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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 CsHAGs, CsHAM, CsHACs, CsHAFs, CsHDAs, CsSRTs, and CsHDTs. Exon/intron structures of these genes are 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 6: Domain composition and gene structure of sweet orange CsHAGs, CsHAM, CsHACs, CsHAFs, CsHDAs, CsSRTs, and CsHDTs. Exon/intron structures of these genes are 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 and domain composition demonstrated that CsHAG25, 20, and 38 were belonged to GCN5, ELP3, and HAT1 class respectively (Supplementary Figure S1). Figure 6 only presented these three proteins domain compositions, while the other members only contained the AT1 conserved domain. In detail, CsHAG25 carried a C-terminal Bromo domain (PF00439) which recognized acetylated lysine residues. CsHAG20 had an N-terminal Elp3 domain, which was conserved in AtHAG3, OsHAG703 and two maize ELP3 proteins. CsHAG38 was a GNAT/MYST-Like (GML; Aiese Cigliano et al., 2013) member featured by N-terminal Hat1_N (PF10394) and an additional MOZ_SAS (PF01853) domain (Figure 6). As regard CsHAM1, it composed by Chromo (PF00385), C2H2 (PF00096), and MOZ_SAS (PF01853) domain which was the typical domain architecture of HAM family. The two CsHACs presented the similar domain compositions, while CsHAC1 had an additional ZnF_TAZ and a ZnF_ZZ domain. Although the two citrus TAFII250-like genes CsHAF1 and CsHAF2 showed high similarity with each other, CsHAF1 only had the TBPb domain and lacked other conserved domains (Figure 6).


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 CsHAGs, CsHAM, CsHACs, CsHAFs, CsHDAs, CsSRTs, and CsHDTs. Exon/intron structures of these genes are 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 6: Domain composition and gene structure of sweet orange CsHAGs, CsHAM, CsHACs, CsHAFs, CsHDAs, CsSRTs, and CsHDTs. Exon/intron structures of these genes are 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 and domain composition demonstrated that CsHAG25, 20, and 38 were belonged to GCN5, ELP3, and HAT1 class respectively (Supplementary Figure S1). Figure 6 only presented these three proteins domain compositions, while the other members only contained the AT1 conserved domain. In detail, CsHAG25 carried a C-terminal Bromo domain (PF00439) which recognized acetylated lysine residues. CsHAG20 had an N-terminal Elp3 domain, which was conserved in AtHAG3, OsHAG703 and two maize ELP3 proteins. CsHAG38 was a GNAT/MYST-Like (GML; Aiese Cigliano et al., 2013) member featured by N-terminal Hat1_N (PF10394) and an additional MOZ_SAS (PF01853) domain (Figure 6). As regard CsHAM1, it composed by Chromo (PF00385), C2H2 (PF00096), and MOZ_SAS (PF01853) domain which was the typical domain architecture of HAM family. The two CsHACs presented the similar domain compositions, while CsHAC1 had an additional ZnF_TAZ and a ZnF_ZZ domain. Although the two citrus TAFII250-like genes CsHAF1 and CsHAF2 showed high similarity with each other, CsHAF1 only had the TBPb domain and lacked other conserved domains (Figure 6).

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