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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.


Related in: MedlinePlus

Evolution of one PC clade in poplar. (A) Phylogenetic relationships and intron insertion; (B) Hypothetical origins of eleven poplar PC genes by retroposition and tandem duplication. The letters “R” and “T” indicate the positions where retroposition and tandem duplication have occurred, respectively. Bright green vertical line represents conserved 1 phase intron insertion position in PCLD as shown in Supplementary Figure S1.
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Figure 4: Evolution of one PC clade in poplar. (A) Phylogenetic relationships and intron insertion; (B) Hypothetical origins of eleven poplar PC genes by retroposition and tandem duplication. The letters “R” and “T” indicate the positions where retroposition and tandem duplication have occurred, respectively. Bright green vertical line represents conserved 1 phase intron insertion position in PCLD as shown in Supplementary Figure S1.

Mentions: Exon–intron structure has been used to explain the evolutionary relationships (Cao et al., 2010; Koralewski and Krutovsky, 2011; Chen and Cao, 2014). Next, we compared the exon–intron organization of the PCs in 10 plants. Supplementary Figure S1 provided a detailed illustration of the position of introns of each PCLD domain. Our results indicated a conserved 1 phase intron insertion in PCLD of most PC paralogs. Interestingly, we also found that this intron insertion has been lost in some poplar PCLD (Supplementary Figure S1). Moreover, these intronless genes in PCLD tended to form species-specific clusters on the poplar chromosomes 2, 6, and 15 (Supplementary Figure S1). It may be the consequences of retroposition and tandem duplications. The loss of intron in these PCs was likely associated with recent evolutionary expansion, like, retroposition and tandem duplication. To test this hypothesis, we identified the candidate donor gene based on the following two criteria. The first criterion is that the retrogene will have identical sequences to the donor gene after retroposition, so they will cluster together in a phylogenetic tree (Kong et al., 2007). Since retrogene comes from retroposition, it usually lacks specific introns compared with the donor gene. Therefore, the second criterion is that the donor gene can be judged from the presence/absence of the specific intron (Kong et al., 2007). Figure 4 shows an example of intron loss caused by gene expansion. Genes with the conserved intron (such as, PtENODL13) usually locate basal positions of the phylogenetic tree, while genes without the intron (such as, others 10 PCs in the clade as shown in Figure 4) often form terminal clades. It is likely that PtENODL13 contains the conserved intron and is their ancestor (donor gene), from which the intronless retrogenes were generated by retroposition and tandem duplication.


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)

Evolution of one PC clade in poplar. (A) Phylogenetic relationships and intron insertion; (B) Hypothetical origins of eleven poplar PC genes by retroposition and tandem duplication. The letters “R” and “T” indicate the positions where retroposition and tandem duplication have occurred, respectively. Bright green vertical line represents conserved 1 phase intron insertion position in PCLD as shown in Supplementary Figure S1.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 4: Evolution of one PC clade in poplar. (A) Phylogenetic relationships and intron insertion; (B) Hypothetical origins of eleven poplar PC genes by retroposition and tandem duplication. The letters “R” and “T” indicate the positions where retroposition and tandem duplication have occurred, respectively. Bright green vertical line represents conserved 1 phase intron insertion position in PCLD as shown in Supplementary Figure S1.
Mentions: Exon–intron structure has been used to explain the evolutionary relationships (Cao et al., 2010; Koralewski and Krutovsky, 2011; Chen and Cao, 2014). Next, we compared the exon–intron organization of the PCs in 10 plants. Supplementary Figure S1 provided a detailed illustration of the position of introns of each PCLD domain. Our results indicated a conserved 1 phase intron insertion in PCLD of most PC paralogs. Interestingly, we also found that this intron insertion has been lost in some poplar PCLD (Supplementary Figure S1). Moreover, these intronless genes in PCLD tended to form species-specific clusters on the poplar chromosomes 2, 6, and 15 (Supplementary Figure S1). It may be the consequences of retroposition and tandem duplications. The loss of intron in these PCs was likely associated with recent evolutionary expansion, like, retroposition and tandem duplication. To test this hypothesis, we identified the candidate donor gene based on the following two criteria. The first criterion is that the retrogene will have identical sequences to the donor gene after retroposition, so they will cluster together in a phylogenetic tree (Kong et al., 2007). Since retrogene comes from retroposition, it usually lacks specific introns compared with the donor gene. Therefore, the second criterion is that the donor gene can be judged from the presence/absence of the specific intron (Kong et al., 2007). Figure 4 shows an example of intron loss caused by gene expansion. Genes with the conserved intron (such as, PtENODL13) usually locate basal positions of the phylogenetic tree, while genes without the intron (such as, others 10 PCs in the clade as shown in Figure 4) often form terminal clades. It is likely that PtENODL13 contains the conserved intron and is their ancestor (donor gene), from which the intronless retrogenes were generated by retroposition and tandem duplication.

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.


Related in: MedlinePlus