Table 2 GO annotations of the 39 DEGs located in the two associated regions

1

BnaC08g40740D

C08

down

Molecular Function: translation initiation factor activity (GO:0003743); Cellular Component: cytoplasm (GO:0005737);

2

BnaA09g45890D

A09

down

Cellular Component: plasma membrane (GO:0005886); Biological Process: phosphate ion transport (GO:0006817); Cellular Component: integral component of membrane (GO:0016021); Biological Process: cellular response to phosphate starvation (GO:0016036);

3

BnaC08g42080D

C08

down

Cellular Component: plasma membrane (GO:0005886); Molecular Function: transferase activity, transferring phosphorus-containing groups (GO:0016772);

4

BnaA09g43250D

A09

up

Cellular Component: mitochondrion (GO:0005739);

5

BnaC08g36200D

C08

down

Cellular Component: chloroplast (GO:0009507); Biological Process: photorespiration (GO:0009853);

6

BnaA09g44650D

A09

down

Cellular Component: plasma membrane (GO:0005886); Biological Process: proteolysis (GO:0006508); Biological Process: lipid transport (GO:0006869); Molecular Function: peptidase activity (GO:0008233); Molecular Function: lipid binding (GO:0008289); Cellular Component: anchored component of membrane (GO:0031225);

7

BnaA09g46080D

A09

down

Cellular Component: nucleus (GO:0005634);

8

BnaC08g37340D

C08

up

Cellular Component: plasma membrane (GO:0005886); Biological Process: proteolysis (GO:0006508); Biological Process: lipid transport (GO:0006869); Molecular Function: peptidase activity (GO:0008233); Molecular Function: lipid binding (GO:0008289); Cellular Component: anchored component of membrane (GO:0031225);

9

BnaC08g41780D

C08

down

Biological Process: sulfur amino acid metabolic process (GO:0000096); Molecular Function: serine-tRNA ligase activity (GO:0004828); Molecular Function: ATP binding (GO:0005524); Cellular Component: mitochondrion (GO:0005739); Biological Process: rRNA processing (GO:0006364); Biological Process: seryl-tRNA aminoacylation (GO:0006434); Biological Process: mitochondrion organization (GO:0007005); Biological Process: cellular amino acid biosynthetic process (GO:0008652); Biological Process: serine family amino acid metabolic process (GO:0009069); Cellular Component: chloroplast (GO:0009507); Biological Process: embryo development ending in seed dormancy (GO:0009793); Biological Process: chloroplast relocation (GO:0009902); Biological Process: leaf morphogenesis (GO:0009965); Biological Process: thylakoid membrane organization (GO:0010027); Biological Process: photosystem II assembly (GO:0010207); Biological Process: vegetative to reproductive phase transition of meristem (GO:0010228); Biological Process: iron-sulfur cluster assembly (GO:0016226); Biological Process: cell differentiation (GO:0030154); Biological Process: regulation of protein dephosphorylation (GO:0035304); Biological Process: cell wall modification (GO:0042545); Biological Process: transcription from plastid promoter (GO:0042793); Biological Process: positive regulation of transcription, DNA-templated (GO:0045893); Biological Process: ovule development (GO:0048481);

10

BnaC08g40810D

C08

up

Molecular Function: protein serine/threonine kinase activity (GO:0004674); Biological Process: protein autophosphorylation (GO:0046777);

11

BnaC08g41540D

C08

down

Molecular Function: N,N-dimethylaniline monooxygenase activity (GO:0004499); Cellular Component: nucleus (GO:0005634); Biological Process: glucosinolate biosynthetic process (GO:0019761); Molecular Function: flavin adenine dinucleotide binding (GO:0050660); Molecular Function: NADP binding (GO:0050661); Biological Process: oxidation-reduction process (GO:0055114); Molecular Function: 8-methylthiopropyl glucosinolate S-oxygenase activity (GO:0080107);

