Genomics of model plant: Brachypodium

Genomic resources have been developed for several annual Brachypodium species, most notably B. distachyon. We propose to develop similar resources for perennial Brachypodium species to elucidate the genetic control of transitions to perenniality and its interaction with the environment, and the origin and mechanisms of allopolyploidy in the genus. Variation in life history strategy, hybridizations and environmental tolerances in this genus represents an untapped resource for deepening our understanding of these key biological and evolutionary aspects. The differences in annual and perennial lifestyle may also lead to significant differences in other areas, including stress response/tolerance. Comparative genomics between closely related annual and perennial species will elucidate the genetic control of perennial/annual switches, the evolutionary dynamics of the hybrid genomes in annual and perennial allopolyploid species, and how differences in growth habit modify plant interaction with the environment. Progress is currently limited, however, by the lack of genomic resources in the genus beyond B. distachyon.

Developing B. sylvaticum as a perennial model and sequencing other perennial species as comparators will help to gain insight into all these areas. Our project also seek to translate the genomic resources gained in Brachypodium to other non-model temperate grasses that show broader diversification, ecology and geographical distributions than the model, and to comparatively investigate the evolution of polyploidy, perenniality and ecological adaptation traits in these model and non-model groups.

Selected papers and books:

.- Gordon SP, Contreras-Moreira B, Levy JJ, Djamei A, Czedik-Eysenberg A, Tartaglio VS, Session A, Martin J, Cartwright A, Katz A, Singan VR, Goltsman E, Barry K, Dinh-Thi VH, Chalhoub B, Diaz-Perez A, Sancho R, Lusinska J, Wolny E, Nibau C, Doonan JH, Mur L, Plott C, Jenkins J, Hazen SP, Lee SJ, Shu S, Goodstein D, Rokhsar D, Schmutz J, Hasterok R, Catalán P, Vogel JP. 2020. Gradual polyploid genome evolution revealed by a pan-genomic analysis of Brachypodium hybridum and its diploid progenitors. Nature Communications 11:3670. A

.- Catalan P, Vogel JP. 2020. Advances on genomics, biology, ecology and evolution of Brachypodium, a bridging model grass system for cereals and biofuel grasses. New Phytologist 227:1587-1590. A

.- Shiposha V, Marques I, López-Álvarez D, Manzaneda A, Hernández P, Olonova M, Catalan P. 2020. Multiple founder events explain the genetic diversity and structure of the model allopolyploid grass Brachypodium hybridum in the Iberian Peninsula hotspot. Annals of Botany 125: 625–638. A

.- Lusinska J, Betekhtin A, López-Álvarez D, Catalán P, Jenkins G, Wolny E, Hasterok R. 2019. Comparatively barcoded chromosomes of Brachypodium perennials tell the story of their karyotype structure and evolution. International Journal of Molecular Sciences 20: 5557; doi:10.3390/ijms20225557. A

.- Scholthof KB, Irigoyen S, Catalan P, Mandadi KK. 2018. Brachypodium: A monocot grass model genus for plant biology. Plant Cell 30:1673-1694, doi: https://doi.org/10.1105/tpc.18.00083). A

.- Díaz-Pérez A, López-Álvarez D, Sancho R, Catalan P. 2018. Reconstructing the biogeography of species’ genomes in the highly reticulate allopolyploid-rich model grass genus Brachypodium using minimum evolution, coalescence and maximum likelihood approaches. Molecular Phylogenetics and Evolution 127: 256-271 (doi 10.1016/j.ympev.2018.06.003). A

.- Sancho R, Cantalapiedra CP, López-Álvarez D, Gordon SP, Vogel JP, Catalan P, Contreras-Moreira B. 2018. Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes. New Phytologist 218: 1631-1644. doi: 10.1111/nph.14926. A

.- Gordon SP, Contreras-Moreira B, Daniel Woods D, Des Marais DL, Burgess D, Shu S, Stritt C, Roulin A, Schackwitz W, Tyler L, Martin J, Lipzen A, Dochy N, Phillips J, Barry K, Geuten K, Juenger TE, Amasino R, Caicedo AL, Goodstein D, Davidson P, Mur L, Figueroa M, Freeling M, Catalan P, Vogel JP. 2017. Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with phenotypic variation. Nature Communications 8(1): 2184. doi: 10.1038/s41467-017-02292-8.

