Genome sequencing and analysis of the model grass Brachypodium distachyonThe International Brachypodium Initiative (TIBI)Nature201046376376810.1038/nature0874720148030

USDA-ARS Western Regional Research Center, Albany, California 94710, USA.
Nature (Impact Factor: 41.46). 02/2010; 463(7282):763-768. DOI: 10.1038/nature08747
Source: PubMed


Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.

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    • "The genomes of these species have been completely sequenced and annotated, and drafts of these sequences are available on the web. These species were: fifteen eudicots (Ricinus communis [22], Populus trichocarpa [23], Medicago truncatula [24], Glycine max [25], Cucumis sativus [26], Prunus persica [27], Fragaria vesca [28], Arabidopsis thaliana [29, 30], Carica papaya [31], Theobroma cacao [32], Vitis vinifera [33], Mimulus guttatus [34]), four monocots (Sorghum bicolor [35], Zea mays [36], Oryza sativa [37, 38], Brachypodium distachyon [39]), one pseudofern (Selaginella moellendorffii [40]), one moss (Physcomitrella patens [41, 42]), and five algae (Chlamydomonas reinhardtii [43], Volvox carteri [44], Coccomyxa subellipsoidea [45], Micromonas pusilla [46], Ostreococcus lucimarinus [47]). All the genomes of these plant species are accessible at Phytozome comparative genomics database, and most of them also at GreenPhylDB comparative genomics database. "
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    ABSTRACT: Background Peptidases are key proteins involved in essential plant physiological processes. Although protein peptidase inhibitors are essential molecules that modulate peptidase activity, their global presence in different plant species remains still unknown. Comparative genomic analyses are powerful tools to get advanced knowledge into the presence and evolution of both, peptidases and their inhibitors across the Viridiplantae kingdom. Results A genomic comparative analysis of peptidase inhibitors and several groups of peptidases in representative species of different plant taxonomic groups has been performed. The results point out: i) clade-specific presence is common to many families of peptidase inhibitors, being some families present in most land plants; ii) variability is a widespread feature for peptidase inhibitory families, with abundant species-specific (or clade-specific) gene family proliferations; iii) peptidases are more conserved in different plant clades, being C1A papain and S8 subtilisin families present in all species analyzed; and iv) a moderate correlation among peptidases and their inhibitors suggests that inhibitors proliferated to control both endogenous and exogenous peptidases. Conclusions Comparative genomics has provided valuable insights on plant peptidase inhibitor families and could explain the evolutionary reasons that lead to the current variable repertoire of peptidase inhibitors in specific plant clades. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-812) contains supplementary material, which is available to authorized users.
    Full-text · Article · Sep 2014 · BMC Genomics
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    • "In contrast to Class I elements, which transpose via an RNA intermediate and therefore copy the original element, CACTAs transpose the original element itself. CACTA elements constitute approximately 2 to 5% of a grass genome [16,18]. However, only few active CACTA elements have been identified in plants [2-6,19]. "
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    ABSTRACT: Background CACTA elements are DNA transposons and are found in numerous organisms. Despite their low activity, several thousand copies can be identified in many genomes. CACTA elements transpose using a 'cut-and-paste' mechanism, which is facilitated by a DDE transposase. DDE transposases from CACTA elements contain, despite their conserved function, different exon numbers among various CACTA families. While earlier studies analyzed the ancestral history of the DDE transposases, no studies have examined exon loss and gain with a view of mechanisms that could drive the changes. Results We analyzed 64 transposases from different CACTA families among monocotyledonous and eudicotyledonous host species. The annotation of the exon/intron boundaries showed a range from one to six exons. A robust multiple sequence alignment of the 64 transposases based on their protein sequences was created and used for phylogenetic analysis, which revealed eight different clades. We observed that the exon numbers in CACTA transposases are not specific for a host genome. We found that ancient CACTA lineages diverged before the divergence of monocotyledons and eudicotyledons. Most exon/intron boundaries were found in three distinct regions among all the transposases, grouping 63 conserved intron/exon boundaries. Conclusions We propose a model for the ancestral CACTA transposase gene, which consists of four exons, that predates the divergence of the monocotyledons and eudicotyledons. Based on this model, we propose pathways of intron loss or gain to explain the observed variation in exon numbers. While intron loss appears to have prevailed, a putative case of intron gain was nevertheless observed.
    Full-text · Article · Sep 2014 · Mobile DNA
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    • "Bd has emerged recently as a novel monocot model plant species in the last 15 years for functional genomics approaches in small-grain cereals [4, 5, 43]. The shortness of its developmental cycle [44], together with the amenability of genetic transformation [45–48] and the availability of mutant collections [49–52] and of the genome sequence [53] makes this plant species an easy model to work with as a host for the interaction with important cereal pathogens such as Magnaporthe grisea [54], Pyrenophora teres [55], Puccinia graminis [56], the Panicum mosaic virus [57] and Fusarium species [6, 58]. This is of particular interest since this allows functional genomics studies to be performed to better understand cereals resistance mechanisms to important diseases. "
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    ABSTRACT: Background Fusarium Head Blight (FHB) caused primarily by Fusarium graminearum (Fg) is one of the major diseases of small-grain cereals including bread wheat. This disease both reduces yields and causes quality losses due to the production of deoxynivalenol (DON), the major type B trichothecene mycotoxin. DON has been described as a virulence factor enabling efficient colonization of spikes by the fungus in wheat, but its precise role during the infection process is still elusive. Brachypodium distachyon (Bd) is a model cereal species which has been shown to be susceptible to FHB. Here, a functional genomics approach was performed in order to characterize the responses of Bd to Fg infection using a global transcriptional and metabolomic profiling of B. distachyon plants infected by two strains of F. graminearum: a wild-type strain producing DON (Fgdon+) and a mutant strain impaired in the production of the mycotoxin (Fgdon-). Results Histological analysis of the interaction of the Bd21 ecotype with both Fg strains showed extensive fungal tissue colonization with the Fgdon+ strain while the florets infected with the Fgdon- strain exhibited a reduced hyphal extension and cell death on palea and lemma tissues. Fungal biomass was reduced in spikes inoculated with the Fgdon- strain as compared with the wild-type strain. The transcriptional analysis showed that jasmonate and ethylene-signalling pathways are induced upon infection, together with genes encoding putative detoxification and transport proteins, antioxidant functions as well as secondary metabolite pathways. In particular, our metabolite profiling analysis showed that tryptophan-derived metabolites, tryptamine, serotonin, coumaroyl-serotonin and feruloyl-serotonin, are more induced upon infection by the Fgdon+ strain than by the Fgdon- strain. Serotonin was shown to exhibit a slight direct antimicrobial effect against Fg. Conclusion Our results show that Bd exhibits defense hallmarks similar to those already identified in cereal crops. While the fungus uses DON as a virulence factor, the host plant preferentially induces detoxification and the phenylpropanoid and phenolamide pathways as resistance mechanisms. Together with its amenability in laboratory conditions, this makes Bd a very good model to study cereal resistance mechanisms towards the major disease FHB. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-629) contains supplementary material, which is available to authorized users.
    Full-text · Article · Jul 2014 · BMC Genomics
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