Table 2. Genes in Cluster 15
NameProtein IDaDescriptionbAverage RPKMcSignificant EffectsdPrimary Functional Categorye
CAH1522126CA, periplasmic, α type1223.8C+S+CSMetabolism
CAH4522732Mitochondrial CA, β type226.5C+S+CSMetabolism
CAH5522733Mitochondrial CA, β type157.3C+S+CSMetabolism
CCP1522130LCI chloroplast envelope protein162.0C+S+CSTransport
CGL28510019RNA binding protein200.7C+S+CSUnknown
CYC6516039Cytochrome c61.2SMetabolism
DNJ15514023DnaJ-like protein12.8SGene Expression
DNJ31518238DnaJ-like protein13.1SGene Expression
*HFO7523344Histone H4<0.1Gene Expression
HLA3518934ATP binding cassette transporter289.5C+STransport
*KIR1526069Keto acid isomerase-like protein<0.1Unknown
LCI1520703LCI membrane protein224.0C+STransport
LCI23523507LCI protein75.8C+SUnknown (TM)
LCIE522129LCIB-like gene1.6SMetabolism
LCR1519760Low-CO2 response regulator79.0C+SGene Expression
LHCSR2525378Stress-related chlorophyll a/b binding protein 245.7C+S+CSMetabolism
LHCSR3525376Stress-related chlorophyll a/b binding protein 351.7C+S+CSMetabolism
NAR1.2524076Anion transporter; LCIA209.7C+STransport
516770PRLI-interacting factor L44.9SSignaling
509757Acetyltransferase27.5C+SUnknown
519249Ser/Thr protein kinase53.5SSignaling
522781ND4.85SUnknown (TM)
516290ND51.5C+STransport
510680ND44.6C+SUnknown (TM)
520458ND20.7S+CSUnknown
512353ND16.8C+S+CSUnknown (TM)
522486ND8.7C+SSignaling
524386ND6.4SUnknown (TM)
524387ND2.3SUnknown
*–512735ND<0.1SUnknown
*–519540ND<0.1Unknown
*–522103ND<0.1Unknown
*–510710ND<0.1Signaling
*–518019ND<0.1Unknown
*–511100ND<0.1Unknown
  • Asterisks indicate genes with an average expression level lower than 0.05 RPKM and “–” indicates unnamed gene.

  • a Augustus 5.0 gene model protein ID.

  • b ND means no description available.

  • c Average RPKM across all six treatment conditions.

  • d Individual effect having a q-value <0.025 by C/S impact test, where “C” means CO2 effect, “S” means strain effect, “CS” means interaction effect, and “–” means no significant C/S impact effect.

  • e Result from our manual curation, where “unknown (TM)” indicates gene of unknown function containing at least one putative transmembrane domain.