Ji L., W.T. Jordan, X. Shi, L. Hu, C. He, and R.J. Schmitz. 2018.  TET-mediated epimutagenesis of the Arabidopsis thaliana methylome. Nat. Commun. 9:895.

Galli, M., A. Khakhar, Z. Lu, Z. Chen, S. Sen, T. Joshi, J.L. Nemhauser, R.J. Schmitz, and A. Gallavotti. 2018. The DNA binding landscape of the maize auxin response factor family. Nat. Commun.  9:4526.

Finnegan, E.J., B. Ford, X. Wallace, F. Pettolino, P.T. Griffin, R.J. Schmitz, P. Zhang, J.M. Barrero, M.J. Hayden, S.A. Boden, C.A. Cavanagh, S.M. Swain, and B. Trevaskis. 2018. Zebularine treatment is associated with deletion of FT-B1 leading to an increase in spikelet number in bread wheat. Plant Cell Environ. 41(6):1346-1360.

Fallon, T.R., S.E. Lower, C.H. Chang, M. Bessho-Uehara, G.J. Martin, A.J. Bewick, M. Behringer, H.J. Debat, I. Wong, J.C. Day, A. Suvorov, C.J. Silva, K.F. Stanger-Hall, D.W. Hall, R.J. Schmitz, D.R. Nelson, S.M. Lewis, S. Shigenobu, S.M. Bybee, A.M. Larracuente, Y. Oba, and J.K. Weng. 2018. Firefly genomes illuminate parallel origins of bioluminescence in beetles. Elife 16:7.

Cunningham, C.B., L. Ji, E.C. McKinney, K.M. Benowitz, R.J. Schmitz, and A.J. Moore. 2018. Changes of gene expression but not cytosine methylation are associated with male parental care reflecting behavioural state, social context, and individual flexibility. J. Exp. Biol. 222, jeb188649.

Kamalanathan, M., C. Xu, K. Schwehr, L. Bretherton, M. Beaver, S.M. Doyle, J. Genzer, J. Hillhouse, J.B. Sylvan, P. Santschi, and A. Quigg. 2018. Extracellular enzyme activity profile in a chemically enhanced water accommodated fraction of surrogate oil: Toward understanding microbial activities after the Deepwater Horizon oil spill. Frontiers in Microbiology 9: 798.

Doyle, S.M., E.A. Whitaker, V. De Pascuale, T.L. Wade, A.H. Knap, P.H. Santschi, A. Quigg, and J.B. Sylvan. 2018. Rapid formation of microbe-oil aggregates and changes in community composition in coastal surface water following exposure to oil and the dispersant Corexit. Frontiers in Microbiology 9:689.

LaVoie, S.P., and A.O. Summers. 2018. Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure. BMC Genomics 19:52.

Publications 2015 - 2017

Huang, G., J. Xu, D.E. Lefever, T.C. Glenn, T. Nagy, and T.L. Guo. 2017. Genistein prevention of hyperglycemia and improvement of glucose tolerance in adult non-obese diabetic mice are associated with alterations of gut microbiome and immune homeostasis. Toxicol Appl Pharmacol.  332:138-148.

Kemp, K.M., J.R. Westrich, M.S. Alabady, M.L. Edwards, E.K. and Lipp. 2017. Abundance and multilocus sequence analysis of Vibrio bacteria associated with diseased elkhorn coral (Acropora palmata) of the Florida Keys. Appl. Environ. Microbiol. 84(2):e01035-17.

Gillespie, E., A. Pauley, M. Haffner, N. Hay, M. Estep, and Z. Murrell. 2017. Fourteen polymorphic microsatellite markers for a widespread limestone endemic, Carex eburnea (Cyperaceae). Applications in Plant Sciences. 5(8) 1700031. http://www.bioone.org/doi/full/10.3732/apps.1700031.

