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Table 4 Subset of genes differentially expressed between Ecodormancy and Swelling buds stages

From: The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

Biological process

Gene function

Ath accession number

Fold change ratio ( Ecodormant bud / Swelling buds )

position in the functional gene network

Genes up-regulated in Ecodormant buds

Ribosome biogenesis

T13C7.4 (60S ribosomal protein L14)

AT2G20450

>100

 

Ribosome biogenesis

F12L6.5 (ribosomal protein L23A)

AT2G39460

>100

 

Ribosome biogenesis

T9J14.13 (ribosomal protei S24e)

AT3G04920

>100

 

Ribosome biogenesis

Ribosomal protein L232A

AT3G55280

>100

 

Ribosome biogenesis

T25K17.40 (ribosomal protein L31e)

AT4G26230

>100

 

Ribosome biogenesis

K16F13.2 (40S ribosomal protein S27-3)

AT5G47930

>100

 

Ribosome biogenesis

MUP24.13 (60S ribosomal protein L12)

AT5G60670

>100

 

Ribosome biogenesis

F10K1.22 (60S ribosomal protein L35a)

AT1G07070

>100

 

Ribosome biogenesis

T2P11.7 (60S ribosomal protein L34)

AT1G26880

>100

 

Ribosome biogenesis

F19K6.12 (60S ribosomal protein L37)

AT1G52300

>100

 

Ribosome biogenesis

STV1 (ribosomal protein L24)

AT3G53020

>100

 

Ribosome biogenesis

Zinc-binding ribosomal protein

AT3G60245

>100

 

Ribosome biogenesis

PRPL11 (plastid ribosomal proteinL11)

AT1G32990

>100

 

Ubiquitin dependent rotein catabolic process

UBC28 (ubiquitin conjugating enzyme 28)

AT1G64230

>100

Neighbors of sbi-miR169r-3p_agpf_35

Ubiquitin dependent protein catabolic process

FKF1 (flavin-binding kelch repeat F box 1)

AT1G68050

>100

Neighbors of ELF3, Neighbors of GI

Ubiquitin dependent protein catabolic process

UBQ11 (ubiquitin 11)

AT4G05050

>100

Neighbors of heat shock

Ubiquitin dependent protein catabolic process

ASK2 (Arabidopsis SKP-Like2)

AT5G42190

>100

 

Ubiquitin dependent protein catabolic process

ATUBA1 (ubiquitin activating enzyme 1)

AT2G30110

>100

 

Response to cold

DREB1A (DREB subfamily A-1)

AT4G25480

>100

Neighbors of cold stress, DREB and CBF

Response to cold

CBF1 (C repeat/DRE binding factor 1)

AT4G25490

>100

Neighbors of cold stress, DREB and CBF

Response to cold

1 (low expression of osmotically responsive gene

AT1G56070

>100

Neighbors of cold stress

Response to cold

LTI30 (Low temperature induce temperature)

AT3G50970

>30

Neighbors of cold stres, ABA and CBF

Response to cold

RCI3 (rare cold inducible gene 3)

AT1G05260

>100

Neighbors of cold stress

Response to cold

Fib (Fibbrilin 1A)

AT4G04020

>50

Neighbors of ABA

Response to water deprivation

ATBI-1 (Bax inhibitor 1)

AT5G47120

>100

Neighbors of drought and COLI

Response to water deprivation

SIP3 (CBL interacting protein kinase 6)

AT4G30960

>100

 

Response to water deprivation

CBL9 (calcineurin B like protein 9)

AT5G47100

>100

Neighbors of ABA, drought and cold

Response to gibberelin stimulus

Gasa1 (GAST1 protein homolg1)

AT1G75750

>100

 

Response to gibberelin stimulus

Gasa2 (GAST1 protein homolg2)

AT4G09610

>100

 

Response to gibberelin stimulus

AGL20 (Agamous like 20)

AT2G45660

>100

Neighbors of AP1

Response to high light intensity

Bag6 (Bcl-2-associated athanogene 6)

AT2G46240

>100

Neighbors of heat shock

Genes up-regulated in swelling buds

DNA dependent DNA replication initiation

MCM6

AT5G44635

>3

 

DNA dependent DNA replication initiation

MCM3

AT5G46280

>3

 

DNA dependent DNA replication initiation

PRL (prolifera)

AT4G02060

>2

Neighbors of cell cycle , DNA replication

DNA dependent DNA replication initiation

CDC45 (cell division cycle 45)

AT3G25100

>6

Neighbors of mitosis , DNA replication

DNA dependent DNA replication initiation

T12C22.19 (MCM2)

AT1G44900

>2

 

Regulation of cell cycle and cell division

CYCB 1;4 (cyclin dependent protein kinase)

AT2G26760

>10

 

Regulation of cell cycle and cell division

CYCD1;1 (cyclin D-type protein)

AT1G70210

>10

Neighbors of CYCD1;1 and CYCD1;3

Regulation of cell cycle and cell division

CYCD5;1 (cyclin D-type protein)

AT4G37630

>100

Neighbors of cell cycle

Regulation of cell cycle and cell division

CYCA3;2 (cyclin D-type protein)

AT1G47210

>2

Neighbors of morphogenesis and cell differenciation

Regulation of cell cycle and cell division

CYCD3;1 (cyclin D-type protein)

AT4G34160

>7

Neighbors of CYCD1;1 and CYCD1;3

Response to auxin

OBP1 (OBF binding protein)

AT3G50410

>3

Neighbors of cell cycle

Response to auxin

Aux1 (auxin influx transporter)

AT2G38120

>6

Neighbors of primordium elongation s and cell differenciation

Response to gibberellin

Gasa4 (Gast1 protein homolog 4)

AT5G15230

>10

Neighbors of heat shock and flower development

Response to gibberellin

Myb26 (MYB domain protein 26)

AT3G13890

>100

Neighbors of cell development

Response to brassinosteroid

Bas1 (cythochrom P450)

AT2G26710

>7

Neighbors of leaf development and hormone

response to brassinosteroid

T5I8.2 (hercule receptor protein kinase 2)

AT1G30570

>40

Neighbors of brassinolide

Response to sucrose stimulation

GBF6 (leucine zipper11)

AT4G34590

>2

 

Response to sucrose stimulation

GASA6 (GA stimulated arabidopsis 6)

AT1G74670

>10

 
  1. The most differentially expressed GO terms identified in the enrichment analysis are indicated in the first column for each dormancy stage.
  2. The localization of the genes in the functional network is indicated in the last column when available.