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Table 2 Identification of putative functions for somatic embryogenesis marker genes based on the reciprocical best hit analysis (BLASTX) using full cDNA sequences, and then co-orthology relationships, inferred by phylogeny, using the deduced amino acid sequences of the AP2 domain for each gene (see Additional file 1 : Figure S1, Additional file 2 : Figure S2, Additional file 3 : Figure S3, Additional file 4 : Figure S4, Additional file 5 : figure S5 and Additional file 6 : Figure S6)

From: Some ethylene biosynthesis and AP2/ERF genes reveal a specific pattern of expression during somatic embryogenesis in Hevea brasiliensis

Gene Callus on ENT Callus on EXP Embryo Reciprocal best hit analysis Phylogenetic analysis
R/NE R/E R/NE R/E Nor/Ab Homology gene Putative function Species Reference Orthologous gene Accession No Putative Function Reference
HbSAMS 0.08 0.04 18.20 5.16   SAMS Precursor for ethylene biosynthesis Eucalyptus [40, 41] .    
HbACS2 0.01 0.01     ACS ACS synthase Ricinus [41, 42] .    
HbETR1 0.35 0.40     HbETR Signal transduction Hevea [41, 42] .    
HbERF-Ia1 0.31 0.15    0.26 DREB Freezing & dehydration tolerance Glycine [4345] ERF53 At2g20880 Regulates drought-responsive gene expression [46]
HbERF-Ib1      0.24 DREB Freezing & dehydration tolerance Populus [4345] . At4g39780 Unknown  
HbERF-Ib3      0.14 DREB Freezing & dehydration tolerance Populus [4345] . At4g39780 Unknown  
HbERF-Ib6      0.18 DREB1p Dwarfed phenotypes,freezing & dehydration tolerance Hevea [44] .    
HbERF-Ib7      0.19 DREB1p Dwarfed phenotypes,freezing & dehydration tolerance Hevea [44] .    
HbERF-Ib8      0.35 DREB1p Dwarfed phenotypes,freezing & dehydration tolerance Hevea [44] .    
HbERF-IIb5      0.09 TINY Affects plant height, hypocotyl elongation, and fertility Populus [47, 48] . At1g44830 Unknown  
HbERF-IIIa1    18.80 3.40   TINY Affects plant height, hypocotyl elongation, and fertility Populus [47, 48] . At1g01250 Unknown  
HbERF-IIIb2    10.70 6.44   ERF025 Control of ethylene-responsive transcription genes Glycine [49] . At1g63040 Unknown  
HbERF-IIIc1    7.84 3.99   CRT/DRE Heat stress tolerance Hevea [50, 51] CBF3/DREB1A At4g25480 Response to low temperature, abscisic acid [52]
CBF2/DREB1C At4g25470 Response to low temperature, abscisic acid, [53]
CBF1/DREB1B At4g25490 Response to low temperature, abscisic acid [52]
CBF4/DREB1D At5g51990 Response to drought stress and abscisic acid [54]
DDF2 At1g63030 Regulates in GA biosynthesis and stress tolerance [55]
DDF1 At1g12610 Regulates in GA biosynthesis and stress tolerance [55]
HbERF-IIIe3    16.20 8.62   TINY Affects plant height, hypocotyl elongation, and fertility Populus [47, 48] TINY At5g25810 Suppresses cell proliferation and exhibits pleiotropic effects [47]
HbERF-IVa1    6.31 9.87   DREB2 Enhances drought stress tolerance Populus [50, 51] DREB2A At5g05410 Drought-responsive gene expression [50]
HbERF-IVa2    5.92 4.83 0.33 DREB2C Heat stress tolerance Ricinus [51]
HbERF-IVa3    2.85 2.52   DREB2B Water deprivation stimulus Arabidopsis [56] .    
HbERF-Vb2    3.24 7.39   RAP2.2 Response to hypoxic stress Arabidopsis [57] .    
HbERF-VI1      3.03 CRF2   Vitis [58] CRF2/TMO3 At4g23750 Related to root initiation at later embryonic stages [58, 59]
HbERF-VI2 0.10 0.06     CRF2 Development of embryos and response to cytokin Arabidopsis [58]
HbERF-VI-L1    5.81 4.97   ERF Control of ethylene-responsive transcription genes Ricinus [60, 61] .    
HbERF-VIIa1      3.65 AP2/ERF Response to biotic and abiotic stress conditions Populus [45] .    
HbERF-VIIa3    4.23   7.07 AP2/ERF Response to biotic and abiotic stress conditions Populus [45] .    
HbERF-VIIa4 0.22 0.21 4.62   5.29 AP2/ERF Response to biotic and abiotic stress conditions Populus [45] .    
HbERF-VIIa17    49.10 9.81   ERF-2 Control of ethylene-responsive transcription genes Gossypium [60, 61] .    
HbERF-VIIIa3 0.15 0.10   017   ERF3 Control of ethylene-responsive transcription genes Arabidopsis [62] .    
HbERF-VIIIa7    4.83 4.32   ATERF-4 Modulates ethylene and abscisic acid responses Arabidopsis [62] .    
HbERF-VIIIa11      0.16 ATERF-4 Modulates ethylene and abscisic acid responses Arabidopsis [62] .    
HbERF-IXb2    2.65 5.07   ERF Control of ethylene-responsive transcription genes Olimarabidopsis [60, 61]   At5g07580 Unknown  
HbERF-IXb4      0.17 ERF Control of ethylene-responsive transcription genes Ricinus [60, 61] .    
HbERF-IXb8      0.07 ERF1 Drought, salt and freezing tolerances Malus [60, 61] . At5g51190 Unknown  
HbERF-IXc4    57.10 10.50   ERF1 Drought, salt and freezing tolerances Ricinus [60, 61] .    
HbERF-Xb1      0.02 AP2/ERF Response to biotic and abiotic stress conditions Populus [45] RRTF1 At4g34410 Regulates redox homeostasis related to photosynthetic stress [63]
HbAP2-1 0.14 0.11     ANT Regulates up-regulation of genes establishing organ polarity and those specifying organ identity Ricinus [19, 64] BBM At5g17430 Promotes cell proliferation and morphogenesis during embryogenesis [18, 65]
HbAP2-3    5.74 4.78   BBM Cell proliferation and morphogenesis during embryogenesis Ricinus [18] AIL7/PLT7 At5g65510 Regulates radial pattern formation process of a shoot apical meristem. [66]
AIL6/PLT3 At5g10510 Regulation of floral meristem growth [67]
HbAP2-5 0.13 0.10     AP2/ERF Response to biotic and abiotic stress conditions Ricinus [45] . At2g41710 Unknown  
HbAP2-7    24.90 12.90   AIL Related to floral development Vitis [64] ANT/DRG/CKC/CKC1 At4g37750 Regulates up—regulation of genes establishing organ polarity and those specifying organ identity [19, 64]
HbAP2-12 0.13 0.10     AP2 Meristem maintenance and cell differentiation Arabidopsis [68, 69] AP2/FLO2/FL1 At4g36920 Meristem maintenance and cell differentiation [68, 69]
HbAP2-18 0.22 0.16     AP2 Vitis
HbRAV-3    43.60 16.40   RAV1 Leaf maturation and senescence Ricinus [70] .    
  1. The ratios between the relative transcript abundance of the regenerant and non-embryogenic lines (R/NE), the regenerant and embryogenic lines (R/E), of the normal and abnormal embryos (Nor/Ab) are presented for only significant down-regulated genes (< 1) and up-regulated (> 1).