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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 ARR genes and their transcriptional responses to CK in Brachypodium and Arabidopsis.Brachypodium ARR family members 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 the read count in tZ treatments divided by the average read count from all other treatments. Stat represents the p-value of the microarray experiment in Arabidopsis treated with t-zeatin for 1 h11 or FDR of RNA-seq data when the count from tZ treatment was compared with all other treatments. log2 ratio is hatched in red if genes are up-regulated. cpm represents the average of log2-scaled read counts per million reads from all experiments.
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f2: Phylogenic tree of ARR genes and their transcriptional responses to CK in Brachypodium and Arabidopsis.Brachypodium ARR family members 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 the read count in tZ treatments divided by the average read count from all other treatments. Stat represents the p-value of the microarray experiment in Arabidopsis treated with t-zeatin for 1 h11 or FDR of RNA-seq data when the count from tZ treatment was compared with all other treatments. log2 ratio is hatched in red if genes are up-regulated. cpm represents the average of log2-scaled read counts per million reads from all experiments.

Mentions: Twenty-three genes were identified as cytokinin-responsive genes in the high-stringency analysis (Data S2). The genes with the term “response to cytokinin stimulus” were enriched in the GOE analysis (Table 7). Genes in the type A ARR family (Bradi2g61000, Bradi4g43090, Bradi5g25860, Bradi3g45930 and Bradi5g11350) were detected as cytokinin-responsive genes (Fig. 2). In contrast, members of the type B ARR gene family were not detected as cytokinin-responsive genes. These results are consistent with the cytokinin response in Arabidopsis18.


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 ARR genes and their transcriptional responses to CK in Brachypodium and Arabidopsis.Brachypodium ARR family members 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 the read count in tZ treatments divided by the average read count from all other treatments. Stat represents the p-value of the microarray experiment in Arabidopsis treated with t-zeatin for 1 h11 or FDR of RNA-seq data when the count from tZ treatment was compared with all other treatments. log2 ratio is hatched in red if genes are up-regulated. cpm represents the average of log2-scaled read counts per million reads from all experiments.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: Phylogenic tree of ARR genes and their transcriptional responses to CK in Brachypodium and Arabidopsis.Brachypodium ARR family members 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 the read count in tZ treatments divided by the average read count from all other treatments. Stat represents the p-value of the microarray experiment in Arabidopsis treated with t-zeatin for 1 h11 or FDR of RNA-seq data when the count from tZ treatment was compared with all other treatments. log2 ratio is hatched in red if genes are up-regulated. cpm represents the average of log2-scaled read counts per million reads from all experiments.
Mentions: Twenty-three genes were identified as cytokinin-responsive genes in the high-stringency analysis (Data S2). The genes with the term “response to cytokinin stimulus” were enriched in the GOE analysis (Table 7). Genes in the type A ARR family (Bradi2g61000, Bradi4g43090, Bradi5g25860, Bradi3g45930 and Bradi5g11350) were detected as cytokinin-responsive genes (Fig. 2). In contrast, members of the type B ARR gene family were not detected as cytokinin-responsive genes. These results are consistent with the cytokinin response in Arabidopsis18.

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.