Stathopoulou, A., J.B. Chhetri, J.C. Ambrose, P.O. Esteve, L. Ji L, H. Erdjument-Bromage, G. Zhang, T.A. Neubert, S. Pradhan, J. Herrero, R.J. Schmitz, and S.K.T. Ooi. 2017. A novel requirement for DROSHA in maintenance of mammalian CG methylation. Nucleic Acids Res. 45:9810.

Mondo, S.J., R.O. Dannebaum, R.C. Kuo, K.B. Louie, A.J. Bewick, K. LaButti, S. Haridas, A. Kuo, A. Salamov, S.R. Ahrendt, R. Lau, B.P. Bowen, A. Lipzen, W. Sullivan, B.B. Andreopoulos, A. Clum, E. Lindquist, C. Daum, T.R. Northen, G. Kunde-Ramamoorthy, R.J. Schmitz, A. Gryganskyi, D. Culley, J. Magnuson, T.Y. James, M.A. O’Malley, J.E. Stajich, J.W. Spatafora, A. Visel, and I.V. Grigoriev. 2017. Widespread adenine N6-methylation of active genes in fungi. Nat. Genet. 49(6):964-968.

Lu, Z., B.T. Hofmeister, C. Vollmers, R.M. DuBois, and R.J. Schmitz. 2017. Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes. Nucleic Acids Res. 45:e41.

Hofmeister, B.T., K. Lee, N.A. Rohr, D.W. Hall, and R.J. Schmitz. 2017. Stable inheritance of DNA methylation allows creation of epigenotype maps and the study of epiallele inheritance patterns in the absence of genetic variation. Genome Biol. 18:155.

Edgar, P.P., R.D. Smith, M.R. McKain, A.M. Cooley, M. Vallejo-Marin, Y. Yuan, A.J. Bewick, L. Ji, A.E. Platts, M.J. Bowman, K.L. Childs, R.J. Schmitz, G.D. Smith, J.C. Pires, and J.R. Puzey. 2017. Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140 year old naturally established neo-allopolyploid monkeyflower. The Plant Cell 29(9):2150-2167.

Bewick, A.J., K.J. Vogel, A.J. Moore, and R.J. Schmitz.2017. Evolution of DNA methylation across insects. Mol. Biol. Evol. 34:654-665.

Bewick, A.J., C.E. Niederhuth, L. Ji, N.A. Rohr, P.T. Griffin, J. Leebens-Mack, and R.J. Schmitz. 2017. The evolution of chromomethylases and gene body DNA methylation in plants. Genome Biol.  18:65.

Borchert, A.J., D.M. Downs. 2017. Endogenously generated 2-aminoacrylate inhibits motility in Salmonella enterica. Scientific Reports. 7:12971.

Lefever, D.E., J. Xu, Y. Chen, G. Huang, N. Tamas, and T.L. Guo. 2016. TCDD modulation of gut microbiome correlated with liver and immune toxicity in streptozotocin (STZ)-induced hyperglycemic mice. Toxicol Appl Pharmacol. 304:48-58.

Rocha, D.M., A. Marques, C.G.T.J. Andrade, R. Guyot, S.R. Chaluvadi, A. Pedrosa-Harand, . . . and A.L.L. Vanzela. 2016. Developmental programmed cell death during asymmetric microsporogenesis in holocentric species of Rhynchospora (Cyperaceae). J. Exp. Bot. 67(18), 5391-5401. 10.1093/jxb/erw300

Franks, S.J., N.C. Kane, N.B. O’Hara, S. Tittes, and J.S. Rest. 2016. Rapid genome-wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendent gene pools. Molecular Ecology 25:3622-3631. doi: 10.1111/mec.13615. Cover article.

Niederhuth, C.E., A.J. Bewick, M.S. Alabady, K.D. Kim, Q. Li, N.A. Rohr, A. Rambani, J.M. Burke, J.A. Udall, C. Egesi, J. Schmutz, J. Grimwood, S.A. Jackson, N.M. Springer, and R.J. Schmitz. 2016. Widespread natural variation of DNA methylation within angiosperms. Genome Biology 17:194.

