Watching Grass Grow: The Emergence of Brachypodium distachyon as a Model for the Poaceae

Lyons, Christopher W. P.; Scholthof, Karen‐Beth G.

doi:10.1007/978-3-319-12185-7_23

Cited by 10 publications

(3 citation statements)

References 53 publications

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“…Despite the significant agricultural relevance of studying grass viral diseases, research on monocot-infecting viruses has generally lagged, compared with studies of dicot-infecting viruses, due to the lack of an amenable plant model similar to Arabidopsis or Nicotiana benthamiana (Mandadi and Scholthof, 2013;Lyons and Scholthof, 2015). Recently, Brachypodium distachyon has gained the status of a model monocot because of its genetic relatedness to key agronomic grasses such as wheat (Triticum aestivum), barley (Hordeum vulgare), maize, and rice (International Brachypodium Initiative, 2010) and because it has a small diploid genome (;272 Mb), short stature, short generation time, and is amenable to Agrobacterium tumefaciens-mediated transformation (Brkljacic et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions in Brachypodium distachyon

2015

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In eukaryotes, alternative splicing (AS) promotes transcriptome and proteome diversity. The extent of genome-wide AS changes occurring during a plant-microbe interaction is largely unknown. Here, using high-throughput, paired-end RNA sequencing, we generated an isoform-level spliceome map of Brachypodium distachyon infected with Panicum mosaic virus and its satellite virus. Overall, we detected ;44,443 transcripts in B. distachyon, ;30% more than those annotated in the reference genome. Expression of ;28,900 transcripts was ‡2 fragments per kilobase of transcript per million mapped fragments, and ;42% of multi-exonic genes were alternatively spliced. Comparative analysis of AS patterns in B. distachyon, rice (Oryza sativa), maize (Zea mays), sorghum (Sorghum bicolor), Arabidopsis thaliana, potato (Solanum tuberosum), Medicago truncatula, and poplar (Populus trichocarpa) revealed conserved ratios of the AS types between monocots and dicots. Virus infection quantitatively altered AS events in Brachypodium with little effect on the AS ratios. We discovered AS events for >100 immune-related genes encoding receptor-like kinases, NB-LRR resistance proteins, transcription factors, RNA silencing, and splicing-associated proteins. Cloning and molecular characterization of SCL33, a serine/arginine-rich splicing factor, identified multiple novel intronretaining splice variants that are developmentally regulated and modulated during virus infection. B. distachyon SCL33 splicing patterns are also strikingly conserved compared with a distant Arabidopsis SCL33 ortholog. This analysis provides new insights into AS landscapes conserved among monocots and dicots and uncovered AS events in plant defense-related genes.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions in Brachypodium distachyon

2015

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“…Such work may also reveal negative host (or virus) outcomes that plant breeders and pathologists could apply to small grains and forage/pasture grasses. Importantly, genetic variation within the Brachypodium genus is maintained in wild populations, which can be used to decipher gene functions for improving agronomic traits and for comparative ecological and evolutionary studies (Lyons & Scholthof, ; Gordon et al , ; Scholthof et al , ).…”

Section: Brachypodium: a Model For Environment–host–virus(n+1) Interamentioning

confidence: 99%

Brachypodium and plant viruses: entwined tools for discovery

Scholthof

2020

New Phytologist

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In just a decade, Brachypodium distachyon (Brachypodium) has fulfilled its initial promise as a key tool for realizing new strategies for understanding host and pathogen biology during virus infections of the Poaceae. For this Tansley Insight, I have identified four areasfrom the laboratory to the fieldthat may be particularly fruitful to explore, with a particular focus on Brachypodium-virus infections. These focus areas include: mechanisms of RNA modification of host plants and viruses; coevolution of virus-host interactions; viruses as tools of discovery; and how to explicate the complex outcomes during multivirus infections. Here, I broadly frame our current knowledge of Brachypodium-virus interactions and how these findings may inform virus studies of grasses in the laboratory, field and natural settings.

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“…Over the past decade, B. distachyon has emerged as one of the preeminent model plant species, for which there are tremendous genetic, molecular and genomic resources (International Brachypodium Initiative, 2010;Mur et al, 2011;Catal an et al, 2014;Gordon et al, 2014). Its flagship plant genome now serves as an anchor for genomic studies across the temperate Pooideae grasses and monocots (Lyons and Scholthof, 2015). Its small genome size, compact genome (e.g.…”

Section: Introductionmentioning

confidence: 99%

Diversity and association of phenotypic and metabolomic traits in the close model grassesBrachypodium distachyon,B. staceiandB. hybridum

López-Álvarez

Zubair

Beckmann

et al. 2016

Ann Bot

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Highly explanatory metabolite signals together with morphological characters revealed concordant patterns of differentiation of the three taxa. Intraspecific phenotypic diversity was observed between northern and southern Iberian populations of B. distachyon and between eastern Mediterranean/south-western Asian and western Mediterranean populations of B. stacei . Significant association was found for pollen grain length and lemma length and ten and six metabolomic signals, respectively. These results would guide the selection of new germplasm lines of the three model grasses in ongoing genome-wide association studies.

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Watching Grass Grow: The Emergence of Brachypodium distachyon as a Model for the Poaceae

Cited by 10 publications

References 53 publications

Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions in Brachypodium distachyon

Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions in Brachypodium distachyon

Brachypodium and plant viruses: entwined tools for discovery

Diversity and association of phenotypic and metabolomic traits in the close model grassesBrachypodium distachyon,B. staceiandB. hybridum

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