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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Research Project #425248

Research Project: Genomics and Bioinformatics Research in Agriculturally Important Organisms

Location: Genomics and Bioinformatics Research

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Evaluation of carbon nanotube based copper nanoparticle composite for the efficient detection of agroviruses - (Peer Reviewed Journal)
Tahir, M.A., Bajwa, S.Z., Mansoor, S., Briddon, R.W., Khan, W.S., Scheffler, B.E., Amin, I. 2018. Evaluation of carbon nanotube based copper nanoparticle composite for the efficient detection of agroviruses. Journal of Hazardous Materials. 346:27–35. doi: 10.1016/j.jhazmat.2017.12.007.

Reference quality assembly of the 3.5 Gb genome of Capsicum annuum form a single linked-read library - (Peer Reviewed Journal)
Hulse, A.M., Maheshwari, S., Stoffel, K., Hill, T.A., Jaffe, D., Williams, S., Weisenfeld, N., Ramakrishnan, S., Kumar, V., Shah, P., Schatz, M.C., Church, D.M., Van Deynze, A. 2018. Reference quality assembly of the 3.5 Gb genome of Capsicum annuum form a single linked-read library. Horticulture Research. 5(4).doi: 10.1038/s41438-017-0011-0.

Subgenome-anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids - (Peer Reviewed Journal)

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea Reprint Icon - (Peer Reviewed Journal)
Bowers, R.M., Kyrpides, N.C., Stepanauskas, R., Harmon-Smith, M., Schulz, F., Doud, D., Reddy, T.K., Jarett, J., Rivers, A.R., Eloe-Fadrosh, E.A., Tringe, S.G., Ivanova, N., Copeland, A., Clum, A., Becraft, E.D., Malmstrom, R.R., Birren, B., Schriml, L., Podar, M., Bork, P., Weinstock, G.W., Banfield, .F., Garrity, G.M., Hugenholtz, P., Parks, D.H., Tyson, G.W., Rinke, C., Dodsworth, J.A., Yooseph, S., Sutton, G., Yilmaz, P., Glöckner, F.O., Meyer, F., Gilbert, J.A., Nelson, W.C., Hallam, S.J., Jungbluth, S.P., Ettema, T.J., Tighe, S., Konstantinidis, K.T., Liu, W., Baker, B.J., Rattei, T., Eisen, J.A., Hedlund, B., Mcmahon, K.D., Fierer, N., Knight, R., Finn, R., Karsch-Mizrachi, I., Eren, A.M., Woyke, T. 2017. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology. 35, 725–731. doi:10.1038/nbt.3893.

Setting the Stage for California Coffee Farming - (Abstract Only)

Patterns and drivers of fungal community depth stratification in Sphagnum peat Reprint Icon - (Peer Reviewed Journal)
Lamit, L.J., Romanowicz, K.J., Potvin, L.R., Rivers, A.R., Singh, K., Lennon, J.T., Tringe, S., Kane, E.S., Lilleskov, E.A. 2017. Patterns and drivers of fungal community depth stratification in Sphagnum peat. FEMS Microbiology Ecology. doi: 10.1093/femsec/fix082.

A developmental transcriptome map for allotetraploid arachis hypogaea Reprint Icon - (Peer Reviewed Journal)
Clevenger, J., Chu, Y., Scheffler, B.E., Ozias-Akins, P. 2016. A developmental transcriptome map for allotetraploid arachis hypogaea. Frontiers in Plant Science. 7:1446. doi: 10.3389/fpls.2016.01446.

Frequent occurrence of tomato leaf curl New Delhi virus in cotton leaf curl disease affected cotton in Pakistan - (Peer Reviewed Journal)
Zaidi, S.S., Shafiq, M., Amin, I., Scheffler, B.E., Scheffler, J.A., Briddon, R.W., Mansoor, S. 2016. Frequent occurrence of tomato leaf curl New Delhi virus in cotton leaf curl disease affected cotton in Pakistan. PLoS One. doi:10.1371/journal.pone.0155520.

