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Table 1 Functional categories based on significantly up-regulated genes associated with ROS metabolism in 2 dpa fibers from the domesticated diploid G. arboreum and wild diploid G. raimondii (p < 0.05 and FDR < 0.01).

From: Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium)

Mechanism

Taxon with significantly greater expression

Functional categorya

Corresponding key genes b

ROS production

G. arboreum

G. raimondii

Photorespiration

Glycolate oxidase activity

NADPH:quinone reductase activity

O2-/H2O2 production process

Long-chain-fatty-acid-CoA ligase activity

GOX, HPR

GOX, HAO

QR-like, SDR

NADPH Oxidase

ACX6

ROS scavenging

G. arboreum

G. raimondii

Peroxidase activity

Antioxidant activity

Glutathione transferase activity

Ascorbate peroxidase activity

Xanthophyll biosynthetic process

Response to toxin

Cellular response to stress

Response to oxidative stress

Epoxide hydrolase activity

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PRX, APX, GST

PRX, GST, Cu/Zn SOD

GSTs

APX, APX (chl)

ZEP

GSTs

GST, NTL

PRX, APX, GST, HSPIII

EPH

Cell signaling

G. arboreum

G. raimondii

Protein kinase regulator activity

ent-kaurene oxidase activity

Carbonic anhydrase activity

Calcium ion signaling

Phosphoglycolate phosphatase activity

Protein kinase activity

Response to salicylic acid stimulus

Response to jasmonic acid stimulus

Response to ethylene stimulus

Cyclin D, CDK

CYP450, GAs

CAs

CaDK, CaATPase, CBP

PGP, HDL

Ser/ThrPK, MAPK4

MAPK, WRKY78, Myb1

LOX, MAPKs, Myb

MYBs, NADPHO, ERF

  1. aBlast2GO http://www.blast2go.de was used as a tool for Gene Ontology functional classification of sequences.
  2. bKey ROS related genes are listed with their corresponding processes (a complete list can be viewed as supplementary material; Additional file 1). Abbreviations: GOX – Glycolate oxidase; HPR – hydroxypyruvate reductase; HAO – hydroxy-acid oxidase; QR-like – quinone reductase-like protein; SDR – Short-chain dehydrogenase/reductase; ACX6 – long chain acyl-CoA synthetase 6; PRX – Peroxidase; APX-Ascorbate peroxidase; APX (chl) – Thylakoid-bound ascorbate peroxidase; GST – Glutathione S-transferase; SOD – Superoxide dismutase; ZEP – zeaxanthin epoxidase; NTL – Nitrilase; HSP – Heat shock protein; EPH – Epoxide hydrolase; CDK – Cyclin dependent kinase; CYP450 – Cytochrome P450 monooxygenase; GA – Gibberellins; CA – Carbonic anhydrase; CaDK – Calcium-dependent protein kinase; CaATPase-calcium-transporting ATPase 1; CBP – Calmodulin-binding protein; PGP – Phosphoglycolate phosphatase; HDL – Hydrolase; Ser/ThrPK – Ser/Thr protein kinase; MAPK4 – Mitogen-activated protein kinase 4; LOX – Lipoxygenase1; ERF – Ethylene response factor 3a.
  3. FDR = False discovery rate.