Structure and evolution of plant genomes

Group Leaders
Josep Mª Casacuberta
CSIC Associate Professor
Carlos Vicient
CSIC Scientist
Group Members
Structure and evolution of plant genomes group


Postdoctoral Researchers

PhD Students

Undergrad or Master Students


The main objective of our group is to increase our knowledge on the structure of plant genomes and study how these genomes evolve. Our group has actively participated in the sequencing and annotation of the Arabidopsis, Physcomitrella patens, melon and almond genomes and is working on 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. One of the major drivers of variability in plants are transposable elements. For this reason we are studying the regulation of transposon activity as well as their impact on the generation of the genetic and epigenetic variability useful for plant adaptation and crop breeding.

Selected Publications

Morata, J., Tormo, M., Alexiou, K.G., Vives, C., Ramos-Onsins, S.E., Garcia-Mas, J., Casacuberta, J.M.
The evolutionary consequences of transposon-related pericentromer expansion in melon
(2018) Genome Biology and Evolution, 10(6), 1584-1595

Ruggieri, V., Alexiou, K.G., Morata, J., Argyris, J., Pujol, M., Yano, R., Nonaka, S., Ezura, H., Latrasse, D., Boualem, A., Benhamed, M., Bendahmane, A., Cigliano, R.A., Sanseverino, W., Puigdomènech, P., Casacuberta, J.M., Garcia-Mas, J.
An improved assembly and annotation of the melon (Cucumis melo L.) reference genome
(2018) Scientific Reports, vol. 8(1), Art. number 8088

Morata, J., Marín, F., Payet, J., Casacuberta, J.M.
Plant lineage-specific amplification of transcription factor binding motifs by miniature inverted-repeat transposable elements (MITEs) 
(2018) Genome Biology and Evolution, 10(5), 1210-1220

Lang D et al (including J. Morata, C. Vives and JM Casacuberta) . 
The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.
(2018) Plant Journal, 93(3), Art. number 1083, pp. 515-533

Vergara, Z, Sequeira-Mendes J, Morata J, Peiro R, Henaff E, Costas C, Casacuberta JM, Gutierrez C. 
Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin. 
(2017) Nucleic Acids Research, 45(14): 8358-8368

Vicient, CM, Casacuberta JM. 
Impact of transposable elements on polyploid plant genomes. 
(2017) Annals of Botany 120(2): 195-207 

Morata J, Puigdomènech P.  
Variability among Cucurbitaceae species (melon, cucumber and watermelon) in a genomic region containing a cluster of NBS-LRR genes. 
(2017) BMC Genomics. 8;18(1):138 

Vives C, Charlot F, Mhiri C, Contreras B, Daniel J, Epert A, Voytas DF, Grandbastien MA, Nogué F, Casacuberta JM. 
Highly efficient gene tagging in the bryophyte Physcomitrella patens using the tobacco (Nicotiana tabacum) Tnt1 retrotransposon. 
(2016) New Phytologist, 212(3): 759-769

Nogué F, Mara K, Collonnier C, Casacuberta JM. 
Genome engineering and plant breeding: impact on trait discovery and development. 
(2016) Plant Cell Reports 35:1475–1486 

Sanseverio W, Hénaff E, Vives C, Pinosio S, Burgos-Paz W, Morgante M, Ramos-Onsins S, Garcia-Mas J, Casacuberta JM. 
Transposon insertion, structural variations and SNPs contribute to the evolution of the melon genome. 
(2015) Molecular Biology and Evolution 32: 2760-2774 

González VM, Müller S, Baulcombe D, Puigdomènech P. 
Evolution of NBS-LRR gene copies among Dicot plants and its regulation by members of the miR482/2118 superfamily of miRNAs. 
(2015) Molecular Plant, vol. 8(2): 329-331

Gómez-Orte E, Vicient CM, Martínez-Izquierdo JA. 
Grande retrotransposons contain an accessory gene in the unusually long 3'-internal region that encodes a nuclear protein transcribed from its own promoter.
(2013) Plant Molecular Biology 81(6): 140-147