Open Access Highly Accessed Research article

Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles

Riccardo Aiese Cigliano1, Walter Sanseverino2, Gaetana Cremona1, Maria R Ercolano2, Clara Conicella1 and Federica M Consiglio1*

  • * Corresponding author: Federica M Consiglio marconsi@unina.it

  • † Equal contributors

Author Affiliations

1 CNR, National Research Council of Italy, Institute of Plant Genetics, Research Division Portici, Via Università 133, 80055, Portici, Italy

2 DISSPAPA, Department of Soil, Plant and Environmental Sciences, University of Naples “Federico II”, Via Università 100, 80055, Portici, Italy

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BMC Genomics 2013, 14:57  doi:10.1186/1471-2164-14-57

Published: 28 January 2013

Additional files

Additional file 1:

Phylogenetic tree of AT1-domain containing proteins. Maximum likelihood phylogenetic tree of predicted proteins from Arabidopsis thaliana (At) and Solanum lycopersicon (Sl) containing an Acetyltrans_1 domain. Bootstrap values higher than 50% are shown. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. GCN5-like, ELP3-like, HAT1-like and HPA2-like proteins are highlighted in spring green, yellow and green, respectively.

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Additional file 2:

Phylogenetic tree of GML proteins. Maximum likelihood phylogenetic tree of predicted proteins from 32 organisms. Bootstrap values are shown for each node. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Ac = Aquilegia coerulea; Al = Arabidopsis lyrata; At = Arabidopsis thaliana; Bd = Brachypodium distachyon; Br = Brassica rapa; Car = Capsella rubella; Cc = Citrus clementina; Cis = Citrus sinensis; Cp = Carica papaya; Cr = Chlamydomonas rheinhardtii; Cs= Cucumis sativus; Es = Ectocarpus siliculosus; Eu = Eucalyptus grandis; Gm = Glycine max; Lu = Linum usitatissimum; Md = Malus domestica; Me = Manihot esculenta; Mg = Mimulus guttatus; Mt = Medicago truncatula; Os = Oryza saliva; Pp = Physcomitrella patens; Pt = Populus trichocarpa; Pv = Phaseolus vulgaris; Sb = Sorghum bicolor; Si = Setaria italica; Sl = Solanum lycopersicon; Ta = Trichoplax adhaerens; Th = Thellungiella halophila; Vc = Volvox cartei; Vv = Vitis vinifera; Zm = Zea mays. The proteins showing both the HAT1_N and the MOZ_SAS domain are highlighted in yellow.

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Additional file 3:

Phylogenetic tree of HAM proteins. Bayesian phylogenetic tree of HAM predicted proteins from Arabidopsis thaliana (At), Oryza sativa (Os), Solanum lycopersicon (Sl) and Zea mays (Zm). Bootstrap values higher than 50% are shown. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site.

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Additional file 4:

Expression profiles of tomatoHDACs. Heat map of RNA-seq expression data from root, leaf, bud, flower, 1cm_fruit, 2cm_fruit, 3cm_fruit, mature green fruit (MG), berry at breaker stage (B) and berry ten days after breaking (B10). HDAs with low, middle and high expression values are reported in A, B and C, respectively. The expression values are measured as reads per kilobase of exon model per million mapped reads (RPKM).

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Additional file 5:

Phylogenetic tree of SRT proteins. Bayesian phylogenetic tree of SRT predicted proteins from Arabidopsis thaliana (At), Oryza sativa (Os), Solanum lycopersicon (Sl) and Zea mays (Zm). Bootstrap values higher than 50% are shown. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site.

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Additional file 6:

Phylogenetic tree of HDT proteins. Bayesian phylogenetic tree of HDT predicted proteins from Arabidopsis thaliana (At), Oryza sativa (Os), Solanum lycopersicon (Sl) and Zea mays (Zm). Bootstrap values higher than 50% are shown. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site.

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Additional file 7:

Phylogenetic tree of PRMT proteins. Maximum likelihood phylogenetic tree of PRMT predicted proteins from Arabidopsis thaliana (At), Oryza sativa (Os), Solanum lycopersicon (Sl) and Zea mays (Zm). Bootstrap values higher than 50% are shown. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site.

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Additional file 8:

Expression profiles of tomato PRMTs. Heat map RNA-seq expression data from root, leaf, bud, flower, 1cm_fruit, 2cm_fruit, 3cm_fruit, mature green fruit (MG), berry at breaker stage (B) and berry ten days after breaking (B10). The expression values are measured as reads per kilobase of exon model per million mapped reads (RPKM).

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Open Data

Additional file 9:

Phylogenetic tree of HDMA proteins. Bayesian phylogenetic tree of HDMA predicted proteins from Arabidopsis thaliana (At), Oryza sativa (Os), Solanum lycopersicon (Sl) and Zea mays (Zm). Bootstrap values higher than 50% are shown. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site.

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Additional file 10:

Expression profiles of tomato HMAs. Heat map of RNA-seq expression data from root, leaf, bud, flower, 1cm_fruit, 2cm_fruit, 3cm_fruit, mature green fruit (MG), berry at breaker stage (B) and berry ten days after breaking (B10). HDMAs with low, middle and high expression values are reported in A, B and C, respectively. The expression values are measured as reads per kilobase of exon model per million mapped reads (RPKM).

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Additional file 11:

Phylogenetic tree of JMJ proteins. Maximum likelihood phylogenetic tree of JMJ predicted proteins from Arabidopsis thaliana (At), Oryza sativa (Os), Solanum lycopersicon (Sl) and Zea mays (Zm). Bootstrap values higher than 50% are shown. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site.

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Additional file 12:

List of the associations between tomato histone modifier genes and introgression lines (ILs).

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Additional file 13:

Expression profiles of CRTISO and putative SDGs involved in carotenoid synthesis. Heat map of CRTISO, SlSDG33 and SlSDG34 RNA-seq expression data from 1cm_fruit, 2cm_fruit, 3cm_fruit, mature green fruit (MG), berry at breaker stage (B) and berry ten days after breaking (B10). The expression values are measured as reads per kilobase of exon model per million mapped reads (RPKM).

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Additional file 14:

List of the histone modifiers from Arabidopsis thaliana, Oryza sativa and Zea mays used in this study.

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Additional file 15:

List of the SlHAG4 homologous sequences used to reconstruct GML evolutionary history.

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Additional file 16:

List of the starting (S) and ending (E) molecular markers, with the corresponding coordinates, used to map tomato ILs.

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