Structure and Evolution of Plant Genomes

Group Structure

Group Leader: Josep Mª Casacuberta (CSIC Associate Professor)
Researchers: Pere Puigdomènech, Matilde José
Postdoctoral Researchers: Víctor Manuel González
PhD Students: María Corujo, Cristina Vives, Elizabeth Hénaff


The main objective of our group is to increase our knowledge on the structure of plant genomes and study how these genomes evolve.

One of the major drivers of variability in plants are transposable elements. However, transpososition is also a highly mutagenic event and, therefore, needs to be tightly controlled. Control of transposition has been a major focus of our research in the last few years, where we analyzed the epigenetic control of the tobacco retrotransposon Tnt1 and the mechanisms of transposition of the Arabidopsis MITE Emigrant. After the sequencing of model plants such as Arabidopsis thaliana, with the development of NGS techniques is now possible to sequence and characterize the genomes of crop species, and it is now possible to study the impact of transposition on the evolution of plant genomes at a genome-wide scale. Our group has actively participated in the sequencing and annotation of the Arabidopsis thaliana and melon genomes and will concentrate in the next future in the study of crop genome evolution using resequencing data from crop varieties. This work should allow us to better understand how genome variability is generated and how this variability correlates with phenotypic variability in traits that have been selected by humans during crop domestication and breeding.

In addition of studying transposons as one of the mechanisms that generate genome variability, we are also studying gene families that show a high degree of plasticity. We have analyzed in detail the genes encoding different types of membrane structural proteins in different crops, and we are now concentrating on the evolution of resistance genes in crops. In particular, we have analyzed the presence/absence polymorphisms of resistance genes in melon and we are now studying their variability and regulation by miRNAs in Cucurbits.

Research Projects

  • Control of plant transposable elements
  • Mechanismsof transposition in plants
  • Impact of transposons in the evolution of crop genes and genomes
  • Evolution of resistance genes in Cucurbits

Selected Publications

Fornale S., Capellades M., Encina A., Wang K., Irar S., Lapierre C., Ruel K., Joseleau J.-P., Berenguer J., Puigdomenech P., Rigau J., Caparros-Ruiz D.
Altered lignin biosynthesis improves cellulosic bioethanol production in transgenic maize plants down-regulated for cinnamyl alcohol dehydrogenase
(2012) Molecular Plant, vol. 5 (4), pp. 817-830

Garcia-Mas J., Benjak A., Sanseverino W., Bourgeois M., Mir G., Gonzalez V.M., Henaff E., Camara F., Cozzuto L., Lowy E., Alioto T., Capella-Gutierrez S., Blancae J., Canizares J., Ziarsolo P., Gonzalez-Ibeas D., Rodriguez-Moreno L., Droege M., Du L., Alvarez-Tejado M., Lorente-Galdos B., Melec M., Yang L., Weng Y., Navarro A., Marques-Bonet T., Aranda M.A., Nuez F., Pico B., Gabaldon T., Roma G., Guigoc R., Casacuberta J.M., Arus P., Puigdomenech P.
The genome of melon (Cucumis melo L.)
(2012) Proceedings of the National Academy of Sciences of the United States of America, vol. 109 (29), pp. 11872-11877

Grandbastien M.-A., Casacuberta J.M.
(2012) Topics in Current Genetics, vol. 24, pp. vii-ix

Guermonprez H., Henaff E., Cifuentes M., Casacuberta J.M.
MITEs, miniature elements with a major role in plant genome evolution
(2012) Topics in Current Genetics, vol. 24, pp. 113-124

Hernandez-Pinzon I., Cifuentes M., Henaff E., Santiago N., Espinas M.L., Casacuberta J.M.
The Tnt1 retrotransposon escapes silencing in tobacco, its natural host
(2012) PLoS ONE, vol. 7 (3), Art. number e33816

Jose-Estanyol M., Puigdomenech P.
Cellular localization of the embryo-specific Hybrid PRP from Zea mays, and characterization of promoter regulatory elements of its gene
(2012) Plant Molecular Biology, vol. 80 (3), pp. 325-335

Gonzalez V.M., Aventin N., Centeno E., Puigdomenech P.
High presence/absence gene variability in defense-related gene clusters of Cucumis melo
(2013) BMC Genomics, vol. 14 (1), Art. number 782

Podevin N., Davies H.V., Hartung F., Nogue F., Casacuberta J.M.
Site-directed nucleases: A paradigm shift in predictable, knowledge-based plant breeding
(2013) Trends in Biotechnology, vol. 31 (6), pp. 375-383

Puigdomenech P.
Dealing with Scientific Integrity Issues: the Spanish Experience
(2013) Archivum Immunologiae et Therapiae Experimentalis, pp. 1-6