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Genome-wide identification of sweet orange (Citrus sinensis) histone modification gene families and their expression analysis during the fruit development and fruit-blue mold infection process.

Xu J, Xu H, Liu Y, Wang X, Xu Q, Deng X - Front Plant Sci (2015)

Bottom Line: In order to gain an insight into the potential roles of these genes in citrus fruit development, 42 CsHMs with high mRNA abundance in fruit tissues were selected to further analyze their expression profiles at six stages of fruit development.Interestingly, a numbers of genes were expressed highly in flesh of ripening fruit and some of them showed the increasing expression levels along with the fruit development.In conclusion, this study presents a comprehensive analysis of the histone modification gene families in sweet orange and further elucidates their behaviors during the fruit development and the blue mold infection responses.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University Wuhan, China.

ABSTRACT
In eukaryotes, histone acetylation and methylation have been known to be involved in regulating diverse developmental processes and plant defense. These histone modification events are controlled by a series of histone modification gene families. To date, there is no study regarding genome-wide characterization of histone modification related genes in citrus species. Based on the two recent sequenced sweet orange genome databases, a total of 136 CsHMs (Citrus sinensis histone modification genes), including 47 CsHMTs (histone methyltransferase genes), 23 CsHDMs (histone demethylase genes), 50 CsHATs (histone acetyltransferase genes), and 16 CsHDACs (histone deacetylase genes) were identified. These genes were categorized to 11 gene families. A comprehensive analysis of these 11 gene families was performed with chromosome locations, phylogenetic comparison, gene structures, and conserved domain compositions of proteins. In order to gain an insight into the potential roles of these genes in citrus fruit development, 42 CsHMs with high mRNA abundance in fruit tissues were selected to further analyze their expression profiles at six stages of fruit development. Interestingly, a numbers of genes were expressed highly in flesh of ripening fruit and some of them showed the increasing expression levels along with the fruit development. Furthermore, we analyzed the expression patterns of all 136 CsHMs response to the infection of blue mold (Penicillium digitatum), which is the most devastating pathogen in citrus post-harvest process. The results indicated that 20 of them showed the strong alterations of their expression levels during the fruit-pathogen infection. In conclusion, this study presents a comprehensive analysis of the histone modification gene families in sweet orange and further elucidates their behaviors during the fruit development and the blue mold infection responses.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic analysis of SDG family between Citrus Sinensis and Arabidopsis. The tree was constructed by the Neighbor-Joining method with MEGA program 5.05 using the conserved SET-domain region.
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Figure 2: Phylogenetic analysis of SDG family between Citrus Sinensis and Arabidopsis. The tree was constructed by the Neighbor-Joining method with MEGA program 5.05 using the conserved SET-domain region.

Mentions: All of the 40 CsSDGs were divided into seven classes according to the classification criteria of SDG family in Arabidopsis (Springer et al., 2003; Figure 2). In detail, CsSDG21 and 22, which were clustered with three AtSDGs, belonged to class I [E(z)-like]. CsSDG21 and 22 commonly had conserved SANT, CXC and SET domain and CsSDG22 had an additional SANT domain (Figure 4). Class II was comprised of four ASH1-like CsSDGs, clustered with five Arabidopsis and five rice ASH1-like proteins. CsSDGs in this class contained the conserved SET, Post-SET and AWS domains, while CsSDG2 and CsSDG7 had an additional PHD and CW domain, respectively. The TRX (TRITHORAX) family (class III) included six CsSDGs which was featured by highly conserved SET and Post-SET domains. CsSDG31 and 34 with a SET and N-terminus PHD domain belonged to class IV. Ten CsSDGs homologous to SU(VAR)3–9 group belonged to class V and were further divided into two main clades. Each of subgroups had five CsSDG members. Three members of Subgroup I contained WIYLD domain and Subgroup II was featured by a conserved SRA domain at the N-terminus. Sixteen CsSDGs clustered within class VI and class VII and eight of them contained Rubis-subs-bind (RBS) domain. As regards CsPRMTs, seven predicted proteins characterized by PRMT5 domain (Figure 4) were categorized to two classes (Supplementary Figure S1) according to the previous study (Aiese Cigliano et al., 2013). CsPRMT2 to 5 proteins were clustered to class I, and CsPRMT1, 6, 7 proteins belonged to class II.


