Julien Boutte

Postdoctoral Research Associate

Ph.D in Genomics and BioinformaticsUniversity of Rennes 1, France (2012-2015).
M.S. in Biological Systems Modelling (Bioinformatics Speciality), University of Rennes 1, France (2010-2012).
B.S. in Mathematics, University of Rennes 1, France (2008-2010).



Boutte, J., Fishbein, M., Liston, A., Cronn, R.C., Straub, S.C.K. A new pipeline to code indel characters from NGS data for phylogenomic analyses: application in milkweed and nematode models. In prep.

Fishbein, M., Livshultz, T., Straub, S.C.K., Simões A.O., Boutte, J., McDonnell, A., Foote, A. Evolution on the backbone: Apocynaceae phylogenomics and new perspectives on growth forms, flowers and fruits. Am. J. Bot. In press.

Fishbein, M., Straub, S.C.K., Boutte, J., Hansen, K., Cronn, R.C., Liston, A. Evolution at the tips: Asclepias (Apocynaceae) phylogenomics and new perspectives on leaf surfaces. Am. J. Bot. In press.


Ferreira de Carvalho, J., Boutte, J., Bourdau, P., Chelaifa, H., Ainouche, K., Salmon, A., Ainouche, M. Gene expression variation in natural populations of hexaploid and allododecaploid Spartina species. Plant Syst. Evol. 303 (8), 1061-1079. doi:10.1007/s00606-017-1446-3.

Keller, J., Rousseau-Gueutin, F., Martin, GE., Morice, J., Boutte, J., Coissac, E., Ourari, M., Ainouche, M., Salmon, M., Cabello-Hurtado, A., Ainouche, A. The evolutionary fate of the chloroplast and nuclear rps16 genes as revealed through the sequencing and comparative analyses of four novel legume chloroplast genomes from Lupinus. DNA Research. 24(4), 343-358. doi:10.1093/dnares/dsx006.

Rousseau, H., Rousseau-Gueutin, M., Dauvergne, X., Boutte, J., Simon, G., Marnet, N., Bouchereau, A., Guiheneuf, S., Bazureau, J.P., Morice, J., Ravanel, S., Cabello-Hurtado, F., Ainouche, A., Salmon, A., Wendel, J.F., Ainouche, M. Evolution of DMSP (dimethylsulfoniopropionate) biosynthesis pathway: Origin and phylogenetic distribution in polyploid Spartina (Poaceae, Chloridoideae). Mol. Phylogenet. and Evol. 114, 401-414. doi:10.1016/j.ympev.2017.07.003.


Boutte, J., Ferreira de Carvalho, J., Rousseau-Gueutin, M., Poulain, J., Da Silva, C., Wincker, P., Ainouche, M., Salmon, A. Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae). GBE, Genome Biol. Evol. 8(9), 3030–3044. doi:10.1093/gbe/evw209.

Boutte, J., Aliaga, B., Lima, O., Ferreira de Carvalho, J., Ainouche, A., Macas, J., Rousseau-Gueutin, M., Coriton, O., Ainouche, M., Salmon, A. Haplotype detection from next generation sequencing in high ploidy-level species: 45S rDNA gene copies in the hexaploid Spartina maritima. G3, Genes | Genomes | Genetics. 6(1), 29-40. doi: 10.1534/g3.115.023242.


Rousseau-Gueutin, M., Bellot, S., Martin, G.E., Boutte, J., Chelaifa, H., Lima, O., Michon-Coudouel, S., Naquin, D., Salmon, A., Ainouche, K., Ainouche, M., 2015. The chloroplast genome of the hexaploid Spartina maritima (Poaceae, Chloridoideae): Comparative analyses and molecular dating. Mol. Phylogenet. Evol. 93, 5-16. 10.1016/j.ympev.2015.06.013.


Ferreira de Carvalho, J., Chelaifa, H., Boutte, J., Poulain, J., Couloux, A., Wincker, P., Bellec, A., Fourment, J., Bergès, H., Salmon, A., Ainouche, M., 2013. Exploring the genome of the salt-marsh Spartina maritima (Poaceae, Chloridoideae) through BAC end sequence analysis. Plant Mol. Biol. 83, 591–606. doi:10.1007/s11103-013-0111-7.

Ferreira de Carvalho, J., Poulain, J., Da Silva, C., Wincker, P., Michon-Coudouel, S., Dheilly, A., Naquin, D., Boutte, J., Salmon, A., Ainouche, M., 2012. Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae). Heredity 110, 181–193. doi:10.1038/hdy.2012.76.

Teaching Experience

Teaching assistant in Plant BiologyUniversity of Rennes 1, UFR SVE, France (2012-2014).

Professional Affiliation

Botanical Society of America (BSA).
Society for the Study of Evolution (SSE).


Reviewer for Systematic Biology Journal.


Julien Boutte

E-mail Link

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