12

BnaC08g40410D

C08

up

Molecular Function: Ran GTPase activator activity (GO:0005098); Cellular Component: nuclear envelope (GO:0005635); Cellular Component: vacuolar membrane (GO:0005774); Cellular Component: endoplasmic reticulum (GO:0005783); Biological Process: nucleocytoplasmic transport (GO:0006913); Biological Process: toxin catabolic process (GO:0009407); Cellular Component: chloroplast (GO:0009507); Biological Process: photomorphogenesis (GO:0009640); Biological Process: response to salt stress (GO:0009651); Biological Process: cullin deneddylation (GO:0010388); Biological Process: lateral root development (GO:0048527);

13

BnaC08g35720D

C08

up

Cellular Component: vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220); Cellular Component: mitochondrion (GO:0005739); Cellular Component: Golgi apparatus (GO:0005794); Biological Process: ATP catabolic process (GO:0006200); Cellular Component: chloroplast (GO:0009507); Molecular Function: hydrogen-translocating pyrophosphatase activity (GO:0009678); Cellular Component: plant-type vacuole membrane (GO:0009705); Molecular Function: hydrogen ion transmembrane transporter activity (GO:0015078); Biological Process: ATP synthesis coupled proton transport (GO:0015986); Biological Process: ATP hydrolysis coupled proton transport (GO:0015991); Molecular Function: ATPase activity (GO:0016887); Biological Process: cellular response to nutrient levels (GO:0031669); Biological Process: sequestering of zinc ion (GO:0032119); Biological Process: vacuolar sequestering (GO:0043181); Molecular Function: nutrient reservoir activity (GO:0045735); Biological Process: vacuolar proton-transporting V-type ATPase complex assembly (GO:0070072); Biological Process: cellular response to salt stress (GO:0071472);

14

BnaC08g42280D

C08

down

Biological Process: telomere maintenance (GO:0000723); Biological Process: double-strand break repair via homologous recombination (GO:0000724); Molecular Function: nucleic acid binding (GO:0003676); Molecular Function: ATP binding (GO:0005524); Cellular Component: nucleus (GO:0005634); Biological Process: DNA replication (GO:0006260); Cellular Component: plasmodesma (GO:0009506); Biological Process: vegetative to reproductive phase transition of meristem (GO:0010228); Molecular Function: ATP-dependent 3′-5′ DNA helicase activity (GO:0043140); Biological Process: cellular response to cold (GO:0070417); Biological Process: cellular response to abscisic acid stimulus (GO:0071215);

15

BnaC08g38300D

C08

down

Molecular Function: nucleotide binding (GO:0000166); Biological Process: mRNA splicing, via spliceosome (GO:0000398); Molecular Function: RNA binding (GO:0003723); Molecular Function: protein binding (GO:0005515); Cellular Component: nucleolus (GO:0005730); Biological Process: sugar mediated signaling pathway (GO:0010182); Cellular Component: nuclear speck (GO:0016607);

16

BnaC08g39990D

C08

up

Biological Process: MAPK cascade (GO:0000165); Molecular Function: protein serine/threonine kinase activity (GO:0004674); Molecular Function: protein serine/threonine/tyrosine kinase activity (GO:0004712); Molecular Function: ATP binding (GO:0005524); Cellular Component: nucleus (GO:0005634); Cellular Component: cytosol (GO:0005829); Biological Process: protein phosphorylation (GO:0006468); Biological Process: protein targeting to membrane (GO:0006612); Biological Process: response to cold (GO:0009409); Biological Process: response to water deprivation (GO:0009414); Biological Process: response to ethylene (GO:0009723); Biological Process: auxin-activated signaling pathway (GO:0009734); Biological Process: abscisic acid-activated signaling pathway (GO:0009738); Biological Process: brassinosteroid mediated signaling pathway (GO:0009742); Biological Process: systemic acquired resistance, salicylic acid mediated signaling pathway (GO:0009862); Biological Process: jasmonic acid mediated signaling pathway (GO:0009867); Biological Process: regulation of signal transduction (GO:0009966); Biological Process: leaf vascular tissue pattern formation (GO:0010305); Biological Process: regulation of plant-type hypersensitive response (GO:0010363); Biological Process: endoplasmic reticulum unfolded protein response (GO:0030968); Biological Process: negative regulation of defense response (GO:0031348); Biological Process: hyperosmotic salinity response (GO:0042538); Biological Process: negative regulation of programmed cell death (GO:0043069); Biological Process: defense response to fungus (GO:0050832);