Behringer, M.G., and D.W. Hall. 2016. Genome-wide estimates of mutation rates and spectrum in Schizosaccharomyces pombe indicate CpG sites are highly mutagenic despite the absence of DNA methylation. G3 Genes Genomes Genetics 6:149-160.

Li, H.-X., K.L. Stevenson, and M.T. Brewer. 2016. Differences in sensitivity to a triazole fungicide among Stagonosporopsis species causing gummy stem blight of cucurbits. Plant Disease 100(10):2106-2112.

Wong, K., T.I. Shaw, A Oladeinde, T.C. Glenn, B. Oakley, and M. Molina. 2016. Rapid microbiome changes in freshly deposited cow feces under field conditions. Frontiers in Microbiology 7:500 doi: 10.3389/fmicb.2016.00500.

Kenny, A.M. and A.L. Sweigart. 2016. Reproductive isolation and introgression between sympatric Mimulus species. Molecular Ecology 25:2499-2517.

Bewick, A.J., L. Ji, C.E. Niederhuth, E.M. Willing, B.T. Hofmeister, X. Shi, L. Wang, Z. Lu, N.A. Rohr, B. Hartwig, C. Kiefer, R.B. Deal, J. Schmutz, J. Grimwood, H. Stroud, S.E. Jacobsen, K. Schneeberger, X. Zhang, and R.J. Schmitz. 2016. On the origin and evolutionary consequences of gene body DNA methylation. Proc. Natl. Acad. Sci. U S A. 113(32):9111-6.

Malakauskas, D.M., R.B. Snipes, A.M. Thompson, and D.W. Schloesser. 2016. Molecular evidence of undescribed Ceratonova sp. (Cnidaria: Myxosporea) in the freshwater polychaete, Manayumkia speciosa, from western Lake Erie. Journal of Invertebrate Pathology 137:49-53.

Hu H., X. Gu, L.-J. Xue, P.S. Swamy, S.A. Harding, and C.-J. Tsai. 2016. Tubulin C-terminal post-translational modifications do not occur in wood-forming tissues of Populus.  Frontiers in Plant Science. 7:1493.

Xue, L.-J., C.J. Frost, C.-J. Tsai, and S.A. Harding. 2016. Drought response transcriptomes are altered in poplar with reduced tonoplast sucrose transporter expression. Scientific Reports. 6:33655.

Yu, P., L. Ji, K.J. Lee, M. Yu, C. He, S. Ambati, E.C. McKinney, C. Jackson, C.A. Baile, R.J. Schmitz, and R.B. Meagher. 2016. Subsets of visceral adipose tissue nuclei with distinct levels of 5-hydroxymethylcytosine. PLoS One  11:e0154949.

Seymour, M., L. Ji, A.M. Santos, M. Kamei, T. Sasaki, E.Y. Basenko, R.J. Schmitz, X. Zhang, and Z.A. Lewis. 2016.  Histone H1 limits DNA methylation in Neurospora crassa. G3 (Bethesda) 6:1879-1889.

Reynolds, D.L., B.T. Hofmeister, L. Cliffe, T.N. Siegel, B.A. Anderson, S.M. Beverley, R.J. Schmitz, and R. Sabatini. 2016. Base J represses genes at the end of polycistronic gene clusters in Leishmania major by promoting RNAP II termination. Mol. Microbiol. 101:559-574.

Reynolds, D., B.T. Hofmeister, L. Cliffe, M. Alabady, T.N. Siegel, R.J. Schmitz, and R. Sabatini R. 2016. Histone H3 variant regulates RNA polymerase II transcription termination and dual strand transcription of siRNA loci in Trypanosoma brucei. PLoS Genet. 12:e1005758.

Panda, K., L. Ji, D.A. Neumann, J. Daron, R.J. Schmitz, R.K. Slotkin. 2016. Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation. Genome Biol. 17:170.

