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Table 3 The carotenoid metabolic genes: Gene families and the conservation of exon number

From: The genes and enzymes of the carotenoid metabolic pathway in Vitis vinifera L.

 

Vitis

Arabidopsis

Populus

Oryza

 

vinifera 1

thaliana 2

trichocarpa 3

sativa 4

 

Accession

Accession

Accession

Accession

Average

Exon (intron)5

Exon (intron)

Exon (intron)

Exon (intron)

Exon number

Gene

Gene family 6

Sub family 7

     

PSY

HOMO01375

ORTHO001026

VV00G37410

AT5G17230

PT00G07390

OS06G51290

6

   

6 (5)

6 (5)

6 (5)

6 (5)

 

PDS

HOM001528

ORTHO003376

VV09G00040

AT4G14210

PT14G09510

OS03G08570

14

   

14 (13)

14 (13)

14 (13)

14 (13)

 

ZDS

HOM001528

ORTHO003216

VV14G05860

AT3G04870

PT00G12105

OS07G10490

14 ± 0.8

   

14 (13)

15 (14)

14 (13)

14 (13)

 

CISO

HOM003569

-

VV08G02490

AT1G06820

PT16G05590

OS11G36440

13

   

13 (12)

13 (12)

13 (12)

13 (12)

 

LECY

HOM001393

ORTHO004775

VV11G01840

AT5G57030

PT06G09650

OS01G39960

9.5 ± 2.4

   

11 (10)

11 (10)

6 (5)

10 (9)

 

ECH

HOM000057

-

VV08G13950

AT3G53130

PT00G01240

OS10G39930

9.3 ± 0.5

   

9 (8)

9 (8)

9 (8)

10 (9)

 

LBCY

HOM001393

ORTHO005684

VV08G15130

AT3G10230

PT16G03200

OS02G09750

1

   

1 (0)

1 (0)

1 (0)

1 (0)

 

BCH

HOM002126

-

VV02G00220

AT4G25700

PT00G07815

OS03G03370

6.8 ± 0.5

   

7 (6)

7 (6)

7 (6)

6 (5)

 

ZEP

HOM004000

-

VV07G11310

AT5G67030

PT05G05140

OS04G37619

16

   

16 (15)

16 (15)

16 (15)

16 (15)

 

VDE

HOM005780

-

VV00G14320

AT1G08550

PT13G04830

OS04G31040

4.3 ± 1.5

   

5 (4)

5 (4)

2 (1)

5 (4)

 

NSY

HOM001393

ORTHO015350

VV00G44920

NA

PT09G01040

NA

1

   

1 (0)

 

1 (0)

  

NCED

HOM000257

ORTHO000562

VV19G09570

AT3G14440

PT11G07980

OS03G44380

1

   

1 (0)

1 (0)

1 (0)

1 (0)

 

CCD

HOM000257

ORTHO003354

VV13G12530

AT3G63520

PT01G17700

OS12G44310

14

   

14 (13)

14 (13)

14 (13)

14 (13)

 
  1. 1Vitis vinifera sequence data from Genoscope v1: http://grup.bio.unipd.it/index.php/Grape_Genome.
  2. 2Arabidopsis thaliana sequence data from TAIR8: http://www.arabidopsis.org/.
  3. 3Populus trichocarpa sequence data from JGI 1.1: http://genome.jgi-psf.org/Poptr1_1/Poptr1_1.home.html.
  4. 4Oryza sativa sequence information from TIGR5: http://rice.plantbiology.msu.edu/.
  5. 5 Accession number from Plaza 1.0 (April 2009): (PLAZA v1: http://bioinformatics.psb.ugent.be/plaza_v1/).
  6. 6 The gene family that the homologues are group into (PLAZA v1: http://bioinformatics.psb.ugent.be/plaza_v1/).
  7. 7 The sub-family that the orthologues group into (PLAZA v1: http://bioinformatics.psb.ugent.be/plaza_v1/).
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BMC Genomics

ISSN: 1471-2164

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