.- Marques I, Shiposha V, López-Álvarez D, Manzaneda A, Hernández P, Olonova M, Catalan P. 2017. Environmental isolation explains Iberian genetic diversity in the highly homozygous model grass Brachypodium distachyon. BMC Evolutionary Biology 17: 139. DOI 10.1186/s12862-017-0996-x. A

.- López-Alvarez D, Zubair H, Beckmann M, Draper J, Catalán P. 2017. Diversity and association of phenotypic and metabolomic traits in the close model grasses Brachypodium distachyon, B. stacei and B. hybridum. Annals of Botany 119 (4): 545-561. doi:101093/aob/mcw239. A.

.- Shiposah V, Catalan P, Olonova M, Marques I. 2016. Genetic structure and diversity of the selfing model grass Brachypodium stacei (Poaceae) in Western Mediterranean: out of the Iberian Peninsula and into the islands. PeerJ 4:e2407; DOI 10.7717/peerj.2407.

.- Catalan P, López-Álvarez D, Bellosta C, Villar L. 2016. Updated taxonomic descriptions, iconography and habitat preferences of Brachypodium distachyon, B. stacei and B. hybridum (Poaceae). Anales del Real Jardín Botánico de Madrid 73 (1): e028 (doi: http://dx.doi.org/10.3989/ajbm.2428). A

.- Catalán P, López-Alvarez D, Díaz-Pérez A, Sancho R, López-Herranz ML. 2016. Phylogeny and evolution of the genus Brachypodium. In Vogel J (ed.). Genetics and genomics of Brachypodium. pp. 9-38. Series Plant Genetics and Genomics: Crops Models. Springer. New York (doi 10.1007/7397_2015_17). A

.- López-Alvarez D, Manzaneda A J, Rey PJ, Giraldo P, Benavente E, Allainguillaume J, Mur LAJ, Caicedo AL, Hazen SP, Breiman A, Ezrati S, Catalán P. 2015. Environmental niche variation and evolutionary diversification of the Brachypodium distachyon grass complex species in their native circum-Mediterranean range. American Journal of Botany 102: 1-16.

.- Catalan P, Chalhoub B, Chochois V, Garvin DF, Hasterok R, Manzaneda AJ, Mur LAJ, Pecchioni N, Rasmussen SK, Vogel JP, Voxeur A. 2014. Update on genomics and basic biology of Brachypodium. Trends in Plant Science 19:414-418.

.- Catalán P, López-Alvarez D, López-Herranz ML. 2013. Código de barras genético de gramíneas modelo (Brachypodium): incremento de la biodiversidad. Conservación Vegetal 17: 3-6.

.- López-Alvarez D, López-Herranz ML, Betekhtin A, Catalán P. 2012. A DNA barcoding method to discriminate between the model plant Brachypodium distachyon and its close relatives B. stacei and B. hybridum (Poaceae). PLoS ONE 7(12): e51058. doi:10.1371/journal.pone.0051058.

.- Catalán P, Müller J, Hasterok R, Jenkins G, Mur LAJ, Langdon T, Betekhtin A, Siwinska D, Pimentel M, López-Alvarez D. 2012. Evolution and taxonomic split of the model grass Brachypodium distachyon (L.) P. Beauv. Annals of Botany 109:385–405.

.- Mur L., Allainguillaume J., Catalán P., Hasterok R., Jenkins G., Lesniewska K., Thomas I., Vogel J. 2011. Exploiting the Brachypodium Tool Box in cereal and grass research. New Phytologist 191: 334-347.

B. distachyon pangenome paper: supplementary information:

Bdistachyon pangenome_Supplementary information

Plant Biology and Evolution

Research Team

Genomics of model plant: Brachypodium