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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 Aux/IAA genes and their transcriptional responses to auxin in Brachypodium and Arabidopsis.Brachypodium Aux/IAA family members were retrieved using the BLAST software. Protein sequences were aligned with MAFFT and similarities (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 IAA treatment divided by the average read count from all other treatments. Stat represents the p-value of the microarray experiment of Arabidopsis treated with IAA11 or the FDR of RNA-seq data when the count of IAA 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 in all experiments.
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f1: Phylogenic tree of Aux/IAA genes and their transcriptional responses to auxin in Brachypodium and Arabidopsis.Brachypodium Aux/IAA family members were retrieved using the BLAST software. Protein sequences were aligned with MAFFT and similarities (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 IAA treatment divided by the average read count from all other treatments. Stat represents the p-value of the microarray experiment of Arabidopsis treated with IAA11 or the FDR of RNA-seq data when the count of IAA 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 in all experiments.

Mentions: One hundred and twenty-five genes were identified as auxin-responsive genes in the high-stringency analysis (Data S1). The genes with the term “response to auxin stimulus” were found to be enriched in the GOE analysis of auxin-responsive genes in Brachypodium (Table 7). As we described in the comparison with rice, many genes in the Aux/IAA family and GH3 family were detected as auxin-responsive genes in Brachypodium. These results are also consistent with the auxin response in Arabidopsis (Fig. 1, Fig. S1). In contrast to the auxin response in Arabidopsis, Brachypodium genes related to ethylene functions were not regulated in the same manner (Fig. S2), although their expression levels were not low (present at sufficiently high levels for analysis) (log2 cpm (number of counts per million reads) >1).


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 Aux/IAA genes and their transcriptional responses to auxin in Brachypodium and Arabidopsis.Brachypodium Aux/IAA family members were retrieved using the BLAST software. Protein sequences were aligned with MAFFT and similarities (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 IAA treatment divided by the average read count from all other treatments. Stat represents the p-value of the microarray experiment of Arabidopsis treated with IAA11 or the FDR of RNA-seq data when the count of IAA 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 in all experiments.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Phylogenic tree of Aux/IAA genes and their transcriptional responses to auxin in Brachypodium and Arabidopsis.Brachypodium Aux/IAA family members were retrieved using the BLAST software. Protein sequences were aligned with MAFFT and similarities (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 IAA treatment divided by the average read count from all other treatments. Stat represents the p-value of the microarray experiment of Arabidopsis treated with IAA11 or the FDR of RNA-seq data when the count of IAA 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 in all experiments.
Mentions: One hundred and twenty-five genes were identified as auxin-responsive genes in the high-stringency analysis (Data S1). The genes with the term “response to auxin stimulus” were found to be enriched in the GOE analysis of auxin-responsive genes in Brachypodium (Table 7). As we described in the comparison with rice, many genes in the Aux/IAA family and GH3 family were detected as auxin-responsive genes in Brachypodium. These results are also consistent with the auxin response in Arabidopsis (Fig. 1, Fig. S1). In contrast to the auxin response in Arabidopsis, Brachypodium genes related to ethylene functions were not regulated in the same manner (Fig. S2), although their expression levels were not low (present at sufficiently high levels for analysis) (log2 cpm (number of counts per million reads) >1).

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.