Limits...
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.


Phylogenetic relationship and intron-exon structure of moso bamboo (Phyllostachys edulis) IQD proteins.(A) Phylogenetic tree of PeIQDs constructed by the neighbour-joining method. Bootstrap values from 1,000 replicates are indicated at each node. The proteins on the tree are divided into four distinct subfamilies. (B) Exons and introns are indicated by yellow rectangles and grey lines, respectively. Untranslated regions (UTRs) are indicated by blue lines.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4837358&req=5

f2: Phylogenetic relationship and intron-exon structure of moso bamboo (Phyllostachys edulis) IQD proteins.(A) Phylogenetic tree of PeIQDs constructed by the neighbour-joining method. Bootstrap values from 1,000 replicates are indicated at each node. The proteins on the tree are divided into four distinct subfamilies. (B) Exons and introns are indicated by yellow rectangles and grey lines, respectively. Untranslated regions (UTRs) are indicated by blue lines.

Mentions: To gain further insights into the structural diversity of moso bamboo IQD genes, we first constructed a separate phylogenetic tree exclusively using the full-length IQD protein sequences of moso bamboo. Moso bamboo proteins were also classified into four independent subfamilies, in good agreement with that described above for the seven plant species (Figs 1A and 2A). It is well known that genetic structural diversity is a possible mechanism for the evolution of multigene families. To gain further insights into the structural diversity of IQD genes, we compared the exon/intron organization in the coding sequences of individual IQD genes in moso bamboo (Fig. 2B). It is interesting to note that we found the intron/exon structure of most sister gene pairs to be conserved, but there are also some differences. For example, the six sister gene pairs (PeIQD24/-14, PeIQD19/-23, PeIQD10/-12, PeIQD11/-16, PeIQD20/-25 and PeIQD2/-29) were found to have the same exon/intron number and intron phase. However, their intron lengths showed great variability, ranging from a few tens of bp to −2 kb. In addition, four sister gene pairs showed greater changes in their structural organizations (PeIQD4/-9, PeIQD18/-21, PeIQD26/-5, PeIQD22/-6) and varying numbers of exons and introns.


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)

Phylogenetic relationship and intron-exon structure of moso bamboo (Phyllostachys edulis) IQD proteins.(A) Phylogenetic tree of PeIQDs constructed by the neighbour-joining method. Bootstrap values from 1,000 replicates are indicated at each node. The proteins on the tree are divided into four distinct subfamilies. (B) Exons and introns are indicated by yellow rectangles and grey lines, respectively. Untranslated regions (UTRs) are indicated by blue lines.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: Phylogenetic relationship and intron-exon structure of moso bamboo (Phyllostachys edulis) IQD proteins.(A) Phylogenetic tree of PeIQDs constructed by the neighbour-joining method. Bootstrap values from 1,000 replicates are indicated at each node. The proteins on the tree are divided into four distinct subfamilies. (B) Exons and introns are indicated by yellow rectangles and grey lines, respectively. Untranslated regions (UTRs) are indicated by blue lines.
Mentions: To gain further insights into the structural diversity of moso bamboo IQD genes, we first constructed a separate phylogenetic tree exclusively using the full-length IQD protein sequences of moso bamboo. Moso bamboo proteins were also classified into four independent subfamilies, in good agreement with that described above for the seven plant species (Figs 1A and 2A). It is well known that genetic structural diversity is a possible mechanism for the evolution of multigene families. To gain further insights into the structural diversity of IQD genes, we compared the exon/intron organization in the coding sequences of individual IQD genes in moso bamboo (Fig. 2B). It is interesting to note that we found the intron/exon structure of most sister gene pairs to be conserved, but there are also some differences. For example, the six sister gene pairs (PeIQD24/-14, PeIQD19/-23, PeIQD10/-12, PeIQD11/-16, PeIQD20/-25 and PeIQD2/-29) were found to have the same exon/intron number and intron phase. However, their intron lengths showed great variability, ranging from a few tens of bp to −2 kb. In addition, four sister gene pairs showed greater changes in their structural organizations (PeIQD4/-9, PeIQD18/-21, PeIQD26/-5, PeIQD22/-6) and varying numbers of exons and introns.

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.