Format: ORAL

Mara ngeles Decena1,2, Rubn Sancho1,2,3, Luis A. Inda1,4, Ernesto Prez-Collazos1,2, Pilar Cataln1,2

1 Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Carretera de Cuarte, km 1, 2071, Huesca, Aragón, España. mdecena@unizar.es, rsancho@unizar.es, ernextop@unizar.es, lainda@unizar.es, pcatalan@unizar.es 2 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, España. C/. Mariano Esquillor Gómez, Edificio I+D, 50018 Zaragoza, España. 3 Estación experimental Aula Dei-CSIC. Avenida Montañana, 1005, 50059 Zaragoza, Aragón, España 4 Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), C/ Miguel Servet, 177, 50013 Zaragoza Aragón, España

The Brachypodium grass species serve as model plants for studying the functional genomics of grass crops, and for elucidating the origins of allopolyploidy and perenniality in monocots. However, significant variations exist in genome sizes among different Brachypodium diploid and polyploid lineages. To explore the composition, abundance, and phylogenetic significance of repetitive elements in these lineages, we utilized low-pass genome sequencing data from 44 representatives. Our study aimed to test the potential mechanisms and consequences of the polyploid genome shock hypothesis (PGSH) in three distinct evolutionary scenarios, analyzing repeat and genome size variations in Brachypodium allopolyploids. Our findings revealed a 3.3-fold difference in the proportion of the genome covered by the repeatome, ranging from 20.77% in B. stacei-2x to 67.97% in B. mexicanum-4x. Changes in genome sizes were attributed to gains or losses in repeat elements. The most prevalent repeat elements in the Brachypodium genomes were LTR-Retand and Tekay retrotransposons. Repeatome phylogenetic networks exhibited high congruence with plastome, nuclear rDNA, and transcriptome trees, distinguishing ancestral outcore lineages from recently evolved core-perennial lineages. The rDNA 5S graph topologies aligned well with ploidy levels and types of subgenomes of Brachypodium polyploids. The core-perennial B. sylvaticum-2x displayed a large repeatome, indicative of a post-polyploid diploidized origin. Our study evidenced that expansions and contractions in the repeatome accounted for three contrasting responses to PGSH: the exacerbated genome expansion of the ancestral allotetraploid B. mexicanum was a consequence of chromosomewide proliferation of TEs and not of WGD, the additive repeatome pattern of young allotetraploid B. hybridum of stabilized post-WGD genome evolution, and the genome shrinkage of recent core perennials polyploids (B. pinnatum, B. phoenicoides) of repeat losses through recombination. Our analyses have contributed to disentangling the evolution of the repeatome and the genome size variation of model Brachypodium grasses.