Publications acknowledging the Genome Center (2017-2021)

  • Meier, J.I., Salazar, P.A., Kučka, M., Davies, R.W., Dréau, A., Aldás, I., Box Power, O., Nadeau, N.J., Bridle, J.R., Rolian, C. et al. (2021) Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. Proc Natl Acad Sci U S A, 118.
     
  • Milani, A., Lutz, U., Galla, G., Scarabel, L., Weigel, D. and Sattin, M. (2021) Population structure and evolution of resistance to acetolactate synthase (ALS)-inhibitors in Amaranthus tuberculatus in Italy. Pest Manag Sci, 77, 2971-2980.
     
  • Barragan, A.C., Collenberg, M., Wang, J., Lee, R.R.Q., Cher, W.Y., Rabanal, F.A., Ashkenazy, H., Weigel, D. and Chae, E. (2021) A Truncated Singleton NLR Causes Hybrid Necrosis in Arabidopsis thaliana. Mol Biol Evol, 38, 557-574.
     
  • Wilches, R., Beluch, W.H., McConnell, E., Tautz, D. and Chan, Y.F. (2021) Independent evolution toward larger body size in the distinctive Faroe Island mice. G3 (Bethesda), 11.
     
  • Renahan, T., Lo, W.S., Werner, M.S., Rochat, J., Herrmann, M. and Sommer, R.J. (2021) Nematode biphasic 'boom and bust' dynamics are dependent on host bacterial load while linking dauer and mouth-form polyphenisms. Environ Microbiol.
     
  • Welter, D.K., Ruaud, A., Henseler, Z.M., De Jong, H.N., van Coeverden de Groot, P., Michaux, J., Gormezano, L., Waters, J.L., Youngblut, N.D. and Ley, R.E. (2021) Free-Living, Psychrotrophic Bacteria of the Genus Psychrobacter Are Descendants of Pathobionts. mSystems, 6.
     
  • Schmidt, V., Enav, H., Spector, T.D., Youngblut, N.D. and Ley, R.E. (2020) Strain-Level Analysis of Bifidobacterium spp. from Gut Microbiomes of Adults with Differing Lactase Persistence Genotypes. mSystems, 5.
     
  • Lang, P.L.M., Weiß, C.L., Kersten, S., Latorre, S.M., Nagel, S., Nickel, B., Meyer, M. and Burbano, H.A. (2020) Hybridization ddRAD-sequencing for population genomics of nonmodel plants using highly degraded historical specimen DNA. Mol Ecol Resour, 20, 1228-1247.
     
  • Weber, R., Chung, M.Y., Keskeny, C., Zinnall, U., Landthaler, M., Valkov, E., Izaurralde, E. and Igreja, C. (2020) 4EHP and GIGYF1/2 Mediate Translation-Coupled Messenger RNA Decay. Cell Rep, 33, 108262.
     
  • Fraser, B.A., Whiting, J.R., Paris, J.R., Weadick, C.J., Parsons, P.J., Charlesworth, D., Bergero, R., Bemm, F., Hoffmann, M., Kottler, V.A. et al. (2020) Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata). Genome Biol Evol, 12, 1789-1805.
     
  • Montgomery, J.S., Giacomini, D., Waithaka, B., Lanz, C., Murphy, B.P., Campe, R., Lerchl, J., Landes, A., Gatzmann, F., Janssen, A. et al. (2020) Draft Genomes of Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri. Genome Biol Evol, 12, 1988-1993.
     
  • Youngblut, N.D., de la Cuesta-Zuluaga, J., Reischer, G.H., Dauser, S., Schuster, N., Walzer, C., Stalder, G., Farnleitner, A.H. and Ley, R.E. (2020) Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity. mSystems, 5.
     
  • Aupalee, K., Wijit, A., Singphai, K., Rödelsperger, C., Zhou, S., Saeung, A. and Streit, A. (2020) Genomic studies on Strongyloides stercoralis in northern and western Thailand. Parasit Vectors, 13, 250.
     
  • Han, Z., Lo, W.S., Lightfoot, J.W., Witte, H., Sun, S. and Sommer, R.J. (2020) Improving Transgenesis Efficiency and CRISPR-Associated Tools Through Codon Optimization and Native Intron Addition in Pristionchus Nematodes. Genetics, 216, 947-956.
     
  • Regalado, J., Lundberg, D.S., Deusch, O., Kersten, S., Karasov, T., Poersch, K., Shirsekar, G. and Weigel, D. (2020) Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe-microbe interaction networks in plant leaves. Isme j, 14, 2116-2130.
     
  • Sieriebriennikov, B., Sun, S., Lightfoot, J.W., Witte, H., Moreno, E., Rödelsperger, C. and Sommer, R.J. (2020) Conserved nuclear hormone receptors controlling a novel plastic trait target fast-evolving genes expressed in a single cell. PLoS Genet, 16, e1008687.
     
  • Dréau, A., Venu, V., Avdievich, E., Gaspar, L. and Jones, F.C. (2019) Genome-wide recombination map construction from single individuals using linked-read sequencing. Nat Commun, 10, 4309.
     
  • Kreiner, J.M., Giacomini, D.A., Bemm, F., Waithaka, B., Regalado, J., Lanz, C., Hildebrandt, J., Sikkema, P.H., Tranel, P.J., Weigel, D. et al. (2019) Multiple modes of convergent adaptation in the spread of glyphosate-resistant Amaranthus tuberculatus. Proc Natl Acad Sci U S A, 116, 21076-21084.
     
