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                    U.S. DEPARTMENT OF AGRICULTURE
 Genomics and Bioinformatics Research: Stoneville, MS
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Sheron  Simpson    Biological Science Technician Phone: (662) 686-3699 Fax:     (662) 686-3567 JWDSRC, Bldg.1, Room 222B 141 Experiment Station Road PO Box 36 Stoneville, MS 38776-0036  Publications(Clicking on the reprint iconReprint Icon  will take you to the publication reprint.)Long-read sequencing  broadens access to genetic and transcript diversity for high-value traits in sorghum-(Abstract Only)Annotated whole-genome sequences of fermentative and spoilage associated Bacilli and Proteobacteria autochthonous to commercial cucumber fermentation-(Peer Reviewed Journal) Page, C.A., Simpson, S.A., Perez Diaz, I.M., Rivers, A.R. 2024. Annotated whole-genome sequences of fermentative and spoilage associated Bacilli and Proteobacteria autochthonous to commercial cucumber fermentation. Microbiology Resource Announcements. 13:e00926-23. https://doi.org/10.1128/mra.00926-23.Molecular Dissection of the 5S Ribosomal RNA-Intergenic Transcribed Spacers in Saccharum spp. and Tripidium spp.-(Peer Reviewed Journal) Pan, Y., Todd, J.R., Lomax, L.E., White Jr, P.M., Simpson, S.A., Scheffler, B.E. 2023. Molecular Dissection of the 5S Ribosomal RNA-Intergenic Transcribed Spacers in Saccharum spp. and Tripidium spp.. Agronomy Journal. https://doi.org/10.3390/agronomy13112728.Discovery of a resistance gene cluster associated with smut resistance in peanut-(Peer Reviewed Journal)Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa-(Peer Reviewed Journal) Huff, M., Babiker, E.M., Hulse-Kemp, A.M., Scheffler, B.E., Youngblood, R.C., Simpson, S.A., Staton, M. 2023. Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa. BMC Genomics. https://doi.org/10.1186/s12864-023-09514-y.Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions-(Peer Reviewed Journal) Waldbieser, G.C., Liu, S., Yuan, Z., Older, C.E., Gao, D., Shi, C., Bosworth, B.G., Li, N., Boa, L., Kirby, M.A., Jin, Y., Wood, M.L., Scheffler, B.E., Simpson, S.A., Youngblood, R.C., Duke, M.V., Ballard, L.L., Phillipy, A., Koren, S., Liu, Z. 2023. Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions. BMC Biology. 21:67. https://doi.org/10.1186/s12915-023-01556-8.Initiation of genomics-assisted breeding in virginia-type peanuts through the generation of a de novo reference genome and informative markers-(Peer Reviewed Journal) Newman, C.S., Andres, R.J., Youngblood, R.C., Campbell, J.D., Simpson, S.A., Cannon, S.B., Scheffler, B.E., Oakley, A.T., Hulse-Kemp, A.M., Dunne, J.C. 2023. Initiation of genomics-assisted breeding in Virginia-type peanuts through the generation of a de novo reference genome and informative markers. Frontiers in Plant Science. 13.Article 1073542. https://doi.org/10.3389/fpls.2022.1073542.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.Clonal diversity, cultivar traits, geographic dispersal, and the ethnotaxonomy of cultivated Qat (Catha edulis, Celastraceae)-(Peer Reviewed Journal) Tembrock, L.R., Simmons, M.P., Richards, C.M., Reeves, P.A., Reilley, A.A., Curto, M.A., Meimberg, H., Ngugi, G., Demissew, S., Abdul Wali, A., Al-Thobhani, M., Simpson, S.A., Varisco, D.M. 2020. Clonal diversity, cultivar traits, geographic dispersal, and the ethnotaxonomy of cultivated Qat (Catha edulis, Celastraceae). Economic Botany. 