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


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 ArabidopsisPhyscomitrella 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 (TEs). TEs are major components of plant genomes and show a high structural diversity. We study the regulation of TE activity as well as their impact on the generation of the genetic and epigenetic variability useful for plant adaptation and crop breeding.

Selected Publications

Castanera R*, de Tomás C, Ruggieri V, Vicient C, Eduardo I, Aranzana MJ, Arús P, Casacuberta JM*.
A phased genome of the highly heterozygous 'Texas' almond uncovers patterns of allele-specific expression linked to heterozygous structural variants.
(2024) Hortic Res. 11:uhae106.

García-Romeral J, Castanera R, Casacuberta J, Domingo C*.
Deciphering the Genetic Basis of Allelopathy in japonica Rice Cultivated in Temperate Regions Using a Genome-Wide Association Study.
(2024) Rice (N Y) 17:22.

Carlos de Tomás, Carlos M Vicient*
The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants
(2023) Epigenomes 8:2.

Perroud PF*, Guyon-Debast A, Casacuberta JM, Paul W, Pichon JP, Comeau D, Nogué F.
Improved prime editing allows for routine predictable gene editing in Physcomitrium patens.
(2023) J Exp Bot. 13;74:6176-6187.

Pulido M, Casacuberta JM*.
Transposable element evolution in plant genome ecosystems.
(2023) Curr Opin Plant Biol. 75:102418.

Castanera R*, Morales-Díaz N, Gupta S, Purugganan M, Casacuberta JM*.
Transposons are important contributors to gene expression variability under selection in rice populations.
(2023) Elife, 12:RP86324.

de Tomás C, Vicient CM*.
Genome-wide identification of Reverse Transcriptase domains of recently inserted endogenous plant pararetrovirus (Caulimoviridae).
(2022) Front Plant Sci. 13:1011565

Vourlaki IT*, Castanera R, Ramos-Onsins SE, Casacuberta JM, Pérez-Enciso M*.
Transposable element polymorphisms improve prediction of complex agronomic traits in rice.
(2022) Theor Appl Genet, 135:3211-3222

de Tomás C, Bardil A, Castanera R, Casacuberta JM*, Vicient CM*.
Absence of major epigenetic and transcriptomic changes accompanying an interspecific cross between peach and almond
(2022) Hortic Res, 9:uhac127

Vendrell-Mir P, Perroud P-F, Haas FB, Meyberg R, Charlot F, Rensing SA, Nogué F*, Casacuberta JM*.
A vertically transmitted amalgavirus is present in certain accessions of the bryophyte Physcomitrium patens
(2021) Plant J., 108:1786-1797/p>

Castanera R*, Vendrell-Mir P, Bardil A, Carpentier MC, Panaud O, Casacuberta JM*.
The amplification dynamics of MITEs and their impact on rice trait variability
(2021) Plant J., 107:118-135

Nieto Feliner G, Casacuberta J, Wendel JF.
Genomics of Evolutionary Novelty in Hybrids and Polyploids.
(2020) Front. Genet., 11:792

Vicient CM, Casacuberta JM.
Additional ORFs in Plant LTR-Retrotransposons
(2020) Front. Plant. Sci., 11:565

Vendrell-Mir P, López-Obando M, Nogue´ F*, Casacuberta JM*.
Different Families of Retrotransposons and DNA Transposons Are Actively Transcribed and May Have Transposed Recently in Physcomitrium (Physcomitrella) patens
(2020) Front. Plant. Sci., 11:1274

Castanera R, Ruggieri V, Pujol M,Garcia-Mas* J, Casacuberta JM*.
An improved melon reference genome with single-molecule sequencing uncovers a recent burst of transposable elements with potential impact on genes
(2020) Front. Plant Sci., 10:1815

Alioto T, Alexiou KG, Bardil A, Barteri F, Castanera R, Cruz F, Dhingra A, Duval H, Fernández i Martí A, Frias L, Galán B, Garcia JL, Howad W, JGómez-GarridoJ, Gut M, Julca I, Morata J, Puigdomènech P, Ribeca P, Rubio Cabetas MJ, Vlasova A, Wirthensohn M, Garcia-Mas J, Gabaldón T, Casacuberta JM*, Arús P*.
Transposons played a major role in the diversification between the closely related almond and peach genomes: Results from the almond genome sequence
(2020) Plant J., 101: 455–472