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                    U.S. DEPARTMENT OF AGRICULTURE
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Justin N Vaughn    Computational Biologist Phone: (706) 546-3185950 College Station Rd,Room 125Athens, GA 30605 Justin Vaughn received his doctoral degree from the University of Tennessee, Knoxville, working with Albecht von Arnim to develop computational pipelines for comparative transcriptomics in plants. As a postdoctoral researcher in Jeff Bennetzen's lab at the University of Georgia, Athens, Dr. Vaughn characterized structural variation in rice populations and used this data to develop new models of tandem duplication formation. He also assisted on numerous genome sequencing projects ranging from orphan grains to culinary herbs. He moved to Zenglu Li's group at the University of Georgia as a postdoctoral researcher and then research scientist. There, he helped in efforts to characterize the global soybean germplasm as well as dissect the genetic architecture of key agronomic traits such as seed composition. He has additionally consulted on the design of the Noble Foundation’s Alfalfa Breeder's Toolbox, which aims to enhance the usefulness of genomic and phenotypic information in cultivar development. He has spoken at numerous academic conferences and given talks internationally for the Health and Safety Institute (HESI) on genetically modified crops.  He joined GBRU in early 2017.  ProjectsIntegrative Applied Agricultural ‘Omics and Bioinformatics ResearchIn-House Appropriated (D)Accession Number:444279Genomic and Informatic Development for Genetic and Phenotypic AnalysisNon-Assistance Cooperative Agreement (S)Accession Number:445040Bioinformatics and Application DevelopmentNon-Assistance Cooperative Agreement (S)Accession Number:438884USDA ARS Research Apprenticeship Program at University of Texas at ArlingtonNon-Assistance Cooperative Agreement (S)Accession Number:442862  Publications(Clicking on the reprint iconReprint Icon  will take you to the publication reprint.)Introgression of a Danbaekkong high protein allele across different genetic backgrounds in soybean-(Peer Reviewed Journal)Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon-(Peer Reviewed Journal) Vaughn, J.N., Branham, S.E., Abernathy, B.L., Hulse-Kemp, A.M., Rivers, A.R., Levi, A., Wechter, W.P. 2022. Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon. Nature Genetics. https://doi.org/10.1038/s41467-022-35621-7.AT homopolymer strings in salmonella enterica subspecies I
contribute to speciation and serovar diversity-(Peer Reviewed Journal) Guard, J.Y., Rivers, A.R., Vaughn, J.N., Rothrock Jr, M.J., Oladeinde, A.A., Shah, D. 2021. AT homopolymer strings in salmonella enterica subspecies I contribute to speciation and serovar diversity. Microorganisms. 9(10):2075. https://doi.org/10.3390/microorganisms9102075.Lessons learned: the importance of biological curation-(Research Notes) Fountain, J., Clevenger, J., Vaughn, J.N., Guo, B. 2021. Lessons learned: the importance of biological curation. Microbiology Resource Announcements. Volume 10 Issue 48.Legacy genetics of arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange-(Peer Reviewed Journal) Bertioli, D.J., Clevenger, J., Godoy, I., Stalker, T., Wood, S., Santos, J., Ballen-Taborda, C., Abernathy, B., Azevedo, V., Campbell, J.D., Chavarro, C., Chu, Y., Farmer, A.D., Fonceka, D., Gao, D., Grimwood, J., Halpin, N., Korani, W., Michelotto, M.D., Ozias-Akins, P., Vaughn, J.N., Youngblood, R., Moretzsohn, M.C., Wright, G.C., Jackson, S.A., Cannon, S.B., Scheffler, B.E., Leal-Bertioli, S.M. 2021. Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange. Proceedings of the National Academy of Sciences(PNAS). 118(38). Article e2104899118. https://doi.org/10.1073/pnas.2104899118.New reference genomes and comparative genomics analyses in Aspergillus flavus-(Abstract Only)Gene disruption by structural mutations drives selection in US rice breeding over the last century-(Peer Reviewed Journal) Vaughn, J.N., Korani, W., Stein, J.C., Edwards, J., Peterson, D.G., Simpson, S.A., Youngblood, R.C., Grimwood, J., Ware, D., Mcclung, A.M., Scheffler, B.E. 2021. Gene disruption by structural mutations drives selection in US rice breeding over the last century. PLoS Genetics. 