Genome-wide identification of sweet orange (Citrus sinensis) histone modification gene families and their expression analysis during the fruit development and fruit-blue mold infection process.

Xu J, Xu H, Liu Y, Wang X, Xu Q, Deng X - Front Plant Sci (2015)

Phylogenetic analysis of SDG family between Citrus Sinensis and Arabidopsis. The tree was constructed by the Neighbor-Joining method with MEGA program 5.05 using the conserved SET-domain region.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4525380&req=5

Figure 2: Phylogenetic analysis of SDG family between Citrus Sinensis and Arabidopsis. The tree was constructed by the Neighbor-Joining method with MEGA program 5.05 using the conserved SET-domain region.
Mentions: All of the 40 CsSDGs were divided into seven classes according to the classification criteria of SDG family in Arabidopsis (Springer et al., 2003; Figure 2). In detail, CsSDG21 and 22, which were clustered with three AtSDGs, belonged to class I [E(z)-like]. CsSDG21 and 22 commonly had conserved SANT, CXC and SET domain and CsSDG22 had an additional SANT domain (Figure 4). Class II was comprised of four ASH1-like CsSDGs, clustered with five Arabidopsis and five rice ASH1-like proteins. CsSDGs in this class contained the conserved SET, Post-SET and AWS domains, while CsSDG2 and CsSDG7 had an additional PHD and CW domain, respectively. The TRX (TRITHORAX) family (class III) included six CsSDGs which was featured by highly conserved SET and Post-SET domains. CsSDG31 and 34 with a SET and N-terminus PHD domain belonged to class IV. Ten CsSDGs homologous to SU(VAR)3–9 group belonged to class V and were further divided into two main clades. Each of subgroups had five CsSDG members. Three members of Subgroup I contained WIYLD domain and Subgroup II was featured by a conserved SRA domain at the N-terminus. Sixteen CsSDGs clustered within class VI and class VII and eight of them contained Rubis-subs-bind (RBS) domain. As regards CsPRMTs, seven predicted proteins characterized by PRMT5 domain (Figure 4) were categorized to two classes (Supplementary Figure S1) according to the previous study (Aiese Cigliano et al., 2013). CsPRMT2 to 5 proteins were clustered to class I, and CsPRMT1, 6, 7 proteins belonged to class II.

Bottom Line: In order to gain an insight into the potential roles of these genes in citrus fruit development, 42 CsHMs with high mRNA abundance in fruit tissues were selected to further analyze their expression profiles at six stages of fruit development.Interestingly, a numbers of genes were expressed highly in flesh of ripening fruit and some of them showed the increasing expression levels along with the fruit development.In conclusion, this study presents a comprehensive analysis of the histone modification gene families in sweet orange and further elucidates their behaviors during the fruit development and the blue mold infection responses.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University Wuhan, China.

ABSTRACT
In eukaryotes, histone acetylation and methylation have been known to be involved in regulating diverse developmental processes and plant defense. These histone modification events are controlled by a series of histone modification gene families. To date, there is no study regarding genome-wide characterization of histone modification related genes in citrus species. Based on the two recent sequenced sweet orange genome databases, a total of 136 CsHMs (Citrus sinensis histone modification genes), including 47 CsHMTs (histone methyltransferase genes), 23 CsHDMs (histone demethylase genes), 50 CsHATs (histone acetyltransferase genes), and 16 CsHDACs (histone deacetylase genes) were identified. These genes were categorized to 11 gene families. A comprehensive analysis of these 11 gene families was performed with chromosome locations, phylogenetic comparison, gene structures, and conserved domain compositions of proteins. In order to gain an insight into the potential roles of these genes in citrus fruit development, 42 CsHMs with high mRNA abundance in fruit tissues were selected to further analyze their expression profiles at six stages of fruit development. Interestingly, a numbers of genes were expressed highly in flesh of ripening fruit and some of them showed the increasing expression levels along with the fruit development. Furthermore, we analyzed the expression patterns of all 136 CsHMs response to the infection of blue mold (Penicillium digitatum), which is the most devastating pathogen in citrus post-harvest process. The results indicated that 20 of them showed the strong alterations of their expression levels during the fruit-pathogen infection. In conclusion, this study presents a comprehensive analysis of the histone modification gene families in sweet orange and further elucidates their behaviors during the fruit development and the blue mold infection responses.

No MeSH data available.


Related in: MedlinePlus