Abstract
The modern Brachypodium distachyon genome consisting in 25,532 genes, 271 Megabases covering five chromosomes derives from a founder grass ancestor structured in 7/12 protochromosomes containing 10,000–15,000 protogenes with a minimal physical coding space size of <50 Megabases. From the grass ancestor, the modern Brachypodium genome evolved through a polyploidization event followed by a diploidization mechanism at the genome level, consisting in centromere-oriented ancestral chromosome fusions leading to chromosome number reduction, and at the gene level, consisting in the deletion of the duplicated gene copies leading to a subgenome dominance. Finally, the Brachypodium genome can be used as a guide for translational research in grasses for applied research in dissecting and improving traits of agricultural relevance.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abrouk M, Murat F, Pont C, Messing J, Jackson S, Faraut T, et al. Palaeogenomics of plants: synteny-based modelling of extinct ancestors. Trends Plant Sci. 2010;15(9):479–87.
Bolot S, Abrouk M, Masood-Quraishi U, Stein N, Messing J, Feuillet C, et al. The ‘inner circle’ of the cereal genomes. Curr Opin Plant Biol. 2009;12(2):119–25.
Dibari B, Murat F, Chosson A, Gautier V, Poncet C, Lecomte P, et al. Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses. BMC Genomics. 2012;13:221.
Dobrovolskaya O, Pont C, Sibout R, Martinek P, Badaeva E, Murat F, et al. FRIZZY PANICLE drives supernumerary spikelets in bread wheat. Plant Physiol. 2015;167(1):189–99.
International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 2010;463(7282):763–8.
International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature. 2005;436:793–800.
Jacquemin J, Chaparro C, Laudié M, Berger A, Gavory F, Goicoechea JL, et al. Long-range and targeted ectopic recombination between the two homeologous chromosomes 11 and 12 in Oryza species. Mol Biol Evol. 2011;28(11):3139–50.
Luo MC, Deal KR, Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, et al. Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae. Proc Natl Acad Sci U S A. 2009;106(37):15780–5.
Massa AN, Wanjugi H, Deal KR, O’Brien K, You FM, Maiti R, et al. Gene space dynamics during the evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes. Mol Biol Evol. 2011;28(9):2537–47.
Murat F, Xu JH, Tannier E, Abrouk M, Guilhot N, Pont C, et al. Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res. 2010;20(11):1545–57.
Murat F, Zhang R, Guizard S, Flores R, Armero A, Pont C, et al. Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes. Genome Biol Evol. 2014a;6(1):12–33.
Murat F, Pont C, Salse J. Paleogenomics in Triticeae for translational research. Curr Plant Biol. 2014b;1:34–9.
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, et al. The Sorghum bicolor genome and the diversification of grasses. Nature. 2009;457(7229):551–6.
Pont C, Murat F, Confolent C, Balzergue S, Salse J. RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.). Genome Biol. 2011;12(12):R119.
Pont C, Murat F, Guizard S, Flores R, Foucrier S, Bidet Y, et al. Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes. Plant J. 2013;76(6):1030–44.
Quraishi UM, Abrouk M, Bolot S, Pont C, Throude M, Guilhot N, et al. Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection. Funct Integr Genomics. 2009;9(4):473–84.
Quraishi UM, Abrouk M, Murat F, Pont C, Foucrier S, Desmaizieres G, et al. Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution. Plant J. 2011a;65(5):745–56.
Quraishi UM, Murat F, Abrouk M, Pont C, Confolent C, Oury FX, et al. Combined meta-genomics analyses unravel candidate genes for the grain dietary fiber content in bread wheat (Triticum aestivum L.). Funct Integr Genomics. 2011b;11(1):71–83.
Salse J, Bolot S, Throude M, Jouffe V, Piegu B, Quraishi UM, et al. Identification and characterization of conserved duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell. 2008;20:11–24.
Salse J, Abrouk M, Murat F, Quraishi UM, Feuillet C. Improved criteria and comparative genomics tool provide new insights into grass paleogenomics. Brief Bioinform. 2009a;10(6):619–30.
Salse J, Abrouk M, Bolot S, Guilhot N, Courcelle E, Faraut T, et al. Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. Proc Natl Acad Sci U S A. 2009b;106:14908–13.
Salse J, Feuillet C. Paleogenomics in cereals: modelling of ancestors for modern species improvement. C R Biol. 2011;334(3):205–11.
Salse J. In silico archeogenomics unveils modern plant genome organization, regulation and evolution. Curr Opin Plant Biol. 2012;15(2):122–30.
Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, et al. The B73 maize genome: complexity, diversity, and dynamics. Science. 2009;326(5956):1112–5.
Schubert I, Lysak MA. Interpretation of karyotype evolution should consider chromosome structural constraints. Trends Genet. 2011;27(6):207–16.
Tang H, Bowers JE, Wang X, Paterson AH. Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc Natl Acad Sci U S A. 2010;107(1):472–7.
Wang X, Tang H, Paterson AH. Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel, in major Poaceae lineages. Plant Cell. 2011;23(1):27–37.
Wicker T, Buchmann JP, Keller B. Patching gaps in plant genomes results in gene movement and erosion of colinearity. Genome Res. 2010;20(9):1229–37.
Acknowledgments
This work has been supported by grants from the Agence Nationale de la Recherche (program ANR Blanc-PAGE, ref: ANR-2011-BSV6-00801). The author gratefully acknowledges Caroline Pont and Florent Murat (INRA Clermont-Ferrand, France) for their contributions in preparing the article illustrations.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Salse, J. (2015). Brachypodium Paleogenomics: From Genome Evolution to Translational Research in Grass Crops. In: Vogel, J. (eds) Genetics and Genomics of Brachypodium. Plant Genetics and Genomics: Crops and Models, vol 18. Springer, Cham. https://doi.org/10.1007/7397_2015_2
Download citation
DOI: https://doi.org/10.1007/7397_2015_2
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-26942-9
Online ISBN: 978-3-319-26944-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)