Hohos, N.M., K. Lee, L. Ji, M. Yu, M.M. Kandasamy, B.G. Phillips, C.A. Baile, C. He, R.J. Schmitz, and R.B. Meagher. 2016. DNA cytosine hydroxymethylation levels are distinct among non-overlapping classes of peripheral blood leukocytes. J. Immunol. Methods  436:1-15.

Griffin, P.T., C.E. Niederhuth, and R.J. Schmitz. 2016. A comparative analysis of 5-azacytidine- and zebularine-induced DNA demethylation. G3 (Bethesda) 6:2773-2780.

Bewick, A.J., B.T. Hofmeister, K. Lee, X. Zhang, D.W. Hall, and R.J. Schmitz. 2016. FASTmC: A suite of predictive models for nonreference-based estimations of DNA methylation. G3 (Bethesda) 2016, 6:447-452.

Bertioli, D.J., S.B. Cannon, L. Froenicke, G. Huang, A.D. Farmer, E.K. Cannon, X. Liu, D. Gao, J. Clevenger, S. Dash, L. Ren, M.C. Moretzsohn, K. Shirasawa, W. Huang, B. Vidigal, B. Abernathy, Y. Chu, C.E. Niederhuth, P. Umale, A.C. Araujo, A. Kozik, K. Do Kim, M.D. Burow, R.K. Varshney, X. Wang, X. Zhang, N. Barkley, P.M. Guimaraes, S. Isobe, B. Guo, B. Liao, H.T. Stalker, R.J. Schmitz, B.E. Scheffler, S.C. Leal-Bertioli, X. Xun, S.A. Jackson, R. Michelmore, and P. Ozias-Akins. 2016. The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat Genet 48:438-446.

Basenko, E.Y., M. Kamei, L. Ji, R.J. Schmitz, and Z.A. Lewis. 2016. The LSH/DDM1 homolog MUS-30 is required for genome stability, but not for DNA methylation in Neurospora crassa. PLoS Genet  12:e1005790.

Yu, M., L. Ji, D.A. Neumann, D.H. Chung, J. Groom, J. Westpheling, C. He, and R.J. Schmitz. 2015. Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing. Nucleic Acids Res. 43:e148.

Vlachogiannis, G., C.E. Niederhuth, S. Tuna, A. Stathopoulou, K. Viiri, D.G. de Rooij, R.G. Jenner, R.J. Schmitz, and S.K. Ooi. 2015. The Dnmt3L add domain controls cytosine methylation establishment during spermatogenesis. Cell Rep. 10(6):944-956.

van der Graaf, A., R. Wardenaar, D.A. Neumann, A. Taudt, R.G. Shaw, R.C. Jansen, R.J. Schmitz, M. Colome-Tatche, and F. Johannes. 2015. Rate, spectrum, and evolutionary dynamics of spontaneous epimutations. Proc Natl Acad Sci U S A  112:6676-6681.

Rancour, D.M., R.D. Hatfield, J.M. Marita, N.A. Rohr, and R.J. Schmitz. 2015. Cell wall composition and digestibility alterations in Brachypodium distachyon achieved through reduced expression of the UDP-arabinopyranose mutase. Front Plant Sci  6:446.

Christensen, S.A., A. Huffaker, F. Kaplan, J. Sims, S. Ziemann, G. Doehlemann, L. Ji, R.J. Schmitz, M.V. Kolomiets, H.T. Alborn, N. Mori, G. Jander, X. Ni, R.C. Sartor, S. Byers, Z. Abdo, and E.A. Schmelz. 2015.  Maize death acids, 9-lipoxygenase-derived cyclopente(a)nones, display activity as cytotoxic phytoalexins and transcriptional mediators. Proc Natl Acad Sci U S A 112(36):11407-12.

Stephens, J.D., W.L. Rogers, K. Heyduk, J.M. Cruse-Sanders, R.O. Determann, T.C. Glenn,  and R. L. Malmberg. 2015. Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment. Molecular Phylogenetics and Evolution 85: 76-87.

