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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.


Biosynthesis pathway of JA and transcriptional responses in Brachypodium and Arabidopsis.Homologs of jasmonate biosynthetic genes in Brachypodium were retrieved using the BLAST software. Brachypodium genes are shown in red and Arabidopsis genes in black. Stat represents the p-value of the microarray experiment. Arabidopsis treated by MJ for 3 hours11 and FDR of RNA-seq data when the count of MJ treatment was compared with all other treatments. log2 ratio represents the gene expression ratio between read counts from the MJ treatment divided by the average read counts from all other treatments. log2 ratio is hatched in red if genes are up-regulated. cpm represents log2 scaled read count per million reads of RNA-seq data from all treatments.
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f4: Biosynthesis pathway of JA and transcriptional responses in Brachypodium and Arabidopsis.Homologs of jasmonate biosynthetic genes in Brachypodium were retrieved using the BLAST software. Brachypodium genes are shown in red and Arabidopsis genes in black. Stat represents the p-value of the microarray experiment. Arabidopsis treated by MJ for 3 hours11 and FDR of RNA-seq data when the count of MJ treatment was compared with all other treatments. log2 ratio represents the gene expression ratio between read counts from the MJ treatment divided by the average read counts from all other treatments. log2 ratio is hatched in red if genes are up-regulated. cpm represents log2 scaled read count per million reads of RNA-seq data from all treatments.

Mentions: Three hundred and eighty-three genes were identified as JA-responsive genes in the high-stringency analysis (Data S5). Genes with the term “response to wounding” were enriched in the GOE analysis (Table 7). Genes involved in the biosynthesis of jasmonic acid (LOX3 homolog (Bradi5g11590), LOX4 homolog (Bradi1g72690), AOS homolog (Bradi3g08160, Bradi1g07480, Bradi1g69330), AOC3 homolog (Bradi1g15840), OPR3 homolog (Bradi3g37650) and OPCL1 homolog (Bradi1g76280) were up-regulated by MJ treatment (Fig. 4). The JAZ genes in Arabidopsis encode JA receptors19. Two members of the JAZ family (Bradi3g23190, Bradi1g58490) were also up-regulated in Brachypodium.


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)

Biosynthesis pathway of JA and transcriptional responses in Brachypodium and Arabidopsis.Homologs of jasmonate biosynthetic genes in Brachypodium were retrieved using the BLAST software. Brachypodium genes are shown in red and Arabidopsis genes in black. Stat represents the p-value of the microarray experiment. Arabidopsis treated by MJ for 3 hours11 and FDR of RNA-seq data when the count of MJ treatment was compared with all other treatments. log2 ratio represents the gene expression ratio between read counts from the MJ treatment divided by the average read counts from all other treatments. log2 ratio is hatched in red if genes are up-regulated. cpm represents 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

f4: Biosynthesis pathway of JA and transcriptional responses in Brachypodium and Arabidopsis.Homologs of jasmonate biosynthetic genes in Brachypodium were retrieved using the BLAST software. Brachypodium genes are shown in red and Arabidopsis genes in black. Stat represents the p-value of the microarray experiment. Arabidopsis treated by MJ for 3 hours11 and FDR of RNA-seq data when the count of MJ treatment was compared with all other treatments. log2 ratio represents the gene expression ratio between read counts from the MJ treatment divided by the average read counts from all other treatments. log2 ratio is hatched in red if genes are up-regulated. cpm represents log2 scaled read count per million reads of RNA-seq data from all treatments.
Mentions: Three hundred and eighty-three genes were identified as JA-responsive genes in the high-stringency analysis (Data S5). Genes with the term “response to wounding” were enriched in the GOE analysis (Table 7). Genes involved in the biosynthesis of jasmonic acid (LOX3 homolog (Bradi5g11590), LOX4 homolog (Bradi1g72690), AOS homolog (Bradi3g08160, Bradi1g07480, Bradi1g69330), AOC3 homolog (Bradi1g15840), OPR3 homolog (Bradi3g37650) and OPCL1 homolog (Bradi1g76280) were up-regulated by MJ treatment (Fig. 4). The JAZ genes in Arabidopsis encode JA receptors19. Two members of the JAZ family (Bradi3g23190, Bradi1g58490) were also up-regulated in Brachypodium.

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.