Publications

How to acknowledge GGF

If work performed for you at the Georgia Genomics Facility (GGF) results in publication, please acknowledge us with one of the following statements, or a similar one, so that we may continue to bring you excellent service:

“This work was performed with the support of the Georgia Genomics Facility at the University of Georgia.” “We thank the Georgia Genomics Facility, which provided the ___________ service.” “The ___________ service was provided by the Georgia Genomics Facility.” “We thank the Georgia Genomics Facility for technical support.” “Samples were shipped to the Georgia Genomics Facility for library preparation and sequencing.” “Paired-end Illumina sequencing was performed on an Illumina NextSeq 500 system using the high output kit v2 with 300 cycles (150 bp PE sequencing) at the Georgia Genomics Facility, University of Georgia, Athens, GA, USA.”

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

Publications 2017 - 2015

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. Accepted for publication at PNAS.

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.

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. doi: 10.1111/nph.13470.

Publications 2012 - 2014

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.

Publications 2009 - 2011

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

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