Sesbania bispinosa, a new host of a begomovirus-betasatellite complex in Pakistan - (Peer Reviewed Journal)
Zaidi, S.S., Amin, I., Iqbal, Z., Akhtar, K.P., Scheffler, B.E., Mansoor, S. 2016. Sesbania bispinosa, a new host of a begomovirus-betasatellite complex in Pakistan. Canadian Journal of Plant Pathology. 38:1, 107-111, DOI:10.1080/07060661.2015.1128980.

Application of genomic, transcriptomic and metabolomic technologies in Arachis species - (Book / Chapter)
Chu, Y., Clevenger, J., Hovav, R., Wang, J., Scheffler, B.E., Jackson, S., Ozias-Akins, P. 2016. Peanuts: genetics, processing, and utilization. In: Elsevier. Application of genomic, transcriptomic and metabolomic technologies in Arachis species. San Diego, CA. p.209-239.

Virus-induced gene silencing in cultivated cotton (Gossypium spp.) using Tobacco rattle virus Reprint Icon - (Peer Reviewed Journal)
Mustafa, R., Shafiq, M., Mansoor, S., Briddon, R.W., Scheffler, B.E., Scheffler, J.A., Amin, I. 2016. Virus-induced gene silencing (VIGS) in cultivated cotton (Gossypium spp.) using Tobacco rattle virus (TRV). Molecular Biotechnology. 58:65–72. doi: 10.1007/s12033-015-9904-z.

Genomic resources for water yam (Dioscorea alata L.): analyses of EST-Sequences, De Novo sequencing and GBS libraries - (Peer Reviewed Journal)
Saski, C.A., Bhattacharjee, R., Scheffler, B.E., Asiedu, R. 2015. Genomic resources for water yam (Dioscorea alata L.): analyses of EST-Sequences, De Novo sequencing and GBS libraries. PLoS One. doi:10.1371/journal.pone.0134031.

Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall sythesis, represses lignification, and prolongs elongation Reprint Icon - (Peer Reviewed Journal)
Tuttle, J.R., Nah, G., Duke, M.V., Alexander, D.C., Guan, X., Song, Q., Chen, Z.J., Scheffler, B.E., Haigler, C.H. 2015. Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall sythesis, represses lignification, and prolongs elongation. Biomed Central (BMC) Genomics. 16:477. doi:10.1186/s12864-015-1708-9.

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.

Transcriptomic changes in zebrafish embryos and larvae following benzo[a]pyrene exposure - (Peer Reviewed Journal)
Fang, X., Corrales, J., Thornton, C., Clerk, T., Scheffler, B.E., Willett, K.L. 2015. Transcriptomic changes in zebrafish embryos and larvae following benzo[a]pyrene exposure. Toxicological Sciences. 146(2):395-411. doi: 10.1093/toxsci/kfv105..

The first nearly cryptic Scorpionfly (Mecoptera: Panorpidae) from North America - (Peer Reviewed Journal)
Bicha, W., Schiff, N., Lancaster, A., Scheffler, B.E. 2015. The first nearly cryptic Scorpionfly (Mecoptera: Panorpidae) from North America. Zootaxa. 3973(3):591–600. doi.org/10.11646/zootaxa.3973.3.12.

BAC-end sequence-based SNP mining in Allotetraploid Cotton (Gossypium) utilizing re-sequencing data, phylogenetic inferences and perspectives for genetic mapping - (Peer Reviewed Journal)
Hulse-Kemp, A.M., Hamid, A., Stoffel, K., Pepper, A.E., Saski, C., Scheffler, B.E., Fang, D.D., Chen, Z., Van Deynze, A., Zheng, X., Stelly, D.M. 2015. BAC-end sequence-based SNP mining in Allotetraploid Cotton (Gossypium) utilizing re-sequencing data, phylogenetic inferences and perspectives for genetic mapping. Genes, Genomes, and Genomics. 5:1095-1105. doi:10.1534/g3.115.017749/-/DC1.

