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Comparative analysis of the phytocyanin gene family in 10 plant species: a focus on Zea mays.

Cao J, Li X, Lv Y, Ding L - Front Plant Sci (2015)

Bottom Line: We found an expansion process of this gene family in evolution.ZmUC16 was strongly expressed after drought treatment.This study will provide a basis for future understanding the characterization of this family.

View Article: PubMed Central - PubMed

Affiliation: Institute of Life Sciences, Jiangsu University Zhenjiang, China.

ABSTRACT
Phytocyanins (PCs) are plant-specific blue copper proteins, which play essential roles in electron transport. While the origin and expansion of this gene family is not well-investigated in plants. Here, we investigated their evolution by undertaking a genome-wide identification and comparison in 10 plants: Arabidopsis, rice, poplar, tomato, soybean, grape, maize, Selaginella moellendorffii, Physcomitrella patens, and Chlamydomonas reinhardtii. We found an expansion process of this gene family in evolution. Except PCs in Arabidopsis and rice, which have described in previous researches, a structural analysis of PCs in other eight plants indicated that 292 PCs contained N-terminal secretion signals and 217 PCs were expected to have glycosylphosphatidylinositol-anchor signals. Moreover, 281 PCs had putative arabinogalactan glycomodules and might be AGPs. Chromosomal distribution and duplication patterns indicated that tandem and segmental duplication played dominant roles for the expansion of PC genes. In addition, gene organization and motif compositions are highly conserved in each clade. Furthermore, expression profiles of maize PC genes revealed diversity in various stages of development. Moreover, all nine detected maize PC genes (ZmUC10, ZmUC16, ZmUC19, ZmSC2, ZmUC21, ZmENODL10, ZmUC22, ZmENODL13, and ZmENODL15) were down-regulated under salt treatment, and five PCs (ZmUC19, ZmSC2, ZmENODL10, ZmUC22, and ZmENODL13) were down-regulated under drought treatment. ZmUC16 was strongly expressed after drought treatment. This study will provide a basis for future understanding the characterization of this family.

No MeSH data available.


Gene locations and genomic duplication in maize (A) and Arabidopsis (B). SyMAP v3.4 (Soderlund et al., 2011) was used to depict the paralogous regions in the putative ancestral constituents of the maize (A) and Arabidopsis(B) genomes. Moreover, some relationship of orthologs or paralogs was confirmed with the Genomicus (http://www.dyogen.ens.fr/genomicus/) online tool (Louis et al., 2013). The segmental duplication regions are supposed to be colored with the same way to the relevant chromosome color. For example, the color key of maize chromosome 1 is red, which means that all red regions on the chromosomes are segmental duplicated from the chromosome 1. Using this method, we can get all of the paralogous regions among different chromosomes in the genome.
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Figure 3: Gene locations and genomic duplication in maize (A) and Arabidopsis (B). SyMAP v3.4 (Soderlund et al., 2011) was used to depict the paralogous regions in the putative ancestral constituents of the maize (A) and Arabidopsis(B) genomes. Moreover, some relationship of orthologs or paralogs was confirmed with the Genomicus (http://www.dyogen.ens.fr/genomicus/) online tool (Louis et al., 2013). The segmental duplication regions are supposed to be colored with the same way to the relevant chromosome color. For example, the color key of maize chromosome 1 is red, which means that all red regions on the chromosomes are segmental duplicated from the chromosome 1. Using this method, we can get all of the paralogous regions among different chromosomes in the genome.

Mentions: Gene duplication, which usually occurs via segmental duplication, tandem duplication and retrotransposition, plays important roles in organismal evolution (Chen et al., 2014; Cao and Li, 2015). To search for duplication mechanisms for PC genes, as examples, we examined their genomic distribution in Arabidopsis and maize. The results showed that PC genes are dispersed throughout Arabidopsis and maize genomes (Figure 3). We also found that about 79.5 and 96.7% of PC genes locate on the duplicated segments of chromosomes in Arabidopsis and maize, respectively. Within identified duplication events, 5 of 11 pairs (AtENDOL14/AtENODL15, AtENODL5/AtENODL6, AtUC4/AtUC5, AtENODL1/AtENODL2, and AtENODL11/AtENODL12) in Arabidopsis and 7 of 20 pairs (ZmUC6/ZmUC10, ZmUC13/ZmUC14, ZmSC1/ZmSC2, ZmUC22/ZmPLC2, ZmENODL4/ZmENODL19, ZmENODL12/ZmENODL21, ZmENODL16/ZmENODL24) in maize are retained (Figure 3). In addition, evolutionary dates of these duplicated PC genes were also estimated (Table 2). The result indicated that duplication events for Arabidopsis six pairs and maize seven pairs occurred within the past 19.73–28.58 million years and 11.72–21.16 million years, respectively (Table 2). These periods coincide with the time of the secondary large-scale genome duplication in Arabidopsis and maize (Gaut et al., 1996; Koch et al., 2000). In addition, we also observed some earlier segmental duplication events occurred around from 41.63 to 58.33 MYA in the PCs of Arabidopsis (AtENODL1/AtENODL2 and AtENODL11/AtENODL12) and maize (ZmUC3/ZmUC23 and ZmUC22/ZmPLC2), nearly within or following grasses origination (Kellogg, 2001). Interestingly, we also found that about 31.67% of PC genes were tandemly clustered in maize, and only one clustered PCs (AtUC7-AtUC3) were also identified in Arabidopsis (Figure 3), suggesting that tandem duplication may be another factor generating the family genes. In a word, segmental duplication and tandem duplication contribute to the expansion of the PC gene family.


