Matthew A. Siemon

Tomato pan-genome

Latest Research

  • Article |

    CRISPR screens identify JNK–JUN family genes as repressors of definitive endoderm differentiation in human pluripotent stem cells. JUN co-occupies stem cell enhancers with OCT4, NANOG, SMAD2 and SMAD3 and inhibits the exit from pluripotency.

    • Qing V. Li
    • , Gary Dixon
    • , Nipun Verma
    • , Bess P. Rosen
    • , Miriam Gordillo
    • , Renhe Luo
    • , Chunlong Xu
    • , Qiong Wang
    • , Chew-Li Soh
    • , Dapeng Yang
    • , Miguel Crespo
    • , Abhijit Shukla
    • , Qing Xiang
    • , Friederike Dündar
    • , Paul Zumbo
    • , Matthew Witkin
    • , Richard Koche
    • , Doron Betel
    • , Shuibing Chen
    • , Joan Massagué
    • , Ralph Garippa
    • , Todd Evans
    • , Michael A. Beer
    •  & Danwei Huangfu
  • Letter |

    The authors present a new genomic prediction method for maize germplasm evaluation under genotype × environment interaction, in which genotype × environment interaction of grain yield components is modeled as genotypic sensitivity to environmental drivers.

    • Emilie J. Millet
    • , Willem Kruijer
    • , Aude Coupel-Ledru
    • , Santiago Alvarez Prado
    • , Llorenç Cabrera-Bosquet
    • , Sébastien Lacube
    • , Alain Charcosset
    • , Claude Welcker
    • , Fred van Eeuwijk
    •  & François Tardieu
  • Article |

    Release of paused Pol II at specific intronic loci or chromatin domains favors the formation of abnormal DNA recombination, leading to cancer-associated chromosomal translocations.

    • Gaetano Ivan Dellino
    • , Fernando Palluzzi
    • , Andrea Maria Chiariello
    • , Rossana Piccioni
    • , Simona Bianco
    • , Laura Furia
    • , Giulia De Conti
    • , Britta A. M. Bouwman
    • , Giorgio Melloni
    • , Davide Guido
    • , Luciano Giacò
    • , Lucilla Luzi
    • , Davide Cittaro
    • , Mario Faretta
    • , Mario Nicodemi
    • , Nicola Crosetto
    •  & Pier Giuseppe Pelicci
  • Article |

    A tomato pan-genome constructed from genome sequences of 725 tomato accessions captures 4,873 genes absent from the reference genome and identifies a rare allele of TomLoxC regulating fruit flavor.

    • Lei Gao
    • , Itay Gonda
    • , Honghe Sun
    • , Qiyue Ma
    • , Kan Bao
    • , Denise M. Tieman
    • , Elizabeth A. Burzynski-Chang
    • , Tara L. Fish
    • , Kaitlin A. Stromberg
    • , Gavin L. Sacks
    • , Theodore W. Thannhauser
    • , Majid R. Foolad
    • , Maria Jose Diez
    • , Jose Blanca
    • , Joaquin Canizares
    • , Yimin Xu
    • , Esther van der Knaap
    • , Sanwen Huang
    • , Harry J. Klee
    • , James J. Giovannoni
    •  & Zhangjun Fei
  • Analysis |

    Exome sequencing of a worldwide panel of 487 wheat genotypes, including landraces, cultivars and modern varieties, sheds light on wheat genomic diversity and the evolution of modern bread wheat.

    • Caroline Pont
    • , Thibault Leroy
    • , Michael Seidel
    • , Alessandro Tondelli
    • , Wandrille Duchemin
    • , David Armisen
    • , Daniel Lang
    • , Daniela Bustos-Korts
    • , Nadia Goué
    • , François Balfourier
    • , Márta Molnár-Láng
    • , Jacob Lage
    • , Benjamin Kilian
    • , Hakan Özkan
    • , Darren Waite
    • , Sarah Dyer
    • , Thomas Letellier
    • , Michael Alaux
    • , Joanne Russell
    • , Beat Keller
    • , Fred van Eeuwijk
    • , Manuel Spannagl
    • , Klaus F. X. Mayer
    • , Robbie Waugh
    • , Nils Stein
    • , Luigi Cattivelli
    • , Georg Haberer
    • , Gilles Charmet
    •  & Jérôme Salse

News & Comment

  • Editorial |

    The field of cancer genomics is currently in an exciting and fast-paced era. With advances in sequencing technologies, computational approaches and tumor models, understanding of cancer processes is at an all-time high, and the application of new methods to studying cancer holds great promise for developing important breakthroughs in cancer treatment and prevention.

  • News & Views |

    The conserved ligand–receptor pair CLAVATA1–CLAVATA3, which maintains homeostasis in shoot apical meristems, responds differently to perturbation in tomato, Arabidopsis and maize. Active compensation occurs in CLE signaling peptides in tomato, but compensation is passive in Arabidopsis.

    • Elizabeth A. Kellogg
  • Comment |

    The Nordic region, comprising primarily Denmark, Estonia, Finland, Iceland, Norway and Sweden, has many of the necessary characteristics for being at the forefront of genome-based precision medicine. These include egalitarian and universal healthcare, expertly curated patient and population registries, biobanks, large population-based prospective cohorts linked to registries and biobanks, and a widely embraced sense of social responsibility that motivates public engagement in biomedical research. However, genome-based precision medicine can be achieved only through coordinated action involving all actors in the healthcare sector. Now is an opportune time to organize scientists in the Nordic region, together with other stakeholders including patient representatives, governments, pharmaceutical companies, academic institutions and funding agencies, to initiate a Nordic Precision Medicine Initiative. We present a roadmap for how this organization can be created. The Initiative should facilitate research, clinical trials and knowledge transfer to meet regional and global health challenges.

    • Pål Rasmus Njølstad
    • , Ole Andreas Andreassen
    • , Søren Brunak
    • , Anders D. Børglum
    • , Joakim Dillner
    • , Tõnu Esko
    • , Paul W. Franks
    • , Nelson Freimer
    • , Leif Groop
    • , Hakon Heimer
    • , David M. Hougaard
    • , Eivind Hovig
    • , Kristian Hveem
    • , Anu Jalanko
    • , Jaakko Kaprio
    • , Gun Peggy Knudsen
    • , Mads Melbye
    • , Andres Metspalu
    • , Preben Bo Mortensen
    • , Juni Palmgren
    • , Aarno Palotie
    • , Wenche Reed
    • , Hreinn Stefánsson
    • , Nathan O. Stitziel
    • , Patrick F. Sullivan
    • , Unnur Thorsteinsdóttir
    • , Marc Vaudel
    • , Eero Vuorio
    • , Thomas Werge
    • , Camilla Stoltenberg
    •  & Kári Stefánsson
  • News & Views |

    Resolving variant-to-function relationships is a key challenge faced by human geneticists. A new study combining statistical fine-mapping with cell-type-specific functional annotations advances the understanding of the regulatory consequences of genetic variants associated with variations in blood-cell traits.

    • Manuel Tardaguila
    •  & Nicole Soranzo
  • News & Views |

    More than one dozen hereditary ataxias are caused by repeat expansions. A newly discovered expansion may be the first known common genetic cause of late-onset ataxia.

    • Vikram Shakkottai
    •  & Henry Paulson

About the Journal

  • Nature Genetics publishes the very highest quality research in genetics, encompassing genetic and functional genomic studies on human and plant traits and on other model organisms.

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