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement - (Peer Reviewed Journal)
Zhang, T., Hu, Y., Jiang, W., Fang, L., Guan, X., Chen, J., Zhang, J., Saski, C., Scheffler, B.E., Stelly, D.M., Hulse-Kemp, A.M., Wan, Q., Liu, B., Liu, C., Wang, S., Pan, M., Wang, Y., Wang, D., Ye, W., Chang, L., Zhang, W., Song, Q., Kirkbride, R.C., Chen, X., Dennis, E., Llewellyn, D.J., Peterson, D.G., Thaxton, P., Jones, D.C., Wang, Q., Xu, X., Zhang, H., Wu, H., Zhou, L., Mei, G., Chen, S., Tian, Y., Xiang, D., Li, X., Ding, J., Zuo, Q., Tao, L., Liu, Y., Li, J., Lin, Y., Hui, Y., Cao, Z., Cai, C., Zhu, X., Jiang, Z., Zhou, B., Guo, W., Li, R., Chen, Z. 2015. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nature Biotechnology. 33(5):531-537. doi:10.1038/nbt.3207.

Development of microsatellites from Fothergilla xintermedia (Hamamelidaceae) and cross transfer to four other genera within Hamamelidaceae Reprint Icon - (Peer Reviewed Journal)
Hatmaker, E., Wadl, P.A., Mantooth, K., Scheffler, B.E., Ownley, B.H., Trigiano, R.N. 2015. Development of microsatellites from Fothergilla xintermedia (Hamamelidaceae) and cross transfer to four other genera within Hamamelidaceae. Applications in Plant Sciences. 3(4):1400123. doi.org/10.3732/apps.1400123. Availiable: http://www.bioone.org/doi/full/10.3732/apps.1400123.

Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection - (Peer Reviewed Journal)
Duitama, J., Silva, A., Sanabria, Y., Cruz, D., Quintero, C., Ballen, C., Lorieux, M., Scheffler, B.E., Farmer, A., Torres, E., Oard, J., Tohme, J. 2015. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection. PLoS One. 10(4):e0124617. doi:10.1371/journal.pone.0124617.

Development of microsatellites from Cornus mas L. (Cornaceae) and characterization of genetic diversity of cornelian cherries from China, central Europe, and the United States Reprint Icon - (Peer Reviewed Journal)
Wadl, P.A., Szyp-Borowska, I., Piórecki, N., Schlarbaum, S.E., Scheffler, B.E., Trigiano, R.N. 2014. Development of microsatellites from Cornus mas L. (Cornaceae) and characterization of genetic diversity of cornelian cherries from China, central Europe, and the United States. Scientia Horticulturae. 179:314-320.

Characterization of 12 polymorphic microsatellite loci of Pityopsis graminifolia var. latifolia Reprint Icon - (Peer Reviewed Journal)
Boggess, S.L., Wadl, P.A., Hadziabdic, D., Scheffler, B.E., Windham, A.S., Klingeman, W.E., Trigiano, R.N. 2014. Characterization of 12 polymorphic microsatellite loci of Pityopsis graminifolia var. latifolia. Conservation Genetics. 6(4):1043-1045. DOI: 10.1007/s12686-014-0282-9.

Effects on specific promoter DNA methylation in zebrafish embryos and larvae following benzo[a]pyrene exposure - (Peer Reviewed Journal)
Corrales, J., Fang, X., Thornton, C., Mei, W., Barbazuk, B.W., Duke, M.V., Scheffler, B.E., Willett, K.L. 2014. Effects on specific promoter DNA methylation in zebrafish embryos and larvae following benzo[a]pyrene exposure. Comparative Biochemistry and Physiology. Part C 163 (2014): 37-46.

Complete genome sequence of channel catfish gastrointestinal sepicemia isolate Edwardsiella tarda C07-087 Reprint Icon - (Peer Reviewed Journal)
Tekedar, H.C., Karsi, A., Williams, M.L., Vamenta, S., Banes, M.M., Duke, M.V., Scheffler, B.E., Lawrence, M.L. 2013. Complete genome sequence of channel catfish gastrointestinal sepicemia isolate Edwardsiella tarda C07-087. American Society for Microbiology. 1(6):e00959-13. doi:10.1128/genomeA.00959-13.