{"entity": "researcher", "timestamp": "2026-09-23T22:45:36.667Z", "family": "Klopp", "given": "Christophe", "initials": "C", "orcid": "0000-0001-7126-5477", "affiliations": ["Plateforme bioinformatique Toulouse Midi-Pyr\u00e9n\u00e9es, INRA, Auzeville Castanet-Tolosan, France."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/2507fcaf0ec6418da9007120d73cab78.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/2507fcaf0ec6418da9007120d73cab78"}}, "publications": [{"entity": "publication", "iuid": "0e2f850002ed44b19c78b9f81127edc3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0e2f850002ed44b19c78b9f81127edc3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0e2f850002ed44b19c78b9f81127edc3"}}, "title": "Oak genome reveals facets of long lifespan.", "authors": [{"family": "Plomion", "given": "Christophe", "initials": "C", "orcid": "0000-0002-3176-2767", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e7f8221d434e49788dfdffadccbe4f67.json"}}, {"family": "Aury", "given": "Jean-Marc", "initials": "JM", "orcid": "0000-0003-1718-3010", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1261c452f6d740579a12006bafc91295.json"}}, {"family": "Amselem", "given": "Jo\u00eblle", "initials": "J"}, {"family": "Leroy", "given": "Thibault", "initials": "T"}, {"family": "Murat", "given": "Florent", "initials": "F"}, {"family": "Duplessis", "given": "S\u00e9bastien", "initials": "S", "orcid": "0000-0002-2072-2989", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/83cb341746a447c493ab89bcddfce4f6.json"}}, {"family": "Faye", "given": "S\u00e9bastien", "initials": "S"}, {"family": "Francillonne", "given": "Nicolas", "initials": "N"}, {"family": "Labadie", "given": "Karine", "initials": "K"}, {"family": "Le Provost", "given": "Gr\u00e9goire", "initials": "G"}, {"family": "Lesur", "given": "Isabelle", "initials": "I"}, {"family": "Bartholom\u00e9", "given": "J\u00e9r\u00f4me", "initials": "J", "orcid": "0000-0002-0855-3828", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ef2baa71c904fb486d6db735a7cc68a.json"}}, {"family": "Faivre-Rampant", "given": "Patricia", "initials": "P"}, {"family": "Kohler", "given": "Annegret", "initials": "A"}, {"family": "Lepl\u00e9", "given": "Jean-Charles", "initials": "JC"}, {"family": "Chantret", "given": "Nathalie", "initials": "N"}, {"family": "Chen", "given": "Jun", "initials": "J"}, {"family": "Di\u00e9vart", "given": "Anne", "initials": "A"}, {"family": "Alaeitabar", "given": "Tina", "initials": "T"}, {"family": "Barbe", "given": "Val\u00e9rie", "initials": "V"}, {"family": "Belser", "given": "Caroline", "initials": "C", "orcid": "0000-0002-8108-9910", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/888f0fb8772444288df8f9bfa92ab3f3.json"}}, {"family": "Berg\u00e8s", "given": "H\u00e9l\u00e8ne", "initials": "H"}, {"family": "Bod\u00e9n\u00e8s", "given": "Catherine", "initials": "C"}, {"family": "Bogeat-Triboulot", "given": "Marie-B\u00e9atrice", "initials": "MB"}, {"family": "Bouffaud", "given": "Marie-Lara", "initials": "ML"}, {"family": "Brachi", "given": "Benjamin", "initials": "B", "orcid": "0000-0001-5988-7150", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/777e360128c1474db4a408d259c09c8d.json"}}, {"family": "Chancerel", "given": "Emilie", "initials": "E"}, {"family": "Cohen", "given": "David", "initials": "D"}, {"family": "Couloux", "given": "Arnaud", "initials": "A"}, {"family": "Da Silva", "given": "Corinne", "initials": "C"}, {"family": "Dossat", "given": "Carole", "initials": "C"}, {"family": "Ehrenmann", "given": "Fran\u00e7ois", "initials": "F"}, {"family": "Gaspin", "given": "Christine", "initials": "C"}, {"family": "Grima-Pettenati", "given": "Jacqueline", "initials": "J"}, {"family": "Guichoux", "given": "Erwan", "initials": "E"}, {"family": "Hecker", "given": "Arnaud", "initials": "A"}, {"family": "Herrmann", "given": "Sylvie", "initials": "S"}, {"family": "Hugueney", "given": "Philippe", "initials": "P"}, {"family": "Hummel", "given": "Ir\u00e8ne", "initials": "I"}, {"family": "Klopp", "given": "Christophe", "initials": "C", "orcid": "0000-0001-7126-5477", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2507fcaf0ec6418da9007120d73cab78.json"}}, {"family": "Lalanne", "given": "C\u00e9line", "initials": "C"}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0730d0f9c2524eb19383640612924701.json"}}, {"family": "Lasserre", "given": "Eric", "initials": "E"}, {"family": "Lemainque", "given": "Arnaud", "initials": "A"}, {"family": "Desprez-Loustau", "given": "Marie-Laure", "initials": "ML"}, {"family": "Luyten", "given": "Isabelle", "initials": "I"}, {"family": "Madoui", "given": "Mohammed-Amin", "initials": "MA"}, {"family": "Mangenot", "given": "Sophie", "initials": "S"}, {"family": "Marchal", "given": "Cl\u00e9mence", "initials": "C", "orcid": "0000-0003-1669-3270", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/45c50312d3f74543be5fd64f115aaa99.json"}}, {"family": "Maumus", "given": "Florian", "initials": "F"}, {"family": "Mercier", "given": "Jonathan", "initials": "J"}, {"family": "Michotey", "given": "C\u00e9lia", "initials": "C"}, {"family": "Panaud", "given": "Olivier", "initials": "O"}, {"family": "Picault", "given": "Nathalie", "initials": "N"}, {"family": "Rouhier", "given": "Nicolas", "initials": "N"}, {"family": "Ru\u00e9", "given": "Olivier", "initials": "O"}, {"family": "Rustenholz", "given": "Camille", "initials": "C"}, {"family": "Salin", "given": "Franck", "initials": "F"}, {"family": "Soler", "given": "Mar\u00e7al", "initials": "M"}, {"family": "Tarkka", "given": "Mika", "initials": "M"}, {"family": "Velt", "given": "Amandine", "initials": "A"}, {"family": "Zanne", "given": "Amy