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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.


P450 genes involved in BR biosynthesis and transcriptional responses to Brz in Brachypodium and Arabidopsis.Brachypodium BR biosynthetic 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 the Brz treatment divided by the average read counts from mock 1-h and Brz+BL treatments. Stat represents the p-value of the microarray experiment, Arabidopsis det2 compared with wild-type11 for Arabidopsis genes or FDR of RNA-seq data when the counts from the Brz treatment were compared with mock 1-h and Brz+BL treatments for Brachypodium genes. log2 ratio is hatched in red if genes are up-regulated and in blue if down-regulated. cpm represents log2 scaled read counts per million reads of RNA-seq data from mock 1-h, Brz and Brz+BL treatments.
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f5: P450 genes involved in BR biosynthesis and transcriptional responses to Brz in Brachypodium and Arabidopsis.Brachypodium BR biosynthetic 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 the Brz treatment divided by the average read counts from mock 1-h and Brz+BL treatments. Stat represents the p-value of the microarray experiment, Arabidopsis det2 compared with wild-type11 for Arabidopsis genes or FDR of RNA-seq data when the counts from the Brz treatment were compared with mock 1-h and Brz+BL treatments for Brachypodium genes. log2 ratio is hatched in red if genes are up-regulated and in blue if down-regulated. cpm represents log2 scaled read counts per million reads of RNA-seq data from mock 1-h, Brz and Brz+BL treatments.

Mentions: Only four genes were detected as DEGs in the Brz220 treatment compared with all other treatments (high-stringency analysis, Data S7). This indicates that the BR-inducible gene expression response is relatively weak compared with those to other hormones, which is consistent with the BR response in Arabidopsis11. When the effects on gene expression of the Brz220 treatment were compared with those of the mock 3-h and Brz220+BL treatments (low-stringency analysis), 474 genes were detected as DEGs (Data S15). Of these genes, those with the term “RNA elongation” were enriched in the GOE analysis (Table 8). Genes with the term “photosynthesis” were also enriched in the GOE analysis. P450 genes involved in the biosynthesis of brassinosteroids (Bradi1g15030, homolog of BR6ox2 and Bradi5g12990, homolog of DWF4) were up-regulated by Brz220 compared to the mock 3-h and Brz220+BL treatments (Fig. 5), although the fold change of Bradi5g12990 was less than twice. This is consistent with the BR response in Arabidopsis; BR6ox2 and DWF4 were up-regulated in the det2 mutant of Arabidopsis compared to the wild-type (Fig. 5).


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)

P450 genes involved in BR biosynthesis and transcriptional responses to Brz in Brachypodium and Arabidopsis.Brachypodium BR biosynthetic 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 the Brz treatment divided by the average read counts from mock 1-h and Brz+BL treatments. Stat represents the p-value of the microarray experiment, Arabidopsis det2 compared with wild-type11 for Arabidopsis genes or FDR of RNA-seq data when the counts from the Brz treatment were compared with mock 1-h and Brz+BL treatments for Brachypodium genes. log2 ratio is hatched in red if genes are up-regulated and in blue if down-regulated. cpm represents log2 scaled read counts per million reads of RNA-seq data from mock 1-h, Brz and Brz+BL treatments.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: P450 genes involved in BR biosynthesis and transcriptional responses to Brz in Brachypodium and Arabidopsis.Brachypodium BR biosynthetic 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 the Brz treatment divided by the average read counts from mock 1-h and Brz+BL treatments. Stat represents the p-value of the microarray experiment, Arabidopsis det2 compared with wild-type11 for Arabidopsis genes or FDR of RNA-seq data when the counts from the Brz treatment were compared with mock 1-h and Brz+BL treatments for Brachypodium genes. log2 ratio is hatched in red if genes are up-regulated and in blue if down-regulated. cpm represents log2 scaled read counts per million reads of RNA-seq data from mock 1-h, Brz and Brz+BL treatments.
Mentions: Only four genes were detected as DEGs in the Brz220 treatment compared with all other treatments (high-stringency analysis, Data S7). This indicates that the BR-inducible gene expression response is relatively weak compared with those to other hormones, which is consistent with the BR response in Arabidopsis11. When the effects on gene expression of the Brz220 treatment were compared with those of the mock 3-h and Brz220+BL treatments (low-stringency analysis), 474 genes were detected as DEGs (Data S15). Of these genes, those with the term “RNA elongation” were enriched in the GOE analysis (Table 8). Genes with the term “photosynthesis” were also enriched in the GOE analysis. P450 genes involved in the biosynthesis of brassinosteroids (Bradi1g15030, homolog of BR6ox2 and Bradi5g12990, homolog of DWF4) were up-regulated by Brz220 compared to the mock 3-h and Brz220+BL treatments (Fig. 5), although the fold change of Bradi5g12990 was less than twice. This is consistent with the BR response in Arabidopsis; BR6ox2 and DWF4 were up-regulated in the det2 mutant of Arabidopsis compared to the wild-type (Fig. 5).

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.