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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

Expression profiles of all CsHMs in response to blue mold (Penicillium digitatum) infection of citrus fruit at different periods (Control, 6, 24, and 48 h) using real-time PCR. Transcripts were normalized to Actin gene expression and the expression level of control was used as the calibrator for relative expression analysis. Hierarchical clustering of each CsHM family was performed using MeV 4.7 software. Genes with log2 value higher than 1.0 (up-regulated) or lower than -1.0 (down-regulated) were marked with yellow box or blue box, respectively.
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Figure 10: Expression profiles of all CsHMs in response to blue mold (Penicillium digitatum) infection of citrus fruit at different periods (Control, 6, 24, and 48 h) using real-time PCR. Transcripts were normalized to Actin gene expression and the expression level of control was used as the calibrator for relative expression analysis. Hierarchical clustering of each CsHM family was performed using MeV 4.7 software. Genes with log2 value higher than 1.0 (up-regulated) or lower than -1.0 (down-regulated) were marked with yellow box or blue box, respectively.

Mentions: A growing body of studies had been revealed the crucial roles of HMs in various abiotic stresses and plant immunity. Blue mold is considered as the most devastating pathogen in citrus fruit post-harvest process and causes lots of rotting losses. In order to determine the CsHMs responding to fruit-blue mold infection, the expression profiles of all CsHMs were detected among the four periods of infection using real-time PCR. The results were visualized by the heat maps and hierarchical clustering was further analyzed in each CsHM family (Figure 10). A numbers of CsHMs were up (yellow color) or down (blue color) regulated by the blue mold infection. According to these data, 20 genes including five CsSDGs, one CsHDMA, four CsJMJs, seven CsHAGs, one CsHDA, and two CsSRTs were selected to present their expression patterns in Supplementary Figure S2 for their expression fold change higher than 2.0 compared with the control. The expression levels of CsSDG6, 7, and 11 were inhibited at 6 h after infection (hai) and recovered at 24 and 48 hai. On the contrast, CsSDG37 was up-regulated by the infection. Three CsJMJs (CsJMJ1, 4, and 14) were strongly down-regulated, while CsJMJ11 were induced by the infection. Five CsHAGs including CsHAG2, 7, 14, 15, and 44 were up-regulated, while the expression levels of CsHAG29 and 31 were strongly inhibited at 6 and 24 hai and then recovered at 48 hai. For CsHDAs, CsHDA3 was selected out and showed the increased expression levels under the infection. Additionally, two CsSRTs (CsSRT3 and 4) presented different responses to infection. CsSRT1 was down-regulated, while CsSRT4 was highly up-regulated at the 6 h and then slightly induced at the 24 and 48 h by the infection.


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)

Expression profiles of all CsHMs in response to blue mold (Penicillium digitatum) infection of citrus fruit at different periods (Control, 6, 24, and 48 h) using real-time PCR. Transcripts were normalized to Actin gene expression and the expression level of control was used as the calibrator for relative expression analysis. Hierarchical clustering of each CsHM family was performed using MeV 4.7 software. Genes with log2 value higher than 1.0 (up-regulated) or lower than -1.0 (down-regulated) were marked with yellow box or blue box, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 10: Expression profiles of all CsHMs in response to blue mold (Penicillium digitatum) infection of citrus fruit at different periods (Control, 6, 24, and 48 h) using real-time PCR. Transcripts were normalized to Actin gene expression and the expression level of control was used as the calibrator for relative expression analysis. Hierarchical clustering of each CsHM family was performed using MeV 4.7 software. Genes with log2 value higher than 1.0 (up-regulated) or lower than -1.0 (down-regulated) were marked with yellow box or blue box, respectively.
Mentions: A growing body of studies had been revealed the crucial roles of HMs in various abiotic stresses and plant immunity. Blue mold is considered as the most devastating pathogen in citrus fruit post-harvest process and causes lots of rotting losses. In order to determine the CsHMs responding to fruit-blue mold infection, the expression profiles of all CsHMs were detected among the four periods of infection using real-time PCR. The results were visualized by the heat maps and hierarchical clustering was further analyzed in each CsHM family (Figure 10). A numbers of CsHMs were up (yellow color) or down (blue color) regulated by the blue mold infection. According to these data, 20 genes including five CsSDGs, one CsHDMA, four CsJMJs, seven CsHAGs, one CsHDA, and two CsSRTs were selected to present their expression patterns in Supplementary Figure S2 for their expression fold change higher than 2.0 compared with the control. The expression levels of CsSDG6, 7, and 11 were inhibited at 6 h after infection (hai) and recovered at 24 and 48 hai. On the contrast, CsSDG37 was up-regulated by the infection. Three CsJMJs (CsJMJ1, 4, and 14) were strongly down-regulated, while CsJMJ11 were induced by the infection. Five CsHAGs including CsHAG2, 7, 14, 15, and 44 were up-regulated, while the expression levels of CsHAG29 and 31 were strongly inhibited at 6 and 24 hai and then recovered at 48 hai. For CsHDAs, CsHDA3 was selected out and showed the increased expression levels under the infection. Additionally, two CsSRTs (CsSRT3 and 4) presented different responses to infection. CsSRT1 was down-regulated, while CsSRT4 was highly up-regulated at the 6 h and then slightly induced at the 24 and 48 h by the infection.

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