74:273-297. https://doi.org/10.1007/s12231-020-09501-4.Development of nuclear microsatellite markers to facilitate germplasm conservation and population genetics studies of five groups of tropical perennial plants with edible fruits and shoots: ranbutan (Nephelium lappaceumt)-(Peer Reviewed Journal) Arias De Ares, R.S., Ballard, L.L., Duke, M.V., Simpson, S.A., Liu, X.F., Orner, V.A., Sobolev, V., Scheffler, B.E., Martinez-Castillo, J. 2020. Development of nuclear microsatellite markers to facilitate germplasm conservation and population genetics studies of five groups of tropical perennial plants with edible fruits and shoots: ranbutan (Nephelium lappaceumt). Genetic Resources and Crop Evolution. https://doi.org/10.1007/s10722-020-00965-w.Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement-(Peer Reviewed Journal) Chen, Z., Sreedasyam, A., Ando, A., Song, Q., De Santiago, L., Hulse-Kemp, A.M., Ding, M., Ye, W., Kirkbride, R., Jenkins, J., Plott, C., Lovell, J., Yu-Ming, L., Vaughn, R., Liu, B., Simpson, S.A., Scheffler, B.E. 2020. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Nature Genetics. https://doi.org/10.1038/s41588-020-0614-5.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.Mitogenome and nuclear-encoded fungicide-target genes of Thecaphora frezii- causal agent of peanut smut-(Peer Reviewed Journal) Arias De Ares, R.S., Cazon, I., Massa, A.N., Scheffler, B.E., Sobolev, V., Lamb, M.C., Duke, M.V., Simpson, S.A., Conforto, C., Paredes, J., Soave, J., Buteler, M., Rago, A.M. 2019. Mitogenome and nuclear-encoded fungicide-target genes of Thecaphora frezii- causal agent of peanut smut. Fungal Genomics and Biology. (9)1:160. https://doi.org/10.35248/2165-8056.19.9.160.New tools to screen wild peanut species for aflatoxin accumulation and genetic fingerprinting-(Peer Reviewed Journal) Arias De Ares, R.S., Sobolev, V., Massa, A.N., Orner, V.A., Walk, T., Simpson, S.A., Ballard, L.L., Puppala, N., Scheffler, B.E., De Blass, F., Tallury, S.P., Guillermo, S. 2018. New tools to screen wild peanut species for aflatoxin accumulation and genetic fingerprinting. Biomed Central (BMC) Plant Biology. https://doi.org/10.1186/s12870-018-1355-9.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)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.Length and nucleotide sequence polymorphism at the trnL and trnF non-coding regions of chloroplast genomes among Saccharum and Erianthus species-(Abstract Only) Pan, Y., Todd, J.R., Scheffler, B.E., Hale, A.L., Lomax, L.E., Simpson, S.A., Liu, F., Grisham, M.P. 2017. Length and nucleotide sequence polymorphism at the trnL and trnF non-coding regions of chloroplast genomes among Saccharum and Erianthus species [abstract]. Journal of the American Society of Sugar Cane Technologists. 37:32.Phylogeography of the wild and cultivated stimulant plant qat (Catha edulis, Celastraceae) in areas of historic cultivation1-(Peer Reviewed Journal) Tembrock, L., Simmons, M., Richards, C.M., Reeves, P.A., Reilley, A.A., Curto, M.A., Meimberg, H., Ngugi, G., Demissew, S., Wali Al Khulaidi, A., Mansoor, A., Simpson, S.A., Varisco, D. 2017. Phylogeography of the wild and cultivated stimulant plant qat (Catha edulis, Celastraceae) in areas of historic cultivation1. American Journal of Botany. 104: 538-549.Colistin resistance mcr-1 gene bearing Escherichia coli from the United States-(Peer Reviewed Journal) Meinersmann, R.J., Ladely, S.R., Plumblee Lawrence, J.R., Hall, M.C., Simpson, S.A., Ballard, L.L., Scheffler, B.E., Genzlinger, L.L., Cook, K.L. 2016. Colistin resistance mcr-1 gene bearing Escherichia coli from the United States. Genome Announcements. 