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Genome-wide identification and expression analysis of the IQD gene family in moso bamboo (Phyllostachys edulis).

Wu M, Li Y, Chen D, Liu H, Zhu D, Xiang Y - Sci Rep (2016)

Bottom Line: We surveyed the putative promoter regions of the PeIQD genes, which showed that largely stress-related cis-elements existed in these genes.The expression profiles of the IQD genes shed light on their functional divergence.Additionally, a yeast two-hybrid assay proved that PeIQD8 can interact with PeCaM2 and that IQ or I in the IQ motif is required for PeIQD8 to combine with CaM2.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.

ABSTRACT
Members of the plant-specific IQ67-domain (IQD) protein family are involved in various aspects of normal plant growth and developmental processes as well as basal defence response. Although hundreds of IQD proteins have been identified, only a small number of IQDs have been functionally characterized. Moreover, no systematic study has been performed on moso bamboo. In this study, we performed for the first time a genome-wide identification and expression analysis of the IQD gene family in moso bamboo. We identified 29 non-redundant PeIQD encoding genes. Analysis of the evolutionary patterns and divergence revealed that the IQD genes underwent a large-scale event around 12 million years ago and the division times of IQD family genes between moso bamboo and rice, and, between moso bamboo and Brachypodium, were found to be 20-35 MYA and 25-40 MYA, respectively. We surveyed the putative promoter regions of the PeIQD genes, which showed that largely stress-related cis-elements existed in these genes. The expression profiles of the IQD genes shed light on their functional divergence. Additionally, a yeast two-hybrid assay proved that PeIQD8 can interact with PeCaM2 and that IQ or I in the IQ motif is required for PeIQD8 to combine with CaM2.

No MeSH data available.


Related in: MedlinePlus

Heat map of the real-time quantitative PCR (qRT-PCR) analysis results of PeIQD genes in leaves under MeJA treatment, with three biological and technical replicates.The scale representing the relative signal intensity values is shown above. Hierarchical clustering was used in the data analysis.
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f8: Heat map of the real-time quantitative PCR (qRT-PCR) analysis results of PeIQD genes in leaves under MeJA treatment, with three biological and technical replicates.The scale representing the relative signal intensity values is shown above. Hierarchical clustering was used in the data analysis.

Mentions: From the heat map of the real-time quantitative PCR (qRT-PCR) analysis results for the PeIQD genes, we can see that all 29 genes were found to be MeJA responsive, but that some differences were observed among these genes (Fig. 8). Similarly, the expression patterns of 29 PeIQD genes under MeJA stress were revealed by qRT-PCR (Figure S6). It can be seen that only nine genes (PeIQD2, −6, −7, −8, −10, −18, −20, −25 and −26) have constitutively weak expression levels under MeJA stress. PeIQD2, −6 and −10 were downregulated during early treatment but upregulated at later time points. For example, PeIQD10 was highly expressed at 12 h (five-fold). Although 20 genes were upregulated by MeJA treatment, PeIQD29 was obviously upregulated at all time points. Eleven PeIQD genes (PeIQD1, −14, −15, −16, -17, −19, −21, −23, −24, −27 and −28) exhibited major changes in expression (relative expression scale changed from 0 to 5 to 0 to 25). The expression of five genes (PeIQD10, −14, −15, −27 and −28) peaked at 12 h; PeIQD16 and PeIQD17 were found to primarily express at 1 h (more than 14-fold and 25-fold, respectively). By contrast, nine genes exhibited minor changes in expression (relative expression scales from 0 to 3 and lower), including PeIQD2, −3, −4, −5, −9, −11, −12, −13 and −22.


Genome-wide identification and expression analysis of the IQD gene family in moso bamboo (Phyllostachys edulis).

Wu M, Li Y, Chen D, Liu H, Zhu D, Xiang Y - Sci Rep (2016)

Heat map of the real-time quantitative PCR (qRT-PCR) analysis results of PeIQD genes in leaves under MeJA treatment, with three biological and technical replicates.The scale representing the relative signal intensity values is shown above. Hierarchical clustering was used in the data analysis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4837358&req=5

f8: Heat map of the real-time quantitative PCR (qRT-PCR) analysis results of PeIQD genes in leaves under MeJA treatment, with three biological and technical replicates.The scale representing the relative signal intensity values is shown above. Hierarchical clustering was used in the data analysis.
Mentions: From the heat map of the real-time quantitative PCR (qRT-PCR) analysis results for the PeIQD genes, we can see that all 29 genes were found to be MeJA responsive, but that some differences were observed among these genes (Fig. 8). Similarly, the expression patterns of 29 PeIQD genes under MeJA stress were revealed by qRT-PCR (Figure S6). It can be seen that only nine genes (PeIQD2, −6, −7, −8, −10, −18, −20, −25 and −26) have constitutively weak expression levels under MeJA stress. PeIQD2, −6 and −10 were downregulated during early treatment but upregulated at later time points. For example, PeIQD10 was highly expressed at 12 h (five-fold). Although 20 genes were upregulated by MeJA treatment, PeIQD29 was obviously upregulated at all time points. Eleven PeIQD genes (PeIQD1, −14, −15, −16, -17, −19, −21, −23, −24, −27 and −28) exhibited major changes in expression (relative expression scale changed from 0 to 5 to 0 to 25). The expression of five genes (PeIQD10, −14, −15, −27 and −28) peaked at 12 h; PeIQD16 and PeIQD17 were found to primarily express at 1 h (more than 14-fold and 25-fold, respectively). By contrast, nine genes exhibited minor changes in expression (relative expression scales from 0 to 3 and lower), including PeIQD2, −3, −4, −5, −9, −11, −12, −13 and −22.

Bottom Line: We surveyed the putative promoter regions of the PeIQD genes, which showed that largely stress-related cis-elements existed in these genes.The expression profiles of the IQD genes shed light on their functional divergence.Additionally, a yeast two-hybrid assay proved that PeIQD8 can interact with PeCaM2 and that IQ or I in the IQ motif is required for PeIQD8 to combine with CaM2.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.

ABSTRACT
Members of the plant-specific IQ67-domain (IQD) protein family are involved in various aspects of normal plant growth and developmental processes as well as basal defence response. Although hundreds of IQD proteins have been identified, only a small number of IQDs have been functionally characterized. Moreover, no systematic study has been performed on moso bamboo. In this study, we performed for the first time a genome-wide identification and expression analysis of the IQD gene family in moso bamboo. We identified 29 non-redundant PeIQD encoding genes. Analysis of the evolutionary patterns and divergence revealed that the IQD genes underwent a large-scale event around 12 million years ago and the division times of IQD family genes between moso bamboo and rice, and, between moso bamboo and Brachypodium, were found to be 20-35 MYA and 25-40 MYA, respectively. We surveyed the putative promoter regions of the PeIQD genes, which showed that largely stress-related cis-elements existed in these genes. The expression profiles of the IQD genes shed light on their functional divergence. Additionally, a yeast two-hybrid assay proved that PeIQD8 can interact with PeCaM2 and that IQ or I in the IQ motif is required for PeIQD8 to combine with CaM2.

No MeSH data available.


Related in: MedlinePlus