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Transcriptome analysis of hormone-induced gene expression in Brachypodium distachyon.

Kakei Y, Mochida K, Sakurai T, Yoshida T, Shinozaki K, Shimada Y - Sci Rep (2015)

Bottom Line: We compared the data with the phytohormone responses that have reported in rice.For example, the expressions of ACC synthase genes were up-regulated by auxin treatment in rice and Arabidopsis, but no orthologous ACC synthase gene was up-regulated in Brachypodium.Our results provide information useful to understand the diversity and similarity of hormone-regulated transcriptional responses between eudicots and monocots.

View Article: PubMed Central - PubMed

Affiliation: Kihara Institute for Biological Research, Yokohama City University, Kanagawa, JAPAN.

ABSTRACT
Brachypodium distachyon is a new model plant closely related to wheat and other cereals. In this study, we performed a comprehensive analysis of hormone-regulated genes in Brachypodium distachyon using RNA sequencing technology. Brachypodium distachyon seedlings were treated with eight phytohormones (auxin, cytokinine, brassinosteroid, gibberelline, abscisic acid, ethylene, jasmonate and salicylic acid) and two inhibitors, Brz220 (brassinosteroid biosynthesis inhibitor) and prohexadione (gibberelline biosynthesis inhibitor). The expressions of 1807 genes were regulated in a phytohormone-dependent manner. We compared the data with the phytohormone responses that have reported in rice. Transcriptional responses to hormones are conserved between Bracypodium and rice. Transcriptional regulation by brassinosteroid, gibberellin and ethylene was relatively weaker than those by other hormones. This is consistent with the data obtained from comprehensive analysis of hormone responses reported in Arabidopsis. Brachypodium and Arabidopsis also shared some common transcriptional responses to phytohormones. Alternatively, unique transcriptional responses to phytohormones were observed in Brachypodium. For example, the expressions of ACC synthase genes were up-regulated by auxin treatment in rice and Arabidopsis, but no orthologous ACC synthase gene was up-regulated in Brachypodium. Our results provide information useful to understand the diversity and similarity of hormone-regulated transcriptional responses between eudicots and monocots.

No MeSH data available.


Phylogenic tree of PR1, its orthologs and transcriptional responses to SA treatment in Brachypodium and Arabidopsis.Brachypodium PR1-like genes were retrieved using the BLAST software. Similarities in protein sequences (percentage identity) are shown as a phylogenetic tree. Brachypodium genes are shown in red and Arabidopsis genes in black. log2 ratio represents the gene expression ratio between read counts from SA treatment divided by the average read counts from all other treatments. Stat represents the p-value of the microarray experiment. Arabidopsis treated with SA for 3 h11 for Arabidopsis genes or FDR of RNA-seq data when the counts from SA treatment were compared with all other treatments for Brachypodium genes. log2 ratio is hatched in red if genes are up-regulated and in blue if down-regulated. cpm represents the log2-scaled read count per million reads of RNA-seq data from all treatments.
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f3: Phylogenic tree of PR1, its orthologs and transcriptional responses to SA treatment in Brachypodium and Arabidopsis.Brachypodium PR1-like genes were retrieved using the BLAST software. Similarities in protein sequences (percentage identity) are shown as a phylogenetic tree. Brachypodium genes are shown in red and Arabidopsis genes in black. log2 ratio represents the gene expression ratio between read counts from SA treatment divided by the average read counts from all other treatments. Stat represents the p-value of the microarray experiment. Arabidopsis treated with SA for 3 h11 for Arabidopsis genes or FDR of RNA-seq data when the counts from SA treatment were compared with all other treatments for Brachypodium genes. log2 ratio is hatched in red if genes are up-regulated and in blue if down-regulated. cpm represents the log2-scaled read count per million reads of RNA-seq data from all treatments.

Mentions: Eighty-one genes were identified as SA-responsive genes in the high-stringency analysis (Data S3). Genes with the term “defense response to fungus” were enriched in GOE analysis (Table 7). A homolog of the PR-1 gene (Bradi1g57590) was up-regulated by SA treatment (Fig. 3).