E", "initials": "AE"}, {"family": "Martin", "given": "Francis", "initials": "F", "orcid": "0000-0002-4737-3715", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7aa217f558f84c4d9c8c89bcbded55c5.json"}}, {"family": "Wincker", "given": "Patrick", "initials": "P"}, {"family": "Quesneville", "given": "Hadi", "initials": "H"}, {"family": "Kremer", "given": "Antoine", "initials": "A"}, {"family": "Salse", "given": "J\u00e9r\u00f4me", "initials": "J"}], "type": "journal article", "published": "2018-07-00", "journal": {"title": "Nat Plants", "issn": "2055-0278", "volume": "4", "issue": "7", "pages": "440-452", "issn-l": "2055-0278"}, "abstract": "Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4 and modelling5 approaches have shown that intra-organismal genetic heterogeneity can be selected for6 and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.", "doi": "10.1038/s41477-018-0172-3", "pmid": "29915331", "labels": [], "xrefs": [{"db": "mid", "key": "EMS78042"}, {"db": "pmc", "key": "PMC6086335"}, {"db": "pii", "key": "10.1038/s41477-018-0172-3"}], "notes": [], "created": "2019-01-17T14:01:07.703Z", "modified": "2026-09-23T06:33:18.225Z"}, {"entity": "publication", "iuid": "a367c28cc6604e33bd8ea03955f5baab", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a367c28cc6604e33bd8ea03955f5baab.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a367c28cc6604e33bd8ea03955f5baab"}}, "title": "Ten steps to get started in Genome Assembly and Annotation.", "authors": [{"family": "Dominguez Del Angel", "given": "Victoria", "initials": "V", "orcid": "0000-0002-5514-6651", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b58d737aa5741b39bfb13121aaab6f4.json"}}, {"family": "Hjerde", "given": "Erik", "initials": "E", "orcid": "0000-0002-6014-1249", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/87ee6188fa184d039bb65e51627301be.json"}}, {"family": "Sterck", "given": "Lieven", "initials": "L", "orcid": "0000-0001-7116-4000", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6637da40e84a4fe788126bd67108489c.json"}}, {"family": "Capella-Gutierrez", "given": "Salvadors", "initials": "S"}, {"family": "Notredame", "given": "Cederic", "initials": "C"}, {"family": "Vinnere Pettersson", "given": "Olga", "initials": "O"}, {"family": "Amselem", "given": "Joelle", "initials": "J", "orcid": "0000-0001-7124-3454", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c75c6cc71c7e4a3eb26b9bbb37b7a94c.json"}}, {"family": "Bouri", "given": "Laurent", "initials": "L", "orcid": "0000-0002-2297-1559", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dcc9c48ac39342269a7762ce7e25895a.json"}}, {"family": "Bocs", "given": "Stephanie", "initials": "S", "orcid": "0000-0001-7850-4426", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/43887f143a404b5a92c7ac67288000e3.json"}}, {"family": "Klopp", "given": "Christophe", "initials": "C", "orcid": "0000-0001-7126-5477", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2507fcaf0ec6418da9007120d73cab78.json"}}, {"family": "Gibrat", "given": "Jean-Francois", "initials": "JF", "orcid": "0000-0002-2623-5698", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0f79c7e9c25d497b8acfcbbab0b96179.json"}}, {"family": "Vlasova", "given": "Anna", "initials": "A", "orcid": "0000-0002-4241-2674", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac5a388dd1344e669272e2ffa23e3c0e.json"}}, {"family": "Leskosek", "given": "Brane L", "initials": "BL"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Binzer-Panchal", "given": "Mahesh", "initials": "M", "orcid": "0000-0003-1675-0677", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fd03c25639c84962b326b35ea434cc79.json"}}, {"family": "Lantz", "given": "Henrik", "initials": "H", "orcid": "0000-0003-2419-0075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc64ba483fcc47d780457af7f24146c7.json"}}], "type": "journal article", "published": "2018-02-05", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "7", "issn-l": "2046-1402"}, "abstract": "As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, intended to be stable over time, and cover all aspects from start to finish of a general assembly and annotation project. Intrinsic properties of genomes are discussed, as is the importance of using high quality DNA. Different sequencing technologies and generally applicable workflows for genome assembly are also detailed. We cover structural and functional annotation and encourage readers to also annotate transposable elements, something that is often omitted from annotation workflows. The importance of data management is stressed, and we give advice on where to submit data and how to make your results Findable, Accessible, Interoperable, and Reusable (FAIR).", "doi": "10.12688/f1000research.13598.1", "pmid": "29568489", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC5850084"}, {"db": "pii", "key": "ELIXIR-148"}, {"db": "figshare", "key": "10.6084/m9.figshare.100940"}], "notes": [], "created": "2026-09-23T07:31:29.741Z", "modified": "2026-09-23T07:31:30.186Z"}]}