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Genome-wide evolutionary characterization and expression analyses of WRKY family genes in Brachypodium distachyon.

Wen F, Zhu H, Li P, Jiang M, Mao W, Ong C, Chu Z - DNA Res. (2014)

Bottom Line: Combining the analysis of phylogenetic tree of BdWRKY genes and the result of expression profiling, results showed that most of clustered gene pairs had higher similarities in the WRKY domain, suggesting that they might be functionally redundant.Neighbour-joining analysis of 301 WRKY domains from Oryza sativa, Arabidopsis thaliana, and B. distachyon suggested that BdWRKY domains are evolutionarily more closely related to O. sativa WRKY domains than those of A. thaliana.The results showed that the expression of BdWRKY genes was rapidly regulated by stresses and phytohormones, and there was a strong correlation between promoter cis-elements and the phytohormones-induced BdWRKY gene expression.

View Article: PubMed Central - PubMed

Affiliation: Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanic Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China.

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NJ analyses of 301 WRKY domains from O. sativa, A. thaliana, and B. distachyon, containing 262 plant WRKY proteins. The domains clustered into eight major subgroups, IN, IC, IIa, IIb, IIc, IId, IIe, and III.
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DST060F3: NJ analyses of 301 WRKY domains from O. sativa, A. thaliana, and B. distachyon, containing 262 plant WRKY proteins. The domains clustered into eight major subgroups, IN, IC, IIa, IIb, IIc, IId, IIe, and III.

Mentions: To further investigate the evolutionary relationships among the WRKY domains from different species, we estimated the phylogeny by using the NJ program from MEGA 5 for the WRKY domains from O. sativa, A. thaliana, and B. distachyon. All subgroups were present in monocots and eudicots (Fig. 3), indicating that the appearance of most WRKY TFs in plants predates the divergence of monocot/eudicots. Meanwhile, no species-specific subgroups and/or clades were observed in O. sativa, A. thaliana, or B. distachyon, implying that WRKY family genes were more conserved during evolution. In addition, WRKY domains from the same lineage tend to cluster together in the phylogenetic tree, suggesting that they experienced duplications after the lineages diverged (Fig. 3). Furthermore, WRKY phylogenetic tree showed almost the same clustering patterns in O. sativa and B. distachyon (Fig. 3 and Supplementary Table S3). In total, about 62 pairs of WRKY domains from O. sativa and B. distachyon were clustered as pairs, indicating that they might be the orthologous WRKY domains (Fig. 3). For example, the WRKY domains of BdWRKY54 and OsWRKY31 are highly similar, indicating that some consensus in domain may have existed before the divergence of B. distachyon and O. sativa. Meanwhile, only two pairs of WRKY domains from B. distachyon and A. thaliana could be clustered as pairs, suggesting that the BdWRKY domains are evolutionarily more closely related to OsWRKY domains, which is consistent with the notion that both B. distachyon and O. sativa belong to monocots. The phylogenetic similarity found in O. sativa and B. distachyon WRKY domain suggests that they may have evolved conservatively.Figure 3.


Genome-wide evolutionary characterization and expression analyses of WRKY family genes in Brachypodium distachyon.

Wen F, Zhu H, Li P, Jiang M, Mao W, Ong C, Chu Z - DNA Res. (2014)

NJ analyses of 301 WRKY domains from O. sativa, A. thaliana, and B. distachyon, containing 262 plant WRKY proteins. The domains clustered into eight major subgroups, IN, IC, IIa, IIb, IIc, IId, IIe, and III.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4060952&req=5

DST060F3: NJ analyses of 301 WRKY domains from O. sativa, A. thaliana, and B. distachyon, containing 262 plant WRKY proteins. The domains clustered into eight major subgroups, IN, IC, IIa, IIb, IIc, IId, IIe, and III.
Mentions: To further investigate the evolutionary relationships among the WRKY domains from different species, we estimated the phylogeny by using the NJ program from MEGA 5 for the WRKY domains from O. sativa, A. thaliana, and B. distachyon. All subgroups were present in monocots and eudicots (Fig. 3), indicating that the appearance of most WRKY TFs in plants predates the divergence of monocot/eudicots. Meanwhile, no species-specific subgroups and/or clades were observed in O. sativa, A. thaliana, or B. distachyon, implying that WRKY family genes were more conserved during evolution. In addition, WRKY domains from the same lineage tend to cluster together in the phylogenetic tree, suggesting that they experienced duplications after the lineages diverged (Fig. 3). Furthermore, WRKY phylogenetic tree showed almost the same clustering patterns in O. sativa and B. distachyon (Fig. 3 and Supplementary Table S3). In total, about 62 pairs of WRKY domains from O. sativa and B. distachyon were clustered as pairs, indicating that they might be the orthologous WRKY domains (Fig. 3). For example, the WRKY domains of BdWRKY54 and OsWRKY31 are highly similar, indicating that some consensus in domain may have existed before the divergence of B. distachyon and O. sativa. Meanwhile, only two pairs of WRKY domains from B. distachyon and A. thaliana could be clustered as pairs, suggesting that the BdWRKY domains are evolutionarily more closely related to OsWRKY domains, which is consistent with the notion that both B. distachyon and O. sativa belong to monocots. The phylogenetic similarity found in O. sativa and B. distachyon WRKY domain suggests that they may have evolved conservatively.Figure 3.

Bottom Line: Combining the analysis of phylogenetic tree of BdWRKY genes and the result of expression profiling, results showed that most of clustered gene pairs had higher similarities in the WRKY domain, suggesting that they might be functionally redundant.Neighbour-joining analysis of 301 WRKY domains from Oryza sativa, Arabidopsis thaliana, and B. distachyon suggested that BdWRKY domains are evolutionarily more closely related to O. sativa WRKY domains than those of A. thaliana.The results showed that the expression of BdWRKY genes was rapidly regulated by stresses and phytohormones, and there was a strong correlation between promoter cis-elements and the phytohormones-induced BdWRKY gene expression.

View Article: PubMed Central - PubMed

Affiliation: Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanic Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China.

Show MeSH