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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.


Gain and loss of the PC genes in plant evolution. Seven internal nodes (V, Viridiplantae; E, Embryophyte; T, Tracheophyte; A, Angiosperm; G, Grass; Eu, eudicots; R, Rosid) are shown in the rectangles. Plus and minus signs indicate gene gain and loss events, respectively.
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Figure 2: Gain and loss of the PC genes in plant evolution. Seven internal nodes (V, Viridiplantae; E, Embryophyte; T, Tracheophyte; A, Angiosperm; G, Grass; Eu, eudicots; R, Rosid) are shown in the rectangles. Plus and minus signs indicate gene gain and loss events, respectively.

Mentions: It has been suggested that the Chlorophycean is the primitive species in Viridiplantae from which all land plants have evolved (Misumi et al., 2008). The earliest PCs possibly originated about 1 billion years ago in algae (Merchant et al., 2007; Misumi et al., 2008). Our search for PCs in Chlamydomonas reinhardtii found only one member. Therefore, the origin of the plant PC genes could be traced to the ancient algae. The PC gene family appeared to expand by duplication events. For example, Physcomitrella patens has 28 PC genes, which soybean exhibites 89 paralogous gene sequences representing about 19% of total 465 identified PCs, which might be due to at least three whole genome duplications (Schmutz et al., 2010). As we know, expansion and conservation of a gene family in evolution imply important roles during organism adaptation to environment (Cao et al., 2011; Cao and Shi, 2012). Next, we also estimated the number of PC genes in the MRCA to better understand how this family gene has evolved in Viridiplantae. Reconciliation of the species phylogeny with the gene trees suggested that one ancestral PC gene exist in the MRCA of Viridiplantae. Furthermore, we identified 32 orthologous genes in the Embryophyte MRCA and 44 in the MRCA of Tracheophyte (Figure 2). We also found that the number of PCs remained relatively increased from the land plants (P. patens) to the angiosperms. Eudicot ancestral PCs once more expanded significantly after the separation from monocot species about 145 million years ago (Xu et al., 2009). We identified about 109 ancestral PC genes in the MRCA of eudicots. After that, many PC genes have lost in the eudicots. It appeared that the PC family had been reduced in all the analyzed eudicot species compared with the number of MRCA in eudicots. For example, the number of PCs decreased approximately 65.1 and 55 percent for Arabidopsis and tomato, respectively. Whereas when compared the number of ancestral PC genes, it appeared that this family had expanded in all the extant species. In addition, this expansion was uneven among these plant species. For instance, there are 77, 60, 41, and 28 genes in poplar, maize, grape, moss, respectively, while the estimated numbers of genes in the MACA of Viridiplantae are seven. Therefore, poplar, maize, grape and moss have gained 70, 53, 34 and 21 genes, respectively, since their splits. The numbers of genes gained in the soybean lineage are much greater than that in other lineages.


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)

Gain and loss of the PC genes in plant evolution. Seven internal nodes (V, Viridiplantae; E, Embryophyte; T, Tracheophyte; A, Angiosperm; G, Grass; Eu, eudicots; R, Rosid) are shown in the rectangles. Plus and minus signs indicate gene gain and loss events, respectively.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4499708&req=5

Figure 2: Gain and loss of the PC genes in plant evolution. Seven internal nodes (V, Viridiplantae; E, Embryophyte; T, Tracheophyte; A, Angiosperm; G, Grass; Eu, eudicots; R, Rosid) are shown in the rectangles. Plus and minus signs indicate gene gain and loss events, respectively.
Mentions: It has been suggested that the Chlorophycean is the primitive species in Viridiplantae from which all land plants have evolved (Misumi et al., 2008). The earliest PCs possibly originated about 1 billion years ago in algae (Merchant et al., 2007; Misumi et al., 2008). Our search for PCs in Chlamydomonas reinhardtii found only one member. Therefore, the origin of the plant PC genes could be traced to the ancient algae. The PC gene family appeared to expand by duplication events. For example, Physcomitrella patens has 28 PC genes, which soybean exhibites 89 paralogous gene sequences representing about 19% of total 465 identified PCs, which might be due to at least three whole genome duplications (Schmutz et al., 2010). As we know, expansion and conservation of a gene family in evolution imply important roles during organism adaptation to environment (Cao et al., 2011; Cao and Shi, 2012). Next, we also estimated the number of PC genes in the MRCA to better understand how this family gene has evolved in Viridiplantae. Reconciliation of the species phylogeny with the gene trees suggested that one ancestral PC gene exist in the MRCA of Viridiplantae. Furthermore, we identified 32 orthologous genes in the Embryophyte MRCA and 44 in the MRCA of Tracheophyte (Figure 2). We also found that the number of PCs remained relatively increased from the land plants (P. patens) to the angiosperms. Eudicot ancestral PCs once more expanded significantly after the separation from monocot species about 145 million years ago (Xu et al., 2009). We identified about 109 ancestral PC genes in the MRCA of eudicots. After that, many PC genes have lost in the eudicots. It appeared that the PC family had been reduced in all the analyzed eudicot species compared with the number of MRCA in eudicots. For example, the number of PCs decreased approximately 65.1 and 55 percent for Arabidopsis and tomato, respectively. Whereas when compared the number of ancestral PC genes, it appeared that this family had expanded in all the extant species. In addition, this expansion was uneven among these plant species. For instance, there are 77, 60, 41, and 28 genes in poplar, maize, grape, moss, respectively, while the estimated numbers of genes in the MACA of Viridiplantae are seven. Therefore, poplar, maize, grape and moss have gained 70, 53, 34 and 21 genes, respectively, since their splits. The numbers of genes gained in the soybean lineage are much greater than that in other lineages.

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.