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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.


Ks , Ka/Ks value and duplication date (MY) distributions of the IQD genes in the genomes of moso bamboo, rice and Brachypodium, and viewed through the frequency distribution of relative Ks and Ka/Ks modes.(A) Distribution of Ks, Ka/Ks values and Duplication date (MY) were obtained from orthologous gene-pairs between the moso bamboo and Brachypodium, and, between the moso bamboo and rice genomes. (B) Distribution of Ks, Ka/Ks values and duplication date (MY) were obtained from paralogous gene-pairs in the moso bamboo genome.
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f4: Ks , Ka/Ks value and duplication date (MY) distributions of the IQD genes in the genomes of moso bamboo, rice and Brachypodium, and viewed through the frequency distribution of relative Ks and Ka/Ks modes.(A) Distribution of Ks, Ka/Ks values and Duplication date (MY) were obtained from orthologous gene-pairs between the moso bamboo and Brachypodium, and, between the moso bamboo and rice genomes. (B) Distribution of Ks, Ka/Ks values and duplication date (MY) were obtained from paralogous gene-pairs in the moso bamboo genome.

Mentions: In comparative genomics, the phylogeny-based and bidirectional best-hit methods are popular strategies for identifying possible paralogous or orthologous genes. Using these two methods, we found nine putative paralogous pairs in the moso bamboo genome, five orthologous pairs between OsIQD and PeIQD, and two orthologous pairs between BdIQD and PeIQD. All gene-pairs are listed in Table S3. To evaluate the divergence times among these three monocotyledon and gramineous plants, we used a relative Ks measure as a proxy for time. Figure 4(A,B) shows the frequency distributions of the relative Ks values obtained from duplicated and paralogous gene-pairs in the moso bamboo, and from thorthologous pairs between moso bamboo and rice, and, between moso bamboo and Brachypodium genomes. The relative Ks distribution peaks around 0.15 in moso bamboo suggested a large-scale event around 12 million years ago (MYA). Peng et al. have found that bamboo underwent whole-genome duplication 7–12 MYA14, according to analyses of clustered gene families, though our results, indicated that IQD family genes underwent a longer large-scale event. Similarly, the relative Ks distribution peaked at 0.25 for the seven duplicated orthologous gene-pairs, indicating division within the three groups of IQD genes at 20 MYA. A previous study estimated that the divergence time of rice and moso bamboo was 48.6 MYA, and for Brachypodium and moso bamboo was 46.9 MYA , and the results of the study by Peng, et al.14 – combined with those of our own study – revealed that the IQD family have undergone gene evolution after separation of the three progenitors.


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)

Ks , Ka/Ks value and duplication date (MY) distributions of the IQD genes in the genomes of moso bamboo, rice and Brachypodium, and viewed through the frequency distribution of relative Ks and Ka/Ks modes.(A) Distribution of Ks, Ka/Ks values and Duplication date (MY) were obtained from orthologous gene-pairs between the moso bamboo and Brachypodium, and, between the moso bamboo and rice genomes. (B) Distribution of Ks, Ka/Ks values and duplication date (MY) were obtained from paralogous gene-pairs in the moso bamboo genome.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4: Ks , Ka/Ks value and duplication date (MY) distributions of the IQD genes in the genomes of moso bamboo, rice and Brachypodium, and viewed through the frequency distribution of relative Ks and Ka/Ks modes.(A) Distribution of Ks, Ka/Ks values and Duplication date (MY) were obtained from orthologous gene-pairs between the moso bamboo and Brachypodium, and, between the moso bamboo and rice genomes. (B) Distribution of Ks, Ka/Ks values and duplication date (MY) were obtained from paralogous gene-pairs in the moso bamboo genome.
Mentions: In comparative genomics, the phylogeny-based and bidirectional best-hit methods are popular strategies for identifying possible paralogous or orthologous genes. Using these two methods, we found nine putative paralogous pairs in the moso bamboo genome, five orthologous pairs between OsIQD and PeIQD, and two orthologous pairs between BdIQD and PeIQD. All gene-pairs are listed in Table S3. To evaluate the divergence times among these three monocotyledon and gramineous plants, we used a relative Ks measure as a proxy for time. Figure 4(A,B) shows the frequency distributions of the relative Ks values obtained from duplicated and paralogous gene-pairs in the moso bamboo, and from thorthologous pairs between moso bamboo and rice, and, between moso bamboo and Brachypodium genomes. The relative Ks distribution peaks around 0.15 in moso bamboo suggested a large-scale event around 12 million years ago (MYA). Peng et al. have found that bamboo underwent whole-genome duplication 7–12 MYA14, according to analyses of clustered gene families, though our results, indicated that IQD family genes underwent a longer large-scale event. Similarly, the relative Ks distribution peaked at 0.25 for the seven duplicated orthologous gene-pairs, indicating division within the three groups of IQD genes at 20 MYA. A previous study estimated that the divergence time of rice and moso bamboo was 48.6 MYA, and for Brachypodium and moso bamboo was 46.9 MYA , and the results of the study by Peng, et al.14 – combined with those of our own study – revealed that the IQD family have undergone gene evolution after separation of the three progenitors.

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.