Plant Genome Evolution and Diversification

Despite evidence pointing to gene duplication, transposition and epigenetic changes going along with plant diversification, the evolutionary significance of such genome dynamics remains elusive. Our work thus integrates evolutionary ecology and genomics to better understand speciation and adaptive radiation under changing environments.

Our projects often (but not only) use polyploid speciation as a model process integrating genomic and ecological changes. They combine high-throughput genomic technologies with experimental and empirical field studies to untangle the genetic and ecological drivers of diversification in alpine and Mediterranean plant populations.

• Transcriptional activity of transposable elements along an elevational gradient in Arabidopsis arenosa
  Wos, Guillaume; Choudhury, Rimjhim Roy; Kolar, Filip; Parisod, Christian
  Mobile Dna,   DOI: 10.1186/s13100-021-00236-0  FEB 27 2021
• The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic
  Nowak, Michael D.; Birkeland, Siri; Mandakova, Terezie; Roy Choudhury, Rimjhim; Guo, Xinyi; et al.
  Molecular Ecology Resources,  DOI: 10.1111/1755-0998.13280 APR 2021
• Climate Change and Alpine Screes: No Future for Glacial Relict Papaver occidentale (Papaveraceae) in Western Prealps
  Fragniere, Yann; Pittet, Loic; Clement, Benoit; Betrisey, Sebastien; Gerber, Emanuel; et al.
  Diversity-basel,  DOI: 10.3390/d12090346 SEP 2020
• Genetic structure of the endemicPapaver occidentaleindicates survival and immigration in the Western Prealps
  Pittet, Loic; Fragniere, Yann; Grunig, Sandra; Betrisey, Sebastien; Clement, Benoit; et al.
  Alpine Botany,   DOI: 10.1007/s00035-020-00238-3  OCT 2020
• Chromosome restructuring among hybridizing wild wheats
  Parisod, Christian; Badaeva, Ekaterina D.
  New Phytologist,  DOI: 10.1111/nph.16415, Early Access: FEB 2020
• Plant defense resistance in natural enemies of a specialist insect herbivore
  Zhang, Xi; van Doan, Cong; Arce, Carla C. M.; Hu, Lingfei; Gruenig, Sandra; Parisod, Christian; Hibbard, Bruce E; Herve, Maxime R.; Nielson, Chad; Robert, Christelle A. M.; Machado, Ricardo A. R.; Erb, Matthias
  Proceedings Of The National Academy Of Sciences Of The United States Of America,  DOI: 10.1073/pnas.1912599116, NOV 12 2019
• Eco-genetic additivity of diploids in allopolyploid wild wheats
  Huynh, Stella; Broennimann, Olivier; Guisan, Antoine; Felber, Francois; Parisod, Christian
  Ecology Letters, DOI: 10.1111/ele.13466, Early Access: FEB 2020
• Hybridization preceded radiation in diploid wheats
  Huynh, S; Marcussen, T; Felber, F; Parisod, C
  MOLECULAR PHYLOGENETICS AND EVOLUTION, 139 10.1016/j.ympev.2019.106554 OCT 2019
• Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae)
  Rogivue A; Choudhury RR; Zoller S; Joost S; Felber F; Kasser M; Parisod C; Gugerli F
  MOLECULAR ECOLOGY RESOURCES, 19 (3):773-787;  https://doi.org/10.1111/1755-0998.12991 MAY 2019
• Impact of polymorphic transposable elements on linkage disequilibrium along chromosomes
  Choudhury, RR; Rogivue, A; Gugerli, F; Parisod, C
  MOLECULAR ECOLOGY, 28 (6):1550-1562; SI  https://doi.org/10.1111/mec.15014 MAR 2019
• Lateral transfers of large DNA fragments spread functional genes among grasses
  Dunning, LT; Olofsson, JK; Parisod, C; Choudhury, RR; Moreno-Villena, JJ; Yang, Y; Dionora, J; Quick, WP; Park, M; Bennetzen, JL; Besnard, G; Nosil, P; Osborne, CP; Christin, PA
  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 116 (10):4416-4425; 10.1073/pnas.1810031116 MAR 5 2019
• Parental transposable element loads influence their dynamics in young Nicotiana hybrids and allotetraploids
  Mhiri, C; Parisod, C; Daniel, J; Petit, M; Lim, KY; de Borne, FD; Kovarik, A; Leitch, AR; Grandbastien, MA
  NEW PHYTOLOGIST, 221 (3):1619-1633; 10.1111/nph.15484 FEB 2019
• …

• Mechanisms of reproductive isolation and speciation
• Polyploidy (hybridization and whole genome duplication)
• Transposable elements and genome dynamics
• Landscape genetics and adaptation to environmental heterogeneity
• Alpine botany

• Integration of genetic variation with environmental heterogeneity at high resolution
• Characterization of genetic resources in wild relatives of crop species
• Genetic diversity for the monitoring of rare endemics or ill-defined species