TABLE 1

Biological processes corresponding to changes in expression ratios accompanying domestication of G. hirsutum and G. barbadense at three fiber developmental stages (5, 10, and 20 DPA)

G. hirsutum comparisonND-biased processes under domesticationGONA-biased processes under domesticationGO
5 DPA60Nuclear poreGO:000564347Methylenetetrahydrofolate reductase (NADPH) activityGO:0004489
Glycerol metabolic processGO:0006071Group transfer coenzyme metabolic processGO:0006752
Unlocalized protein complexGO:0005941Ceramidase activityGO:0017040
Nucleoside metabolic processGO:0009116Malate transportGO:0015743
Signal transductionGO:0007165PathogenesisGO:0009405
Protein targetingGO:0006605rRegulation of translational fidelityGO:0006450
Kinase activityGO:0016301Coenzyme biosynthetic processGO:0009108
Phosphoethanolamine N-methyltransferase activityGO:0000234Golgi apparatus partGO:0044431
Hydrolase activityGO:0016823PlastidGO:0009536
Trypsin activityGO:0004295
UTP:glucose-1-phosphate uridylyltransferase activityGO:0003983
Pyrimidine dimer repairGO:0006290
Aldehyde dehydrogenase (NAD) activityGO:0004029
3-oxo-5-α-steroid 4-dehydrogenase activityGO:0003865
Amidase activityGO:0004040
10 DPA78Response to ethylene stimulusGO:000972359Methylenetetrahydrofolate reductase (NADPH) activityGO:0004489
Sugar bindingGO:0005529Group transfer coenzyme metabolic processGO:0006752
Cell communicationGO:0007154Cell cycleGO:0007049
Kinase activityGO:0016301Lipid bindingGO:0008289
Nucleoside metabolic processGO:0009116ATP metabolic processGO:0046034
Aromatic compound metabolic processGO:0006725Regulation of translational fidelityGO:0006450
UDP-sugar pyrophosphorylase activityGO:0051748DNA ligase activityGO:0003909
amidase activityGO:0004040Malate transportGO:0015743
Chlorophyll bindingGO:0016168Fructokinase activityGO:0008865
Selenium bindingGO:0008430
Pectin metabolic processGO:0045488
Cellular morphogenesis during vegetative growthGO:0000903
ESCRT III complexGO:0000815
Cytosolic large ribosomal subunit (sensu Bacteria)GO:0009282
3-Hydroxyacyl-CoA dehydratase activityGO:0018812
Negative regulation of programmed cell deathGO:0043069
Aminomethyltransferase activityGO:0004047
Aldehyde dehydrogenase (NAD) activityGO:0004029
Pyrimidine dimer repairGO:0006290
20 DPA71Unlocalized protein complexGO:000594154Methylenetetrahydrofolate reductase (NADPH) activityGO:0004489
Transferase activity, transferring phosphorus-containing groupsGO:0016772Cation-transporting ATPase activityGO:0019829
Nucleobase, nucleoside, nucleotide kinase activityGO:0019205Cell divisionGO:0051301
Kinase activityGO:0016301Methionine metabolic processGO:0006555
Glycerol-3-phosphate dehydrogenase complexGO:0009331DNA ligase activityGO:0003909
Two-component signal transduction system (phosphorelay)GO:0000160Xanthophyll metabolic processGO:0016122
Electron transportGO:00061185S rRNA bindingGO:0008097
Magnesium ion bindingGO:0000287Regulation of translational fidelityGO:0006450
Phosphoric ester hydrolase activityGO:0042578Dipeptidase activityGO:0016805
Oxidoreductase activity, acting on the CH-CH group of donorsGO:0016627β-Carotene hydroxylase activityGO:0042411
Pectin biosynthetic processGO:0045489
Amidase activityGO:0004040
Cellular morphogenesis during vegetative growthGO:0000903
Negative regulation of apoptosisGO:0043066
Pyrimidine dimer repairGO:0006290
Aldehyde dehydrogenase (NAD) activityGO:0004029
Chlorophyll bindingGO:0016168
G. barbadense comparisonND-biased biological processes under domesticationGONA-biased biological processes under domesticationGO
5 DPA17GTPase activityGO:00039247Protein phosphatase type 2A activityGO:0000158
ATP-binding cassette (ABC) transporter complexGO:0043190FK506 bindingGO:0005528
Protein polymerizationGO:0051258
Microtubule-based movementGO:0007018
Positive regulation of protein kinase activityGO:0045860
Plastid membraneGO:0042170
10 DPA13Peptidyl-proline 4-dioxygenase activityGO:003154511Detection of cytokinin stimulusGO:0009722
NAD biosynthetic processGO:0009435Bis(5′-adenosyl)-triphosphatase activityGO:0047710
Phosphoglucomutase activityGO:0004614Regulation of actin filament lengthGO:0030832
Pollen germinationGO:0009846FK506 bindingGO:0005528
Regulation of protein kinase activityGO:0045859Membrane-bound vesicleGO:0031988
G-protein signaling, coupled to IP3 second messengerGO:0007200Peptidyl-prolyl cis-trans isomerase activityGO:0003755
Protein kinase activityGO:0004672
20 DPA21Pollen germinationGO:000984625Cystathionine γ-synthase activityGO:0003962
Fatty acid metabolic processGO:0006631Vesicle docking during exocytosisGO:0006904
Peptidyl-amino acid modificationGO:0018193ATP citrate synthase activityGO:0003878
Nucleotide diphosphatase activityGO:0004551Antioxidant activityGO:0016209
Oxidoreductase activityGO:0016705Actin filament organizationGO:0007015
Hydrolase activity, acting on ester bondsGO:0016788Response to cytokinin stimulusGO:0009735
G-protein signaling, coupled to IP3 second messengerGO:0007200
Nucleoside-triphosphatase activityGO:0017111
  • Data are partitioned into processes corresponding to genes biased toward either the A-genome or D-genome homeolog. Blast2GO (http://www.blast2go.de/) was used to identify biochemical pathways involved in a given comparison and to calculate the statistical significance of each pathway. Blast2GO includes the Gossip package (Bluthgen et al. 2005) for statistical assessment of annotation differences between two sets of sequences, using Fisher's exact test for each GO term. P-values (P < 0.05) were used for the assessment of significant metabolic pathways. A complete list of genes is at (http://www.eeob.iastate.edu/faculty/WendelJ/ranhovav.htm).