17

BnaC08g36100D

C08

down

Cellular Component: cytoplasm (GO:0005737); Biological Process: ER to Golgi vesicle-mediated transport (GO:0006888);

18

BnaA09g48320D

A09

down

Molecular Function: structural constituent of ribosome (GO:0003735); Cellular Component: nucleolus (GO:0005730); Biological Process: translation (GO:0006412); Cellular Component: chloroplast (GO:0009507); Cellular Component: cytosolic large ribosomal subunit (GO:0022625);

19

BnaA09g45000D

A09

down

Biological Process: RNA splicing, via endonucleolytic cleavage and ligation (GO:0000394); Molecular Function: DNA binding (GO:0003677); Cellular Component: transcription factor TFIID complex (GO:0005669); Biological Process: DNA-templated transcription, initiation (GO:0006352); Biological Process: transcription from RNA polymerase II promoter (GO:0006366); Biological Process: cytokinin-activated signaling pathway (GO:0009736); Biological Process: jasmonic acid mediated signaling pathway (GO:0009867); Biological Process: regulation of ethylene-activated signaling pathway (GO:0010104); Molecular Function: protein heterodimerization activity (GO:0046982);

20

BnaC08g39130D

C08

up

Molecular Function: copper ion binding (GO:0005507); Molecular Function: calmodulin binding (GO:0005516); Molecular Function: ATP binding (GO:0005524); Cellular Component: mitochondrion (GO:0005739); Cellular Component: cytosol (GO:0005829); Biological Process: gluconeogenesis (GO:0006094); Biological Process: glycolytic process (GO:0006096); Biological Process: protein folding (GO:0006457); Biological Process: tryptophan catabolic process (GO:0006569); Biological Process: response to heat (GO:0009408); Biological Process: response to cold (GO:0009409); Cellular Component: chloroplast thylakoid membrane (GO:0009535); Cellular Component: chloroplast stroma (GO:0009570); Biological Process: response to high light intensity (GO:0009644); Biological Process: response to salt stress (GO:0009651); Biological Process: chloroplast organization (GO:0009658); Biological Process: indoleacetic acid biosynthetic process (GO:0009684); Cellular Component: chloroplast envelope (GO:0009941); Biological Process: isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway (GO:0019288); Biological Process: cysteine biosynthetic process (GO:0019344); Biological Process: response to endoplasmic reticulum stress (GO:0034976); Biological Process: response to hydrogen peroxide (GO:0042542); Biological Process: response to cadmium ion (GO:0046686); Cellular Component: apoplast (GO:0048046); Biological Process: ovule development (GO:0048481); Molecular Function: chaperone binding (GO:0051087); Biological Process: positive regulation of superoxide dismutase activity (GO:1901671);

21

BnaA09g45260D

A09

down

Cellular Component: chloroplast (GO:0009507);

22

BnaA09g45300D

A09

down

Molecular Function: serine-type carboxypeptidase activity (GO:0004185); Cellular Component: extracellular region (GO:0005576); Cellular Component: vacuole (GO:0005773); Biological Process: proteolysis (GO:0006508);

23

BnaC08g39020D

C08

up

Cellular Component: cytosol (GO:0005829); Cellular Component: plasmodesma (GO:0009506);

24

BnaC08g38200D

C08

down

Cellular Component: nucleus (GO:0005634); Molecular Function: oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628);