Comparative analysis of the phytocyanin gene family in 10 plant species: a focus on Zea mays.

Cao J, Li X, Lv Y, Ding L - Front Plant Sci (2015)

Gene locations and genomic duplication in maize (A) and Arabidopsis (B). SyMAP v3.4 (Soderlund et al., 2011) was used to depict the paralogous regions in the putative ancestral constituents of the maize (A) and Arabidopsis(B) genomes. Moreover, some relationship of orthologs or paralogs was confirmed with the Genomicus (http://www.dyogen.ens.fr/genomicus/) online tool (Louis et al., 2013). The segmental duplication regions are supposed to be colored with the same way to the relevant chromosome color. For example, the color key of maize chromosome 1 is red, which means that all red regions on the chromosomes are segmental duplicated from the chromosome 1. Using this method, we can get all of the paralogous regions among different chromosomes in the genome.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
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Figure 3: Gene locations and genomic duplication in maize (A) and Arabidopsis (B). SyMAP v3.4 (Soderlund et al., 2011) was used to depict the paralogous regions in the putative ancestral constituents of the maize (A) and Arabidopsis(B) genomes. Moreover, some relationship of orthologs or paralogs was confirmed with the Genomicus (http://www.dyogen.ens.fr/genomicus/) online tool (Louis et al., 2013). The segmental duplication regions are supposed to be colored with the same way to the relevant chromosome color. For example, the color key of maize chromosome 1 is red, which means that all red regions on the chromosomes are segmental duplicated from the chromosome 1. Using this method, we can get all of the paralogous regions among different chromosomes in the genome.
Mentions: Gene duplication, which usually occurs via segmental duplication, tandem duplication and retrotransposition, plays important roles in organismal evolution (Chen et al., 2014; Cao and Li, 2015). To search for duplication mechanisms for PC genes, as examples, we examined their genomic distribution in Arabidopsis and maize. The results showed that PC genes are dispersed throughout Arabidopsis and maize genomes (Figure 3). We also found that about 79.5 and 96.7% of PC genes locate on the duplicated segments of chromosomes in Arabidopsis and maize, respectively. Within identified duplication events, 5 of 11 pairs (AtENDOL14/AtENODL15, AtENODL5/AtENODL6, AtUC4/AtUC5, AtENODL1/AtENODL2, and AtENODL11/AtENODL12) in Arabidopsis and 7 of 20 pairs (ZmUC6/ZmUC10, ZmUC13/ZmUC14, ZmSC1/ZmSC2, ZmUC22/ZmPLC2, ZmENODL4/ZmENODL19, ZmENODL12/ZmENODL21, ZmENODL16/ZmENODL24) in maize are retained (Figure 3). In addition, evolutionary dates of these duplicated PC genes were also estimated (Table 2). The result indicated that duplication events for Arabidopsis six pairs and maize seven pairs occurred within the past 19.73–28.58 million years and 11.72–21.16 million years, respectively (Table 2). These periods coincide with the time of the secondary large-scale genome duplication in Arabidopsis and maize (Gaut et al., 1996; Koch et al., 2000). In addition, we also observed some earlier segmental duplication events occurred around from 41.63 to 58.33 MYA in the PCs of Arabidopsis (AtENODL1/AtENODL2 and AtENODL11/AtENODL12) and maize (ZmUC3/ZmUC23 and ZmUC22/ZmPLC2), nearly within or following grasses origination (Kellogg, 2001). Interestingly, we also found that about 31.67% of PC genes were tandemly clustered in maize, and only one clustered PCs (AtUC7-AtUC3) were also identified in Arabidopsis (Figure 3), suggesting that tandem duplication may be another factor generating the family genes. In a word, segmental duplication and tandem duplication contribute to the expansion of the PC gene family.

Bottom Line: We found an expansion process of this gene family in evolution.ZmUC16 was strongly expressed after drought treatment.This study will provide a basis for future understanding the characterization of this family.

View Article: PubMed Central - PubMed

Affiliation: Institute of Life Sciences, Jiangsu University Zhenjiang, China.

ABSTRACT
Phytocyanins (PCs) are plant-specific blue copper proteins, which play essential roles in electron transport. While the origin and expansion of this gene family is not well-investigated in plants. Here, we investigated their evolution by undertaking a genome-wide identification and comparison in 10 plants: Arabidopsis, rice, poplar, tomato, soybean, grape, maize, Selaginella moellendorffii, Physcomitrella patens, and Chlamydomonas reinhardtii. We found an expansion process of this gene family in evolution. Except PCs in Arabidopsis and rice, which have described in previous researches, a structural analysis of PCs in other eight plants indicated that 292 PCs contained N-terminal secretion signals and 217 PCs were expected to have glycosylphosphatidylinositol-anchor signals. Moreover, 281 PCs had putative arabinogalactan glycomodules and might be AGPs. Chromosomal distribution and duplication patterns indicated that tandem and segmental duplication played dominant roles for the expansion of PC genes. In addition, gene organization and motif compositions are highly conserved in each clade. Furthermore, expression profiles of maize PC genes revealed diversity in various stages of development. Moreover, all nine detected maize PC genes (ZmUC10, ZmUC16, ZmUC19, ZmSC2, ZmUC21, ZmENODL10, ZmUC22, ZmENODL13, and ZmENODL15) were down-regulated under salt treatment, and five PCs (ZmUC19, ZmSC2, ZmENODL10, ZmUC22, and ZmENODL13) were down-regulated under drought treatment. ZmUC16 was strongly expressed after drought treatment. This study will provide a basis for future understanding the characterization of this family.

No MeSH data available.