  • Rowan, B.A., Heavens, D., Feuerborn, T.R., Tock, A.J., Henderson, I.R. and Weigel, D. (2019) An Ultra High-Density Arabidopsis thaliana Crossover Map That Refines the Influences of Structural Variation and Epigenetic Features. Genetics, 213, 771-787.
     
  • Zhou, S., Fu, X., Pei, P., Kucka, M., Liu, J., Tang, L., Zhan, T., He, S., Chan, Y.F., Rödelsperger, C. et al. (2019) Characterization of a non-sexual population of Strongyloides stercoralis with hybrid 18S rDNA haplotypes in Guangxi, Southern China. PLoS Negl Trop Dis, 13, e0007396.
     
  • Castro, J.P., Yancoskie, M.N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., Beluch, W.H., Naumann, R., Skuplik, I., Cobb, J. et al. (2019) An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. Elife, 8.
     
  • Barragan, C.A., Wu, R., Kim, S.T., Xi, W., Habring, A., Hagmann, J., Van de Weyer, A.L., Zaidem, M., Ho, W.W.H., Wang, G. et al. (2019) RPW8/HR repeats control NLR activation in Arabidopsis thaliana. PLoS Genet, 15, e1008313.
     
  • Gutaker, R.M., Weiß, C.L., Ellis, D., Anglin, N.L., Knapp, S., Luis Fernández-Alonso, J., Prat, S. and Burbano, H.A. (2019) The origins and adaptation of European potatoes reconstructed from historical genomes. Nat Ecol Evol, 3, 1093-1101.
     
  • Weng, M.L., Becker, C., Hildebrandt, J., Neumann, M., Rutter, M.T., Shaw, R.G., Weigel, D. and Fenster, C.B. (2019) Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in Arabidopsis thaliana. Genetics, 211, 703-714.
     
  • Poole, A.C., Goodrich, J.K., Youngblut, N.D., Luque, G.G., Ruaud, A., Sutter, J.L., Waters, J.L., Shi, Q., El-Hadidi, M., Johnson, L.M. et al. (2019) Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes. Cell Host Microbe, 25, 553-564.e557.
     
  • Lightfoot, J.W., Wilecki, M., Rödelsperger, C., Moreno, E., Susoy, V., Witte, H. and Sommer, R.J. (2019) Small peptide-mediated self-recognition prevents cannibalism in predatory nematodes. Science, 364, 86-89.
     
  • Zhu, W., Zaidem, M., Van de Weyer, A.L., Gutaker, R.M., Chae, E., Kim, S.T., Bemm, F., Li, L., Todesco, M., Schwab, R. et al. (2018) Modulation of ACD6 dependent hyperimmunity by natural alleles of an Arabidopsis thaliana NLR resistance gene. PLoS Genet, 14, e1007628.
     
  • Rödelsperger, C., Röseler, W., Prabh, N., Yoshida, K., Weiler, C., Herrmann, M. and Sommer, R.J. (2018) Phylotranscriptomics of Pristionchus Nematodes Reveals Parallel Gene Loss in Six Hermaphroditic Lineages. Curr Biol, 28, 3123-3127.e3125.
     
  • Prabh, N., Roeseler, W., Witte, H., Eberhardt, G., Sommer, R.J. and Rödelsperger, C. (2018) Deep taxon sampling reveals the evolutionary dynamics of novel gene families in Pristionchus nematodes. Genome Res, 28, 1664-1674.
     
  • Karasov, T.L., Almario, J., Friedemann, C., Ding, W., Giolai, M., Heavens, D., Kersten, S., Lundberg, D.S., Neumann, M., Regalado, J. et al. (2018) Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales. Cell Host Microbe, 24, 168-179.e164.
     
  • Exposito-Alonso, M., Vasseur, F., Ding, W., Wang, G., Burbano, H.A. and Weigel, D. (2018) Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana. Nat Ecol Evol, 2, 352-358.
     
  • Lazzarano, S., Kučka, M., Castro, J.P.L., Naumann, R., Medina, P., Fletcher, M.N.C., Wombacher, R., Gribnau, J., Hochepied, T., Van Montagu, M. et al. (2018) Genetic mapping of species differences via in vitro crosses in mouse embryonic stem cells. Proc Natl Acad Sci U S A, 115, 3680-3685.
     
  • Liu, C., Cheng, Y.J., Wang, J.W. and Weigel, D. (2017) Prominent topologically associated domains differentiate global chromatin packing in rice from Arabidopsis. Nat Plants, 3, 742-748.
     
  • Durvasula, A., Fulgione, A., Gutaker, R.M., Alacakaptan, S.I., Flood, P.J., Neto, C., Tsuchimatsu, T., Burbano, H.A., Pico, F.X., Alonso-Blanco, C. et al. (2017) African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana. Proc Natl Acad Sci U S A, 114, 5213-5218.
     
  • Zhu, W., Hu, B., Becker, C., Doğan, E.S., Berendzen, K.W., Weigel, D. and Liu, C. (2017) Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid. Genome Biol, 18, 157.
     
  • Swarts, K., Gutaker, R.M., Benz, B., Blake, M., Bukowski, R., Holland, J., Kruse-Peeples, M., Lepak, N., Prim, L., Romay, M.C. et al. (2017) Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America. Science, 357, 512-515.