25

BnaC08g41720D

C08

down

Molecular Function: aspartic-type endopeptidase activity (GO:0004190); Cellular Component: extracellular region (GO:0005576); Cellular Component: vacuole (GO:0005773); Cellular Component: cytosol (GO:0005829); Biological Process: glycolytic process (GO:0006096); Biological Process: proteolysis (GO:0006508); Biological Process: protein targeting to vacuole (GO:0006623); Biological Process: lipid metabolic process (GO:0006629); Biological Process: water transport (GO:0006833); Biological Process: hyperosmotic response (GO:0006972); Biological Process: Golgi organization (GO:0007030); Biological Process: response to temperature stimulus (GO:0009266); Cellular Component: plasmodesma (GO:0009506); Biological Process: response to salt stress (GO:0009651); Biological Process: response to cadmium ion (GO:0046686); Biological Process: organ development (GO:0048513);

26

BnaC08g42450D

C08

down

Biological Process: response to molecule of bacterial origin (GO:0002237); Molecular Function: protein serine/threonine kinase activity (GO:0004674); Molecular Function: ATP binding (GO:0005524); Cellular Component: plasma membrane (GO:0005886); Biological Process: N-terminal protein myristoylation (GO:0006499); Biological Process: protein targeting to membrane (GO:0006612); Biological Process: membrane fusion (GO:0006944); Biological Process: response to oxidative stress (GO:0006979); Biological Process: transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169); Biological Process: systemic acquired resistance (GO:0009627); Biological Process: seed germination (GO:0009845); Biological Process: stomatal complex morphogenesis (GO:0010103); Biological Process: regulation of plant-type hypersensitive response (GO:0010363); Cellular Component: integral component of membrane (GO:0016021); Biological Process: negative regulation of programmed cell death (GO:0043069); Biological Process: protein autophosphorylation (GO:0046777); Biological Process: stamen development (GO:0048443); Cellular Component: micropyle (GO:0070825);

27

BnaC08g35850D

C08

up

Molecular Function: microtubule motor activity (GO:0003777); Molecular Function: ATP binding (GO:0005524); Cellular Component: cytoplasm (GO:0005737); Cellular Component: kinesin complex (GO:0005871); Cellular Component: microtubule (GO:0005874); Cellular Component: plasma membrane (GO:0005886); Biological Process: microtubule-based movement (GO:0007018); Molecular Function: microtubule binding (GO:0008017); Cellular Component: plasmodesma (GO:0009506);

28

BnaC08g40320D

C08

up

Molecular Function: chromatin binding (GO:0003682); Molecular Function: sequence-specific DNA binding transcription factor activity (GO:0003700); Cellular Component: nucleus (GO:0005634); Biological Process: regulation of transcription, DNA-templated (GO:0006355); Biological Process: membrane fusion (GO:0006944); Molecular Function: identical protein binding (GO:0042802); Molecular Function: sequence-specific DNA binding (GO:0043565); Biological Process: Golgi vesicle transport (GO:0048193);

29

BnaA09g45310D

A09

up

–

30

BnaC08g41180D

C08

down

Molecular Function: DNA binding (GO:0003677); Cellular Component: nucleus (GO:0005634); Molecular Function: zinc ion binding (GO:0008270);

31

BnaA09g44370D

A09

down

Molecular Function: DNA binding (GO:0003677); Molecular Function: chromatin binding (GO:0003682); Molecular Function: sequence-specific DNA binding transcription factor activity (GO:0003700); Cellular Component: nucleus (GO:0005634); Biological Process: regulation of transcription, DNA-templated (GO:0006355); Biological Process: protein targeting to membrane (GO:0006612); Biological Process: response to salt stress (GO:0009651); Biological Process: response to ethylene (GO:0009723); Biological Process: response to auxin (GO:0009733); Biological Process: response to abscisic acid (GO:0009737); Biological Process: response to gibberellin (GO:0009739); Biological Process: response to salicylic acid (GO:0009751); Biological Process: response to jasmonic acid (GO:0009753); Biological Process: positive regulation of flavonoid biosynthetic process (GO:0009963); Biological Process: regulation of plant-type hypersensitive response (GO:0010363); Biological Process: response to cadmium ion (GO:0046686);

32

BnaA09g47900D

A09

down

Molecular Function: zinc ion binding (GO:0008270);