Transcriptome analysis of hormone-induced gene expression in Brachypodium distachyon.

Kakei Y, Mochida K, Sakurai T, Yoshida T, Shinozaki K, Shimada Y - Sci Rep (2015)

Phylogenic tree of PR1, its orthologs and transcriptional responses to SA treatment in Brachypodium and Arabidopsis.Brachypodium PR1-like genes were retrieved using the BLAST software. Similarities in protein sequences (percentage identity) are shown as a phylogenetic tree. Brachypodium genes are shown in red and Arabidopsis genes in black. log2 ratio represents the gene expression ratio between read counts from SA treatment divided by the average read counts from all other treatments. Stat represents the p-value of the microarray experiment. Arabidopsis treated with SA for 3 h11 for Arabidopsis genes or FDR of RNA-seq data when the counts from SA treatment were compared with all other treatments for Brachypodium genes. log2 ratio is hatched in red if genes are up-regulated and in blue if down-regulated. cpm represents the log2-scaled read count per million reads of RNA-seq data from all treatments.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4588574&req=5

f3: Phylogenic tree of PR1, its orthologs and transcriptional responses to SA treatment in Brachypodium and Arabidopsis.Brachypodium PR1-like genes were retrieved using the BLAST software. Similarities in protein sequences (percentage identity) are shown as a phylogenetic tree. Brachypodium genes are shown in red and Arabidopsis genes in black. log2 ratio represents the gene expression ratio between read counts from SA treatment divided by the average read counts from all other treatments. Stat represents the p-value of the microarray experiment. Arabidopsis treated with SA for 3 h11 for Arabidopsis genes or FDR of RNA-seq data when the counts from SA treatment were compared with all other treatments for Brachypodium genes. log2 ratio is hatched in red if genes are up-regulated and in blue if down-regulated. cpm represents the log2-scaled read count per million reads of RNA-seq data from all treatments.
Mentions: Eighty-one genes were identified as SA-responsive genes in the high-stringency analysis (Data S3). Genes with the term “defense response to fungus” were enriched in GOE analysis (Table 7). A homolog of the PR-1 gene (Bradi1g57590) was up-regulated by SA treatment (Fig. 3).

Bottom Line: We compared the data with the phytohormone responses that have reported in rice.For example, the expressions of ACC synthase genes were up-regulated by auxin treatment in rice and Arabidopsis, but no orthologous ACC synthase gene was up-regulated in Brachypodium.Our results provide information useful to understand the diversity and similarity of hormone-regulated transcriptional responses between eudicots and monocots.

View Article: PubMed Central - PubMed

Affiliation: Kihara Institute for Biological Research, Yokohama City University, Kanagawa, JAPAN.

ABSTRACT
Brachypodium distachyon is a new model plant closely related to wheat and other cereals. In this study, we performed a comprehensive analysis of hormone-regulated genes in Brachypodium distachyon using RNA sequencing technology. Brachypodium distachyon seedlings were treated with eight phytohormones (auxin, cytokinine, brassinosteroid, gibberelline, abscisic acid, ethylene, jasmonate and salicylic acid) and two inhibitors, Brz220 (brassinosteroid biosynthesis inhibitor) and prohexadione (gibberelline biosynthesis inhibitor). The expressions of 1807 genes were regulated in a phytohormone-dependent manner. We compared the data with the phytohormone responses that have reported in rice. Transcriptional responses to hormones are conserved between Bracypodium and rice. Transcriptional regulation by brassinosteroid, gibberellin and ethylene was relatively weaker than those by other hormones. This is consistent with the data obtained from comprehensive analysis of hormone responses reported in Arabidopsis. Brachypodium and Arabidopsis also shared some common transcriptional responses to phytohormones. Alternatively, unique transcriptional responses to phytohormones were observed in Brachypodium. For example, the expressions of ACC synthase genes were up-regulated by auxin treatment in rice and Arabidopsis, but no orthologous ACC synthase gene was up-regulated in Brachypodium. Our results provide information useful to understand the diversity and similarity of hormone-regulated transcriptional responses between eudicots and monocots.

No MeSH data available.