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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).