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7. High quality genome sequence reveals important events during domestication of White Lupin

Author

Hufnagel, B., Marques, A., Sallet, Erika, Marande, William, Soriano, A., Arribat, Sandrine, Nelson, M., Divol, F., Marques, L., Gallardo, Karine, Salse, Jerome, Guyot, R., Delaux, Pierre-Marc, Geuflores, F., Berges, Helene, Gouzy, Jerome, Péret, Benjamin, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut de Recherche pour le Développement (IRD), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (UCPH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), University of Copenhagen = Københavns Universitet (KU), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], [SDE] Environmental Sciences, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology
Abstract

Prod 2019-88m BAP GEAPSI INRA; International audience; White lupin (Lupinus albus; 2n=50) is the only crop producing cluster roots, an outstanding developmental adaptation to low phosphate soils. We report a high-quality chromosome-scale assembly of white lupin genome, together with an extensive transcriptome data from ten different organs. We used singlemolecule real-time technology, in combination with short-reads sequencing and optical and genetic maps to have a successful assembly. The final assembly size is 443 Mb with a N50 of 17 Mb. About 98% of the assembled genome is included on the 25 pseudo-chromosomes. The structural annotation identified 38258 coding genes and 3,129 ncRNA, being 97.3% genes anchored on the pseudo-chromosomes. Genome of white lupin is laden with gene duplications and repetitive elements, which represent ~55% of the genome. A comparative evolutionary analysis of white lupin with other legumes revealed that it experienced a whole genome triplication in about 10 M years ago. We resequenced other 15 white lupin accessions, including a landrace and a non-domesticated variety. This has shown a highly polymorphic genome that has been impacted by domestication in different ways. Some transposons families present on the non-domesticated variety have disappeared in modern accessions, as well as the protein content of the seed has changed. Interestingly, the domestication has also modified cluster root formation. The cluster roots are formed earlier on time and closer to topsoil in the cultivated varieties. Altogether, this genome is a valuable resource and represents a keystone for legume genomics research.

Published
2019

18. FRANCE

Author

Rébelliau, Alfred, Monod, Gabriel, Guignebert, Ch., Jullian, C., Guyot, R., and Hauser, H.

Published
1907

19. Automatic curation of LTR retrotransposon libraries from plant genomes through machine learning

Author

Orozco-Arias Simon, Candamil-Cortes Mariana S., Jaimes Paula A., Valencia-Castrillon Estiven, Tabares-Soto Reinel, Isaza Gustavo, and Guyot Romain

Subjects
curation, deep neural networks, k-mer-based methods, ltr retrotransposons, machine learning, nesting insertions, Biotechnology, TP248.13-248.65
Abstract

Transposable elements are mobile sequences that can move and insert themselves into chromosomes, activating under internal or external stimuli, giving the organism the ability to adapt to the environment. Annotating transposable elements in genomic data is currently considered a crucial task to understand key aspects of organisms such as phenotype variability, species evolution, and genome size, among others. Because of the way they replicate, LTR retrotransposons are the most common transposable elements in plants, accounting in some cases for up to 80% of all DNA information. To annotate these elements, a reference library is usually created, a curation process is performed, eliminating TE fragments and false positives and then annotated in the genome using the homology method. However, the curation process can take weeks, requires extensive manual work and the execution of multiple time-consuming bioinformatics software. Here, we propose a machine learning-based approach to perform this process automatically on plant genomes, obtaining up to 91.18% F1-score. This approach was tested with four plant species, obtaining up to 93.6% F1-score (Oryza granulata) in only 22.61 s, where bioinformatics methods took approximately 6 h. This acceleration demonstrates that the ML-based approach is efficient and could be used in massive sequencing projects.

Published
2022
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20. Arsen

Author

Hartwich, C., Toggenburg, F., Cormimboeuf, H., Guyot, R., Sjollema, B., Hollins, C., Zwicknagl, Karl, and Fenner, G.

