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.


Phylogeny and distribution of IQD protein from seven plant species.(A) Phylogenetic tree of IQD proteins from Arabidopsis, rice, tomato, Brachypodium, soybean, Populus and moso bamboo. The tree was generated with Clustal X 2.0 software using the neighbour-joining method. (B) Percentage representation of IQD proteins across the seven plant species within each subfamily. Colours correspond to the plant taxa as listed in (C). (C) Percentage representation of distributions for IQD proteins within each plant species.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Phylogeny and distribution of IQD protein from seven plant species.(A) Phylogenetic tree of IQD proteins from Arabidopsis, rice, tomato, Brachypodium, soybean, Populus and moso bamboo. The tree was generated with Clustal X 2.0 software using the neighbour-joining method. (B) Percentage representation of IQD proteins across the seven plant species within each subfamily. Colours correspond to the plant taxa as listed in (C). (C) Percentage representation of distributions for IQD proteins within each plant species.

Mentions: To examine the phylogenetic relationship of the IQD domain proteins among the three grass subfamilies – including Pooideae (Brachypodium distachyon), Ehrhartoideae (rice), Bambusoideae (Phyllostachys edulis) and four dicots (Arabidopsis thaliana, soybean, tomato and the woody plant poplar), a rooted tree was constructed from alignments of the full-length IQD protein sequences (Fig. 1A). The phylogenetic tree was constructed using MEGA 6.0 software by employing the Nneighbor-joining (NJ), minimal evolution and maximum parsimony methods. The tree topologies produced by the three algorithms were largely comparable with only minor modifications at interior branches (data not shown). Therefore, only the NJ phylogenetic tree was further analyzed in our study. The NJ phylogenetic tree comprised 226 full-length IQD protein sequences from Oryza sativa (28), Brachypodium distachyon (23), Arabidopsis thaliana (34), Populus trichocarpa (40), Glycine max (67) and Solanum lycopersicum (34)612131617. The characteristics of the IQD genes–including pI, MW, chromosome location, ORF length and amino acids – are showed in Table S1. As indicated in Fig. 1A, the phylogenetic tree highlighted that the IQD family of proteins could be divided into four well-conserved subfamilies, IQD I-VI, as described previously and with significant statistical support61213. We further examined each of the subfamilies containing the IQD genes. The IQDI subfamily was divided into four clades designated as clade a, b, c and d, which was consistent with the nomenclature in previous studies of Arabidopsis, rice and soybean61213. The other three subfamilies were separated into two clades (a and b) (Fig. 1A). The phylogenetic tree revealed that the plant IQD sequence distribution predominates with species bias (Fig. 1B). The largest subfamilies of the plant species were found to contain mostly IQD I genes . In contrast, the IQD II subfamily contained the fewest IQD genes – except in the case of Brachypodium and tomato, where IQD IV contained the fewest. It also appeared that more IQD IV genes were present in moso bamboo and soybean IQD IV than in other species. In fact, we found nine and ten IQD IV genes to be present in moso bamboo and soybean, respectively, while only three and two IQD IV genes were present in Brachypodium and tomato, respectively. The percentage distribution of the IQD proteins among each subfamily was calculated for all seven species (Fig. 1C). Remarkably, there were fewer IQD genes in each subfamily for monocotyledonous than for dicotyledonous.


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)

Phylogeny and distribution of IQD protein from seven plant species.(A) Phylogenetic tree of IQD proteins from Arabidopsis, rice, tomato, Brachypodium, soybean, Populus and moso bamboo. The tree was generated with Clustal X 2.0 software using the neighbour-joining method. (B) Percentage representation of IQD proteins across the seven plant species within each subfamily. Colours correspond to the plant taxa as listed in (C). (C) Percentage representation of distributions for IQD proteins within each plant species.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Phylogeny and distribution of IQD protein from seven plant species.(A) Phylogenetic tree of IQD proteins from Arabidopsis, rice, tomato, Brachypodium, soybean, Populus and moso bamboo. The tree was generated with Clustal X 2.0 software using the neighbour-joining method. (B) Percentage representation of IQD proteins across the seven plant species within each subfamily. Colours correspond to the plant taxa as listed in (C). (C) Percentage representation of distributions for IQD proteins within each plant species.
Mentions: To examine the phylogenetic relationship of the IQD domain proteins among the three grass subfamilies – including Pooideae (Brachypodium distachyon), Ehrhartoideae (rice), Bambusoideae (Phyllostachys edulis) and four dicots (Arabidopsis thaliana, soybean, tomato and the woody plant poplar), a rooted tree was constructed from alignments of the full-length IQD protein sequences (Fig. 1A). The phylogenetic tree was constructed using MEGA 6.0 software by employing the Nneighbor-joining (NJ), minimal evolution and maximum parsimony methods. The tree topologies produced by the three algorithms were largely comparable with only minor modifications at interior branches (data not shown). Therefore, only the NJ phylogenetic tree was further analyzed in our study. The NJ phylogenetic tree comprised 226 full-length IQD protein sequences from Oryza sativa (28), Brachypodium distachyon (23), Arabidopsis thaliana (34), Populus trichocarpa (40), Glycine max (67) and Solanum lycopersicum (34)612131617. The characteristics of the IQD genes–including pI, MW, chromosome location, ORF length and amino acids – are showed in Table S1. As indicated in Fig. 1A, the phylogenetic tree highlighted that the IQD family of proteins could be divided into four well-conserved subfamilies, IQD I-VI, as described previously and with significant statistical support61213. We further examined each of the subfamilies containing the IQD genes. The IQDI subfamily was divided into four clades designated as clade a, b, c and d, which was consistent with the nomenclature in previous studies of Arabidopsis, rice and soybean61213. The other three subfamilies were separated into two clades (a and b) (Fig. 1A). The phylogenetic tree revealed that the plant IQD sequence distribution predominates with species bias (Fig. 1B). The largest subfamilies of the plant species were found to contain mostly IQD I genes . In contrast, the IQD II subfamily contained the fewest IQD genes – except in the case of Brachypodium and tomato, where IQD IV contained the fewest. It also appeared that more IQD IV genes were present in moso bamboo and soybean IQD IV than in other species. In fact, we found nine and ten IQD IV genes to be present in moso bamboo and soybean, respectively, while only three and two IQD IV genes were present in Brachypodium and tomato, respectively. The percentage distribution of the IQD proteins among each subfamily was calculated for all seven species (Fig. 1C). Remarkably, there were fewer IQD genes in each subfamily for monocotyledonous than for dicotyledonous.

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.