4(5):898-16.Development of a large set of microsatellite markers in Zapote Maney (Pouteria sapota (Jacq.) (H.E. Moore & Stearn) and their potential use in the study of the species-(Peer Reviewed Journal) Arias De Ares, R.S., Castillo, J.M., Sobolev, V., Blancarte-Jasso, N.H., Simpson, S.A., Ballard, L.L., Duke, M.V., Liu, X.F., Irish, B.M., Scheffler, B.E. 2015. Development of a large set of microsatellite markers in Zapote Maney (Pouteria sapota (Jacq.) (H.E. Moore & Stearn) and their potential use in the study of the species. Molecules. 20(60):11400-11417.Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences-(Peer Reviewed Journal) Gardner, E.M., Laricchia, K.M., Murphy, M., Ragone, D., Scheffler, B.E., Simpson, S.A., Williams, E., Zerega, N.C. 2015. Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences. Applications in Plant Sciences. 3(9):1500049. doi:10.3732/apps.1500049.Ecology, Behavior and Bionomics: First Genotyping of Spodoptera frugiperda (J. E. Smith)(Lepidoptera: Noctuidae) Progeny from Crosses between Bt-Resistant and Bt-Susceptible Populations, and 65-Locus Discrimination of Isofami-(Peer Reviewed Journal) Arias De Ares, R.S., Portilla, M., Ray, J.D., Blanco, C.A., Simpson, S.A., Scheffler, B.E. 2015. Ecology, Behavior and Bionomics: First Genotyping of Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) Progeny from Crosses between Bt-Resistant and Bt-Susceptible Populations, and 65-Locus Discrimination of Isofamilies. The Journal of Botanical Society. 4:18-29.Diversity of the breadfruit complex (Artocarpus, Moraceae): Genetic characterization of critical germplasm-(Peer Reviewed Journal) Zerega, N., Wiesner-Hanks, T., Ragone, D., Irish, B.M., Scheffler, B.E., Simpson, S.A., Zee, F.T. 2015. Diversity of the breadfruit complex (Artocarpus, Moraceae): Genetic characterization of critical germplasm. Tree Genetics and Genomes. doi: 10.1007/s11295-014-0824-z.Musa spp. germplasm management: microsatellite fingerprinting of USDA-ARS National Plant Germplasm System (NPGS) collection-(Peer Reviewed Journal) Irish, B.M., Cuevas, H.E., Simpson, S.A., Scheffler, B.E., Sardos, J., Ploetz, R., Goenaga, R.J. 2014. Musa spp. germplasm management: microsatellite fingerprinting of USDA-ARS National Plant Germplasm System (NPGS) collection. Crop Science. 54:2140-2151.Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species-(Peer Reviewed Journal) Witherup, C., Ragone, D., Wiesner-Hanks, T., Irish, B.M., Scheffler, B.E., Simpson, S.A., Zee, F.T., Zuberi, M., Zerega, N. 2013. Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species. Applications in Plant Sciences. 1(7):1200423. doi: org/10.3732/apps.1200423.Batch Isolation of Microsatellites for Tropical Plant Species Pyrosequencing-(Abstract Only) Arias De Ares, R.S., Irish, B.M., Ballard, L.L., Duke, M.V., Liu, X.F., Simpson, S.A., Scheffler, B.E. 2010. Batch Isolation of Microsatellites for Tropical Plant Species Pyrosequencing. Plant and Animal Genome. Abstract P089.UPIC + GO: Zeroing in on informative markers-(Other) Ford, D., Arias, R.S., Ballard, L.L., Scheffler, B.E., Duke, M.V., Simpson, S.A., Newsome, A. 2010. UPIC + GO: Zeroing in on informative markers. Eighth Annual Rocky Mountain Bioinformatics Conference, International Society of Computational Biology (ISCB), December 09-11, 2010, Aspen, CO. Meeting Proceedings.


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