Schrey, A.W., R.K. Evans, M. Netherland, K.G. Ashton, H.R. Mushinsky, and E.D. McCoy. 2015. Phylogeography of the peninsula crowned snake (Tantilla relicta relicta) on the Lake Wales Ridge in Central Florida. Journal of Herpetology 49(3):415-419.

Stewart, J.E., A.N. Turner, and M.T. Brewer. 2015. Evolutionary history and variation in host range of three Stagonosporopsis species causing gummy stem blight of cucurbits. Fungal Biology 119: 370-382.

Stewart. J.E., K. Brooks, P.M. Brannen, W.O. Cline, and M.T. Brewer. 2015. Elevated genetic diversity in the emerging blueberry pathogen Exobasidium maculosum. PLOS ONE 10(7): e0132545.

Cunningham, C.B., L. Ji, R.A.W. Wiberg, J. Shelton, E.C. McKinney, D.J. Parker, R.B. Meagher, K.M. Benowitz, E.M. Roy-Zokan, M.G. Ritchie, S.J. Brown, R.J. Schmitz, and A.J. Moore. 2015. The Genome and methylome of a beetle with complex social behavior, Nicrophorus vespilloides (Coleoptera: Silphidae). Genome Biology and Evolution 7:3383-3396.

Roy-Zokan. E.M., C.B. Cunningham, L.E. Hebb, E.C. McKinney, and A.J. Moore. 2015. Vitellogenin and vitellogenin receptor gene expression is associated with male and female parenting in a subsocial insect. Proc. R. Soc. B 282:20150787.

Varaljay, V.A., J. Robidart, C.M. Preston, S.M. Gifford, B.P. Durham, A.S. Burns, J.P. Tyan, R. Marin III, R.P. Keine, J.P. Zehr, C.A. Scholin, and M.A. Moran. 2015. Single-taxon field measurements of bacterial gene regulation controlling DMSP fate. ISME Journal 9(7):1677-1686.

Xue, L.-J., M.S. Alabady, M. Mohebbi, and C.-J. Tsai. 2015. Exploiting genome variation to improve next-generation sequencing data analysis and genome editing efficiency in Populus tremula x alba 717-1B4. Tree Genetics and Genomes 11:82.

Zhou, X., T B. Jacobs, L.-J. Xue, S.A. Harding, and C.-J. Tsai. 2015. Exploiting SNPs for biallelic CRISPR mutations in the outcrossing woody perennial Populus reveals 4-coumarate: CoA ligase specificity and redundancy. New Phytologist. 208:298-301.

Alabady, M.S., W.L. Rogers, R.L. Malmberg. 2015. Development of transcriptomic markers for population analysis using restriction site associated RNA sequencing (RARseq). PLOS ONE 10(8):e0134855.

Publications 2012 - 2014

Chaluvadi, S.R., S. Khanam, M.A.M. Aly, and J.L. Bennetzen. 2014. Genetic diversity and population structure of native and introduced date palm (Phoenix dactylifera) germplasm in the United Arab Emirates. Trop. Plant Biol. 7(1), 30-41. 10.1007/s12042-014-9135-7

Vaughn, J.N., S.R. Chaluvadi, Tushar, L. Rangan, and J.L. Bennetzen. 2014. Whole plastome sequences from five ginger species facilitate marker development and define limits to barcode methodology. PLOS ONE 9(10), 8 pages. 10.1371/journal.pone.0108581

Ji L., T. Sasaki, X. Sun, P. Ma, Z.A. Lewis, and R.J. Schmitz. 2014. Methylated DNA is over-represented in whole-genome bisulfite sequencing data. Front Genet. 5:341

Brewer, M.T., A.N. Turner, P.M. Brannen, W.O. Cline, and E.A. Richardson. 2014. Exobasidium maculosum, a new species causing leaf and fruit spots on blueberry in the southeastern USA and its relationship with other Exobasidium spp. parasitic to blueberry and cranberry. Mycologia 106(3):415-423.

