Selected publications

Evolution of sex chromosomes

The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication.

Badouin H, Velt A, Gindraud F, Flutre T, Dumas V, Vautrin S, Marande W, Corbi J, Sallet E, Ganofsky J, Santoni S, Guyot D, Ricciardelli E, Jepsen K, Käfer J, Berges H, Duchêne E, Picard F, Hugueney P, Tavares R, Bacilieri R, Rustenholz C, Marais GAB.

Genome Biol. 2020 Sep 7;21(1):223. (Genome Biology’s featured research)

An efficient RNA-seq-based segregation analysis identifies the sex chromosomes of Cannabis sativa.

Prentout D, Razumova O, Rhoné B, Badouin H, Henri H, Feng C, Käfer J, Karlov G, Marais GAB.

Genome Res. 2020 Feb;30(2):164-172.

Genomic imprinting mediates dosage compensation in a young plant XY system.

Muyle A, Zemp N, Fruchard C, Cegan R, Vrana J, Deschamps C, Tavares R, Hobza R, Picard F, Widmer A, Marais GAB.

Nat Plants. 2018 Sep;4(9):677-680. (recommended by PCI Evol. Biol.)

Rapid de novo evolution of X chromosome dosage compensation in Silene latifolia, a plant with young sex chromosomes.

Muyle A, Zemp N, Deschamps C, Mousset S, Widmer A, Marais GA.

PLoS Biol. 2012;10(4):e1001308. (PLoS Biol Editor’s choice, recommended by F1000)

Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome.

Pessia E, Makino T, Bailly-Bechet M, McLysaght A, Marais GA.

Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5346-51. (from the cover, commented in PNAS)

Evolution of plant sexual systems

On the rarity of dioecy in flowering plants.

Käfer J, Marais GA, Pannell JR.

Mol Ecol. 2017 Mar;26(5):1225-1241. (recommended by F1000)

An angiosperm-wide analysis of the gynodioecy-to-dioecy pathway

Dufaÿ M, Champelovier P, Käfer J, Henry JP, Mousset S, Marais GA.

Ann Bot. 2014 Sep;114(3):539-48.

Dioecy is associated with higher diversification rates in flowering plants.

Käfer J, de Boer HJ, Mousset S, Kool A, Dufay M, Marais GA.

J Evol Biol. 2014 Jul;27(7):1478-90

Silene as a model system in ecology and evolution.

Bernasconi G, Antonovics J, Biere A, Charlesworth D, Delph LF, Filatov D, Giraud T, Hood ME, Marais GA, McCauley D, Pannell JR, Shykoff JA, Vyskot B, Wolfe LM, Widmer A.

Heredity (Edinb). 2009 Jul;103(1):5-14.

Plant genomics and phenotypic evolution

The Rosa genome provides new insights into the domestication of modern roses.

Raymond O, Gouzy J, Just J, Badouin H, Verdenaud M, Lemainque A, Vergne P, Moja S, Choisne N, Pont C, Carrère S, Caissard JC, Couloux A, Cottret L, Aury JM, Szécsi J, Latrasse D, Madoui MA, François L, Fu X, Yang SH, Dubois A, Piola F, Larrieu A, Perez M, Labadie K, Perrier L, Govetto B, Labrousse Y, Villand P, Bardoux C, Boltz V, Lopez-Roques C, Heitzler P, Vernoux T, Vandenbussche M, Quesneville H, Boualem A, Bendahmane A, Liu C, Le Bris M, Salse J, Baudino S, Benhamed M, Wincker P, Bendahmane M. Nat Genet. 2018 Jun;50(6):772-777. (commented in Nat Genet., recommended by F1000)

The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes.

Cubry P, Tranchant-Dubreuil C, Thuillet AC, Monat C, Ndjiondjop MN, Labadie K, Cruaud C, Engelen S, Scarcelli N, Rhoné B, Burgarella C, Dupuy C, Larmande P, Wincker P, François O, Sabot F, Vigouroux Y. Curr Biol. 2018 Jul 23;28(14):2274-2282.e6. (commented in Curr. Biol., recommended by F1000)

Evolutionary interplay between sister cytochrome P450 genes shapes plasticity in plant metabolism.

Liu Z, Tavares R, Forsythe ES, André F, Lugan R, Jonasson G, Boutet-Mercey S, Tohge T, Beilstein MA, Werck-Reichhart D, Renault H. Nat Commun. 2016 Oct 7;7:13026.

Structural, functional, and evolutionary analysis of the unusually large stilbene synthase gene family in grapevine.

Parage C, Tavares R, Réty S, Baltenweck-Guyot R, Poutaraud A, Renault L, Heintz D, Lugan R, Marais GA, Aubourg S, Hugueney P.

Plant Physiol. 2012 Nov;160(3):1407-19.

Testing the recent theories for the origin of the hermaphrodite flower by comparison of the transcriptomes of gymnosperms and angiosperms.

Tavares R, Cagnon M, Negrutiu I, Mouchiroud D. BMC Evol Biol. 2010 Aug 3;10:240.

Methodological developments

MareyMap Online: A User-Friendly Web Application and Database Service for Estimating Recombination Rates Using Physical and Genetic Maps.

Siberchicot A, Bessy A, Guéguen L, Marais GAB.

Genome Biol Evol. 2017 Oct 1;9(10):2506-2509.

SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms.

Muyle A, Käfer J, Zemp N, Mousset S, Picard F, Marais GA.

Genome Biol Evol. 2016 Aug 29;8(8):2530-43.