17(3): e1009389. https://doi.org/10.1371/journal.pgen.1009389.In vivo assembly of sorgoleone biosynthetic pathway and its impact on agroinfiltrated leaves of Nicotiana benthamiana-(Peer Reviewed Journal) Pan, Z., Bajsa Hirschel, J.N., Vaughn, J.N., Rimando, A.M., Baerson, S.R., Duke, S.O. 2021. In vivo assembly of sorgoleone biosynthetic pathway and its impact on agroinfiltrated leaves of Nicotiana benthamiana. New Phytologist. 230:683-697.Draft genome sequences of one Aspergillus parasiticus isolate and nine Aspergillus flavus isolates with varying stress tolerance and aflatoxin production-(Peer Reviewed Journal) Fountain, J.C., Clevenger, J.P., Nadon, B.D., Wang, H., Abbas, H.K., Kemerait, R.C., Scully, B.T., Vaughn, J.N., Guo, B. 2020. Draft genome sequences of one Aspergillus parasiticus idolate and nine Aspergillus flavus isolates with varying stress tolerance and aflatoxin production. Microbiology Resource Announcements. 9e00478-20. https://doi.org/10.1128/MRA.00478-20.Two new Aspergillus flavus reference genomes reveal a large insertion potentially contributing to isolate stress tolerance and aflatoxin production-(Peer Reviewed Journal) Fountain, J.C., Clevenger, J.P., Nadon, B.D., Youngblood, R.C., Chang, P., Starr, D., Wang, H., Wiggins, R., Kemerait, R.C., Bhatnagar, D., Ozias-Akins, P., Varshney, R.K., Scheffler, B.E., Vaughn, J.N., Guo, B. 2020. Two new Aspergillus flavus reference genomes reveal a large insertion potentially contributing to isolate stress tolerance and aflatoxin production. Genes, Genomes, and Genomics. 10(9). https://doi.org/10.1534/g3.120.401405.Gene disruption by structural mutations drives selection in U.S. rice breeding over the last century-(Proceedings) Vaughn, J.N., Stein, J.C., Korani, W., Edwards, J., Peterson, D.G., Simpson, S.A., Grimwood, J., Ware, D., McClung, A.M., Scheffler, B.E. 2021. Gene disruption by structural mutations drives selection in U.S. rice breeding over the last century. Proceedings of 38th Rice Technical Working Group Meeting, February 24-27, 2020, Orange Beach, Alabama. p 77. Electronic Publication.Genomic selection for yield and seed composition traits within an applied soybean breeding program-(Peer Reviewed Journal) Stewart-Brown, B.B., Song, Q., Vaughn, J., Li, Z. 2019. Genomic selection for yield and seed composition traits within an applied soybean breeding program . G3, Genes/Genomes/Genetics. https://doi.org/10.1534/g3.118.200917.Dissecting the role of oxidative stress in host-Aspergillus flavus interactions using genomics and genetic engineering-(Abstract Only)Transcriptome responses to the phytotoxin t-Chalcone in Arabidopsis thaliana L.-(Peer Reviewed Journal) Diaz-Tielas, C., Grana, E., Sanchez-Moreiras, A.M., Reigosa, M.J., Vaughn, J.N., Pan, Z., Bajsa Hirschel, J.N., Duke, S.O. 2019. Transcriptome responses to the phytotoxin t-Chalcone in Arabidopsis thaliana L. Pest Management Science. https://doi.org/10.1002/ps.5405.Crossword: A data-driven simulation language for the design of genetic-mapping experiments and breeding strategies-(Peer Reviewed Journal) Korani, W., Vaughn, J.N. 2019. Crossword: A data-driven simulation language for the design of genetic-mapping experiments and breeding strategies. bioRxiv. 9:4386. http://dx.doi.org/10.1101/330563.The hunt for the "silver bullet": Reference genome development and comparative genomics analysis of field isolates of Aspergillus flavus for identification of aflatoxin regulators-(Abstract Only)Use of omics methods to determine the mode of action of natural phytotoxins-(Book / Chapter) Duke, S.O., Pan, Z., Bajsa Hirschel, J.N., Sanchez-Moreiras, A.M., Vaughn, J.N. 2018. Use of omics methods to determine the mode of action of natural phytotoxins. American Chemical Society Symposium Series. 1294:33-46.A Reference Genome for US Rice-(Abstract Only) Scheffler, B.E., Edwards, J., Stein, J., Ware, D., Vaughn, J.N., Schmutz, J., Peterson, D., Youngblood, C., Duke, M.V., Grimwood, J., Simpson, S.A., Mcclung, A.M. 2018. A Reference Genome for US Rice. Meeting Abstract. 37th Rice Technical Working Group.p.50.  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