33

BnaC08g41390D

C08

down

Cellular Component: plant-type vacuole (GO:0000325); Molecular Function: sucrose alpha-glucosidase activity (GO:0004575); Biological Process: carbohydrate metabolic process (GO:0005975); Biological Process: polyamine catabolic process (GO:0006598); Biological Process: calcium ion transport (GO:0006816); Biological Process: iron ion transport (GO:0006826); Biological Process: Golgi organization (GO:0007030); Cellular Component: plant-type cell wall (GO:0009505); Biological Process: response to wounding (GO:0009611); Biological Process: response to bacterium (GO:0009617); Biological Process: response to salt stress (GO:0009651); Biological Process: coumarin biosynthetic process (GO:0009805); Biological Process: cellular response to iron ion starvation (GO:0010106); Biological Process: response to nitrate (GO:0010167); Biological Process: nitrate transport (GO:0015706); Biological Process: brassinosteroid biosynthetic process (GO:0016132); Biological Process: cellular modified amino acid biosynthetic process (GO:0042398); Biological Process: cellular response to gibberellin stimulus (GO:0071370); Biological Process: primary root development (GO:0080022);

34

BnaA09g45610D

A09

up

Cellular Component: nucleus (GO:0005634);

35

BnaC08g35880D

C08

down

Cellular Component: cytosol (GO:0005829); Biological Process: ubiquitin-dependent protein catabolic process (GO:0006511); Cellular Component: chloroplast (GO:0009507);

36

BnaC08g36360D

C08

up

Molecular Function: nucleotide binding (GO:0000166); Molecular Function: catalytic activity (GO:0003824); Cellular Component: mitochondrial respiratory chain complex I (GO:0005747); Biological Process: ubiquitin-dependent protein catabolic process (GO:0006511); Biological Process: response to salt stress (GO:0009651); Biological Process: photorespiration (GO:0009853); Molecular Function: coenzyme binding (GO:0050662); Biological Process: response to misfolded protein (GO:0051788); Biological Process: proteasome core complex assembly (GO:0080129);

37

BnaC08g37460D

C08

down

Biological Process: mitotic cell cycle (GO:0000278); Molecular Function: RNA binding (GO:0003723); Molecular Function: polynucleotide adenylyltransferase activity (GO:0004652); Molecular Function: protein binding (GO:0005515); Cellular Component: nucleus (GO:0005634); Biological Process: transcription, DNA-templated (GO:0006351); Biological Process: RNA polyadenylation (GO:0043631);

38

BnaC08g39120D

C08

up

–

39

BnaA09g45320D

A09

down

Molecular Function: copper ion binding (GO:0005507); Molecular Function: calmodulin binding (GO:0005516); Molecular Function: ATP binding (GO:0005524); Cellular Component: mitochondrion (GO:0005739); Cellular Component: cytosol (GO:0005829); Biological Process: gluconeogenesis (GO:0006094); Biological Process: glycolytic process (GO:0006096); Biological Process: protein folding (GO:0006457); Biological Process: tryptophan catabolic process (GO:0006569); Biological Process: response to heat (GO:0009408); Biological Process: response to cold (GO:0009409); Cellular Component: chloroplast thylakoid membrane (GO:0009535); Cellular Component: chloroplast stroma (GO:0009570); Biological Process: response to high light intensity (GO:0009644); Biological Process: response to salt stress (GO:0009651); Biological Process: chloroplast organization (GO:0009658); Biological Process: indoleacetic acid biosynthetic process (GO:0009684); Cellular Component: chloroplast envelope (GO:0009941); Biological Process: isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway (GO:0019288); Biological Process: cysteine biosynthetic process (GO:0019344); Biological Process: response to endoplasmic reticulum stress (GO:0034976); Biological Process: response to hydrogen peroxide (GO:0042542); Biological Process: response to cadmium ion (GO:0046686); Cellular Component: apoplast (GO:0048046); Biological Process: ovule development (GO:0048481); Molecular Function: chaperone binding (GO:0051087); Biological Process: positive regulation of superoxide dismutase activity (GO:1901671)