Published
1918
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21. Structural, functional and evolutionary analysis of the unusually large stilbene synthase gene family in grapevine (Vitis vinifera)

Author

Parage, C., Tavares, R., Réty, S., Baltenweck-Guyot, R., Poutaraud, A., Renault, L., Heintz, D., Lugan, R., Marais, Gabriel, Aubourg, S., Hugueney, P., Sexe et évolution, Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)

Subjects
[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2012

24. Rapid genome divergence at orthologous low molecular weight glutenin loci of the A and Amgenomes of wheat

Author

Wicker, T, Yahiaoui, N, Guyot, R, Schlagenhauf, E, Liu, ZD, Dubcovsky, J, and Keller, B

Subjects
food and beverages
Abstract

To study genome evolution in wheat, we have sequenced and compared two large physical contigs of 285 and 142 kb covering orthologous low molecular weight (LMW) glutenin loci on chromosome 1AS of a diploid wheat species (Triticum monococcum subsp monococcum) and a tetraploid wheat species (Triticum turgidum subsp durum). Sequence conservation between the two species was restricted to small regions containing the orthologous LMW glutenin genes, whereas >90% of the compared sequences were not conserved. Dramatic sequence rearrangements occurred in the regions rich in repetitive elements. Dating of long terminal repeat retrotransposon insertions revealed different insertion events occurring during the last 5.5 million years in both species. These insertions are partially responsible for the lack of homology between the intergenic regions. In addition, the gene space was conserved only partially, because different predicted genes were identified on both contigs. Duplications and deletions of large fragments that might be attributable to illegitimate recombination also have contributed to the differentiation of this region in both species. The striking differences in the intergenic landscape between the A and Amgenomes that diverged 1 to 3 million years ago provide evidence for a dynamic and rapid genome evolution in wheat species.

Published
2003
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30. Ancestral genome duplication in rice.

Author

Guyot, R. and Keller, B.

Subjects
*GENOMES, *GENETIC code, *NUCLEOTIDE sequence, *PLANT genetics, RICE genetics
Abstract

The recent availability of the pseudochromosome sequences of rice allows for the first time the investigation of the extent of intra-genomic duplications on a large scale in this agronomically important species. Using a dot-matrix plotter as a tool to display pairwise comparisons of ordered predicted coding sequences along rice pseudochromosomes, we found that the rice genome contains extensive chromosomal duplications accounting for 53% of the available sequences. The size of duplicated blocks is considerably larger than previously reported. In the rice genome, a duplicated block size of >1 Mb appears to be the rule and not the exception. Comparative mapping has shown high genetic colinearity among chromosomes of cereals, promoting rice as a model for studying grass genomes. Further comparative genome analysis should allow the study of the conservation and evolution of these duplication events in other important cereals such as rye, barley, and wheat. [ABSTRACT FROM AUTHOR]

Published
2004
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38. NOTES BIBLIOGRAPHIQUES

Author

Bémont, Ch., Guyot, R., Isaac, J., Lécrivain, Ch., and Morel-Fatio, A.

Published
1921

39. NOTES BIBLIOGRAPHIQUES

Author

Isaac, J., Lécrivain, Ch., Lévy-Guenot, Roger, Guyot, R., and Guignebert, Ch.

Published
1923

41. NOTES BIBLIOGRAPHIQUES

Author

Halphen, L., Petit-Dutaillis, Ch., Bourgin, G., Guyot, R., Lécrivain, Ch., Jordan, E., Masson-Oursel, P., Gorceix, Septime, and Duchesne, E.

Published
1924

43. NOTES BIBLIOGRAPHIQUES

Author

Albertini, E., Hauser, Henri, Guyot, R., Bourgin, Georges, Sée, Henri, Eisenmann, L., Laloy, Émile, Constant, G., Blanchet, Adrien, Coornaert, E., Pascal, P., Lantier, R., Kagarov, Eugène, and Jordan, E.

Published
1934

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