Lenz, P.H., V. Roncalli, R.P. Hassett, L.-S. Wu, M.C. Cieslak, D.K. Hartline, and A.E. Christie. 2014. De Novo Assembly of a Transcriptome for Calanus finmarchicus (Crustacea, Copepoda) – The Dominant Zooplankter of the North Atlantic Ocean. PLOS One 9(2): e88589. doi:10.1371/journal.pone.0088589.

Christie, A.E., T.M. Fontanilla, V. Roncalli, M.C. Cieslak, and P.H. Lenz. 2014. Diffusible gas transmitter signaling in the copepod crustacean Calanus finmarachicus: Identification of the biosynthetic enzymes of nitric oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H₂S) using a de novo assembled transcriptome. General and Comparative Endocrinology 202: 76-86.

Christie, A.E., T.M. Fontanilla, V. Roncalli, M.C. Cieslak, and P.H. Lenz. 2014. Identification and developmental expression of the enzymes responsible for dopamine, histamine, octopamine and serotonin biosynthesis in the copepod crustacean Calanus finmarchicus. General and Comparative Endocrinology 195: 28-39.

Reisch, C.R., W.M. Crabb, S.M. Gifford, Q. Teng, M.J. Stoudemayer, M.A. Moran, and W.B. Whitman. 2013. Metabolism of dimethylsulphoniopropionate by Ruegeria pomeroyi DSS-3. Molecular Microbiology 89(4): 774-791.

Sarmiento, F., J. Mrázek, and W.B. Whitman. 2013. Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis. PNAS 110(12): 4726-31.

Christie, A.E., V. Roncalli, L.S. Wu., C.L. Ganote., T. Doak, and P.H. Lenz. 2013. Peptidergic signaling in Calanus finmarchicus (Crustacea, Copepoda): In silico identification of putative peptide hormones and their receptors using a de novo assembled transcriptome. General and Comparative Endocrinology 187: 117-135.

Christie, A.E., T.M. Fontanilla, K.T. Nesbit, and P.H. Lenz. 2013. Prediction of the protein components of a putative Calanus finmarchicus (Crustacea, Copepoda) circadian signaling system using a de novo assembled transcriptome. Comparative Biochemistry and Physiology Part D 8: 165-193.

Sarmiento, F., J. Mrázek, and W.B. Whitman. 2013. Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis. PNAS 110(12):4726-4731.

Srivastava, A., K. Winker, T.I. Shaw, K.L. Jones, and T.C. Glenn. 2012. Transcriptome analysis of a North American songbird, Melospiza melodia. DNA Research 19(4): 325-33.

Crawford, N.G., B.C. Faircloth, J.E. McCormack, R.T. Brumfield, K. Winker and T.C. Glenn. 2012. More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biology Letters 8(5):783-6.

Faircloth, B.C., J.E. McCormack, N.G. Crawford, M.G. Harvey, R.T. Brumfield, and T.C. Glenn. 2012. Ultraconserved elements anchor thousands of genetic markers for target enrichment spanning multiple evolutionary timescales. Systematic Biology 61(5):717-26.

Faircloth, B.C. and T.C. Glenn. 2012. Not all sequence tags are created equal: Designing and validating sequence identification tags robust to indels. PLoS ONE 7(8):e42543, 66.

St. John, J.A., E.L. Braun, S.R. Isberg, L.G. Miles, A.Y. Chong, J. Gongora, P. Dalzell, C. Moran, B. Bed’Hom, A. Abzhanov, S.C. Burgess, A.M. Cooksey, T.A. Castoe, N.G. Crawford, L.D. Densmore, J.C. Drew, S.V. Edwards, B.C. Faircloth, M.K. Fujita, M.J. Greenwold, F.G. Hoffmann, J.M. Howard, T. Iguchi, D.E. Janes, S.Y. Khan, S. Kohno, A.P.J. de Koning, S.L. Lance, F.M. McCarthy, J.E. McCormack, M.E. Merchant, D.G. Peterson, D.D. Pollock, N. Pourmand, B.J. Raney, K.A. Roessler, J R. Sanford, R.H. Sawyer, C.J. Schmidt, E.W. Triplett, T. D. Tuberville, M. Venegas-Anaya, E.D. Jarvis, L.J. Guillette Jr., T. . Glenn, R.E. Green, and D.A. Ray. 2012. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology 13:415.

