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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

Domain composition and gene structure of sweet orange JMJs and HDMAs. Exon/intron structures of these genes were placed on the right side of the domain composition. Exon(s) and intron(s) were represented by green boxes and black lines, respectively. The blue box represented UTR region of gene upstream and/or downstream.
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Figure 5: Domain composition and gene structure of sweet orange JMJs and HDMAs. Exon/intron structures of these genes were placed on the right side of the domain composition. Exon(s) and intron(s) were represented by green boxes and black lines, respectively. The blue box represented UTR region of gene upstream and/or downstream.

Mentions: The Phylogenetic tree of HDMAs was clustered to two main clades (Supplementary Figure S1) and all of three CsHDMAs were characterized by conserved N-terminal SWIRM (PF04433) domain and C-terminal Amino_oxidase (PF01593) domain. JMJ family was grouped into five classes based on sequence similarities, including JMJ-only (class I), KDM3 (class II), KDM4 (class III), KDM5 (class IV), and JMJD6 (class V) groups (Figure 3; Lu et al., 2008). JMJ-only class included four citrus members (CsJMJ9 and CsJMJ18-20) which only had JmjC domain and were not clustered to other groups. However, amino acid analysis of Arabidopsis and rice JMJ-only members indicated that they could be active demethylases (Lu et al., 2008). KDM3 class had six citrus members (CsJMJ10-13, CsJMJ16, and CsJMJ17), featured by a JmjC domain at the C-terminal with Ring finger domains (SM000184) ahead of it (Figure 5). The CsJMJs of KDM4 class fell into two main subclasses corresponding to the domain composition. Subclass I was characterized by four tandem repeats of ZnF_C2H2 domain (SM000355), while subclass II contained a zf-C5HC2 domain (PF02928) at the C-terminal. KDM5 group was also divided into two main subclasses which contain one (CsJMJ3) and three citrus members (CsJMJ1, 2, and 8), respectively. Additionally, the class of JMJD6 had two citrus members which had JmjC and N-terminal FBOX domain.


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)

Domain composition and gene structure of sweet orange JMJs and HDMAs. Exon/intron structures of these genes were placed on the right side of the domain composition. Exon(s) and intron(s) were represented by green boxes and black lines, respectively. The blue box represented UTR region of gene upstream and/or downstream.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 5: Domain composition and gene structure of sweet orange JMJs and HDMAs. Exon/intron structures of these genes were placed on the right side of the domain composition. Exon(s) and intron(s) were represented by green boxes and black lines, respectively. The blue box represented UTR region of gene upstream and/or downstream.
Mentions: The Phylogenetic tree of HDMAs was clustered to two main clades (Supplementary Figure S1) and all of three CsHDMAs were characterized by conserved N-terminal SWIRM (PF04433) domain and C-terminal Amino_oxidase (PF01593) domain. JMJ family was grouped into five classes based on sequence similarities, including JMJ-only (class I), KDM3 (class II), KDM4 (class III), KDM5 (class IV), and JMJD6 (class V) groups (Figure 3; Lu et al., 2008). JMJ-only class included four citrus members (CsJMJ9 and CsJMJ18-20) which only had JmjC domain and were not clustered to other groups. However, amino acid analysis of Arabidopsis and rice JMJ-only members indicated that they could be active demethylases (Lu et al., 2008). KDM3 class had six citrus members (CsJMJ10-13, CsJMJ16, and CsJMJ17), featured by a JmjC domain at the C-terminal with Ring finger domains (SM000184) ahead of it (Figure 5). The CsJMJs of KDM4 class fell into two main subclasses corresponding to the domain composition. Subclass I was characterized by four tandem repeats of ZnF_C2H2 domain (SM000355), while subclass II contained a zf-C5HC2 domain (PF02928) at the C-terminal. KDM5 group was also divided into two main subclasses which contain one (CsJMJ3) and three citrus members (CsJMJ1, 2, and 8), respectively. Additionally, the class of JMJD6 had two citrus members which had JmjC and N-terminal FBOX domain.

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