Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources

Mochida, Keiichi; Uehara‐Yamaguchi, Yukiko; Takahashi, Fumiyuki; Yoshida, Takuhiro; Sakurai, Tetsuya; Shinozaki, Kazuo

doi:10.1371/journal.pone.0075265

Cited by 28 publications

(27 citation statements)

References 41 publications

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“…Most of the queried transcripts were allocated to the annotated gene regions of the Brachypodium genome; some were allocated to the non-annotated regions. These results suggest that there are potential transcription units of Brachypodium with conserved homology to cDNAs in Triticeae plants that have not yet been annotated (Mochida et al 2013a) (Fig. 3B).…”

Section: Study Of Brachypodium and Its Roles In Pooideae Genomicsmentioning

confidence: 99%

Unlocking Triticeae genomics to sustainably feed the future

Mochida

Shinozaki

2013

Plant and Cell Physiology

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The tribe Triticeae includes the major crops wheat and barley. Within the last few years, the whole genomes of four Triticeae species—barley, wheat, Tausch’s goatgrass (Aegilops tauschii) and wild einkorn wheat (Triticum urartu)—have been sequenced. The availability of these genomic resources for Triticeae plants and innovative analytical applications using next-generation sequencing technologies are helping to revitalize our approaches in genetic work and to accelerate improvement of the Triticeae crops. Comparative genomics and integration of genomic resources from Triticeae plants and the model grass Brachypodium distachyon are aiding the discovery of new genes and functional analyses of genes in Triticeae crops. Innovative approaches and tools such as analysis of next-generation populations, evolutionary genomics and systems approaches with mathematical modeling are new strategies that will help us discover alleles for adaptive traits to future agronomic environments. In this review, we provide an update on genomic tools for use with Triticeae plants and Brachypodium and describe emerging approaches toward crop improvements in Triticeae.

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Section: Study Of Brachypodium and Its Roles In Pooideae Genomicsmentioning

confidence: 99%

Unlocking Triticeae genomics to sustainably feed the future

Mochida

Shinozaki

2013

Plant and Cell Physiology

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“…Brachypoideae belongs to a tribe which configures the core Pooideae with Littledaleeae, Bromeae and Triticeae (Soreng et al ., ), and a small grass, B. distachyon , is used as an experimental model plant for economically important cereals such as wheat, barley and rice because of its short life cycle, self‐fertility and small diploid genome (Kellogg, ). The complete genome sequence and cDNA database of the standard accession Bd21 and a number of accessions are available (Vogel et al ., , , ; Mochida et al ., ). Various major crop pathogens can infect B. distachyon (Sandoya & Buanafina, ; Fitzgerald et al ., ).…”

Section: Introductionmentioning

confidence: 97%

Salicylic acid‐dependent immunity contributes to resistance against Rhizoctonia solani, a necrotrophic fungal agent of sheath blight, in rice and Brachypodium distachyon

et al. 2017

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Summary Rhizoctonia solani is a soil‐borne fungus causing sheath blight. In consistent with its necrotrophic life style, no rice cultivars fully resistant to R. solani are known, and agrochemical plant defense activators used for rice blast, which upregulate a phytohormonal salicylic acid (SA)‐dependent pathway, are ineffective towards this pathogen. As a result of the unavailability of genetics, the infection process of R. solani remains unclear.We used the model monocotyledonous plants Brachypodium distachyon and rice, and evaluated the effects of phytohormone‐induced resistance to R. solani by pharmacological, genetic and microscopic approaches to understand fungal pathogenicity.Pretreatment with SA, but not with plant defense activators used in agriculture, can unexpectedly induce sheath blight resistance in plants. SA treatment inhibits the advancement of R. solani to the point in the infection process in which fungal biomass shows remarkable expansion and specific infection machinery is developed. The involvement of SA in R. solani resistance is demonstrated by SA‐deficient NahG transgenic rice and the sheath blight‐resistant B. distachyon accessions, Bd3‐1 and Gaz‐4, which activate SA‐dependent signaling on inoculation.Our findings suggest a hemi‐biotrophic nature of R. solani, which can be targeted by SA‐dependent plant immunity. Furthermore, B. distachyon provides a genetic resource that can confer disease resistance against R. solani to plants.

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“…Subsequently, the technology has been used in grass species, including O. sativa ( Kikuchi et al 2003 ), Triticum aestivum ( Ogihara et al 2004 , Kawaura et al 2009 ), Hordeum vulgare ( Sato et al 2009 , Matsumoto et al 2011 ), Z. mays ( Soderlund et al . 2009 ) and Brachypodium distachyon ( Mochida et al 2013 ).…”

Section: Introductionmentioning

confidence: 99%

MOROKOSHI: Transcriptome Database in Sorghum bicolor

Makita

Shimada

Kawashima

et al. 2014

Plant and Cell Physiology

110

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In transcriptome analysis, accurate annotation of each transcriptional unit and its expression profile is essential. A full-length cDNA (FL-cDNA) collection facilitates the refinement of transcriptional annotation, and accurate transcription start sites help to unravel transcriptional regulation. We constructed a normalized FL-cDNA library from eight growth stages of aerial tissues in Sorghum bicolor and isolated 37,607 clones. These clones were Sanger sequenced from the 5′ and/or 3′ ends and in total 38,981 high-quality expressed sequence tags (ESTs) were obtained. About one-third of the transcripts of known genes were captured as FL-cDNA clone resources. In addition to these, we also annotated 272 novel genes, 323 antisense transcripts and 1,672 candidate isoforms. These clones are available from the RIKEN Bioresource Center. After obtaining accurate annotation of transcriptional units, we performed expression profile analysis. We carried out spikelet-, seed- and stem-specific RNA sequencing (RNA-Seq) analysis and confirmed the expression of 70.6% of the newly identified genes. We also downloaded 23 sorghum RNA-Seq samples that are publicly available and these are shown on a genome browser together with our original FL-cDNA and RNA-Seq data. Using our original and publicly available data, we made an expression profile of each gene and identified the top 20 genes with the most similar expression. In addition, we visualized their relationships in gene co-expression networks. Users can access and compare various transcriptome data from S, bicolor at http://sorghum.riken.jp.

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Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources

Cited by 28 publications

References 41 publications

Unlocking Triticeae genomics to sustainably feed the future

Unlocking Triticeae genomics to sustainably feed the future

Salicylic acid‐dependent immunity contributes to resistance against Rhizoctonia solani, a necrotrophic fungal agent of sheath blight, in rice and Brachypodium distachyon

MOROKOSHI: Transcriptome Database in Sorghum bicolor

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