Zhu, Q., S.M. Smith, M. Ayele, L. Yang, and A. Jogi, S.R. Chaluvadi, and J.L. Bennetzen. 2012. High-throughput discovery of mutations in tef semi-dwarfing genes by next-generation sequencing analysis. Genetics 192(3), 819-+. 10.1534/genetics.112.144436

Publications 2009 - 2011

Al-Dous, E.K., B. George, M.E. Al-Mahmoud, M.Y. Al-Jaber, H. Wang, Y.M. Salameh, S. Chaluvadi,. . . J.A. Malek. 2011. De novo genome sequencing and comparative genomics to date palm (Phoenix dactylifera). Nat. Biotechnol. 29(6), 521-U84. 10.1038/nbt.1860

Glenn, T.C. 2011. Field guide to next-generation DNA sequencers. Molecular Ecology Resources 11(5):759-769. doi: 10.1111/j.1755-0998.2011.03024.x

Srivastava, A., W.L. Rogers, C.M. Breton, L. Cai, and R.L. Malmberg. 2011. Transcriptome analysis of Sarracenia, an insectivorous plant. DNA Res. 18(4):253-61.

Tsyusko, O., T. Glenn, Y. Yi, G. Joice, K. Jones, K. Aizawa, D. Coughlin, J. Zimbrick, and T. Hinton. 2011. Differential genetic responses to ionizing irradiation in individual families of Japanese medaka, Oryzias latipes. Mutation Research – Genetic Toxicology and Environmental Mutagenesis 718(1-2): 18-23. doi: 10.1016/j.mrgentox.2010.11.001.

Miles, L.G., S.R. Isberg, P.C. Thomson, T.C. Glenn, S.L. Lance, and C. Moran. 2009. QTL mapping for two commercial traits in farmed saltwater crocodiles (Crocodylus porosus ). Animal Genetics 41:142-149.

Miles, L.G., S.R. Isberg, T.C. Glenn, S.L. Lance, P. Dazell, P.C. Thomson, and C. Moran. 2009. A genetic linkage map for the saltwater crocodile (Crocodylus porosus). BMC Genomics 10:339. [Highly Accessed; top 100 PubMedCentral, August 2009]

Miles, L.G., S.L. Lance, S.R. Isberg, C. Moran, and T.C. Glenn. 2009. Cross-species amplification of microsatellites in crocodilians: assessment and applications for the future. Conservation Genetics 10:935-954. (Online in 2008).

Miles, L.G., S.R. Isberg, C. Moran, C. Hagen, and T.C. Glenn. 2009. 253 novel polymorphic microsatellites for the saltwater crocodile (Crocodylus porosus ). Conservation Genetics 10:963-980. (Online in 2008).

Faircloth, B.C., T.M. Terhune, N.A. Schable, T.C. Glenn, W.E. Palmer, and J.P. Carroll. 2009. Ten microsatellite loci from the Northern Bobwhite (Colinus virginianus ). Conservation Genetics 10:535-538. (Online in 2008).

Dalzell, P., L.G. Miles, S.R. Isberg, T.C. Glenn, C. King, V. Murtagh, and C. Moran. 2009. Standardized reference ideogram for physical mapping in the saltwater crocodile (Crocodylus porosus). Cytogenetic and Genome Research 127(2-4): 204-212. doi: 10.1159/000293286

Lance, S.L., T.D. Tuberville, L. Dueck, C. Holz-Schietinger, P.L. Trosclair III, R. M. Elsey, and T.C. Glenn. 2009. Multiyear multiple paternity and mate fidelity in the American alligator, Alligator mississippiensis. Molecular Ecology 18(21): 4508-4520. Cover Photo. doi: 10.1111/j.1365-294X.2009.04373.x