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Table 3 Subset of differentially expressed genes (DEG) in cotton flower buds in response to feeding by cotton boll weevil larvae

From: Transcriptome analysis of Gossypium hirsutum flower buds infested by cotton boll weevil (Anthonomus grandis) larvae

Contigs cotton

Gene symbol

TAIR annotation

SubjectID

logFold change

Adjusted P-value

GO:0010200 - Response to chitin

contig7179*

 

Protein kinase family protein with leucine-rich repeat domain

AT5g25930

2.02

5.33E-09

contig14965

Kin3

Encodes a putative serine/threonine-specific protein kinase

AT2g17220

2.03

1.20E-08

contig21694

 

Protein kinase superfamily

AT1g18390

2.65

5.45E-10

contig2968

CPK28

Member of Calcium Dependent Protein Kinase

AT5g66210

2.47

0.01

contig17371

CCR4

Serine/threonine-protein kinase-like domain

AT5g47850

3.51

0

contig2100

MAPK3

Encodes a mitogen-activated kinase

AT5g57510

4.27

8.61E-07

contig2102

MAPK3

Encodes a mitogen-activated kinase

AT3g45640

2.17

2.57E-10

contig14909

MKK9

Member of MAP Kinase Kinase family

AT1g73500

2.22

1.58E-10

contig7892

MAPKKK14

Member of MEKK subfamily

AT2g30040

2.96

4.79E-11

contig4523

 

ATPase E1-E2 type family protein/haloacid dehalogenase-like hydrolase family protein

AT3g63380

3.3

0

contig11388

 

ATPase E1-E2 type family protein/haloacid dehalogenase-like hydrolase family protein

AT3g63380

2.2

7.24E-11

contig18754

 

ATPase E1-E2 type family protein/haloacid dehalogenase-like hydrolase family protein

AT3g63380

2.15

3.53E-09

contig7822

CML38

Calmodulin-like 38 (CML38)

AT1g76650

4.87

1.56E-06

contig7823

CML38

Calmodulin-like 38 (CML38)

AT1g76650

3.32

0

contig535

CML24

Encodes a protein with 40% similarity to calmodulin

AT5g37770

3.48

0

contig2687

 

C2 calcium-dependent membrane targeting

AT2g25460

4.02

0

contig12364

 

Calcium-binding EF-hand family protein

AT4g27280

4.1

0

contig2688

 

C2 calcium-dependent membrane targeting

AT2g25460

3.89

1.72E-11

contig14266*

ACA2

Encodes a calmodulin-regulated Ca(2+)-pump located in the endoplasmic reticulum

AT4g37640

2.17

2.26E-10

contig2595*

ACA2

Encodes a calmodulin-regulated Ca(2+)-pump located in the endoplasmic reticulum

AT4g37640

2.15

7.16E-10

contig8294*

EDA39

Encodes a calmodulin-binding protein involved in stomatal movement

AT4g33050

2.61

3.93E-12

contig1798

PUMP5

Encodes one of the mitochondrial dicarboxylate carriers (DIC)

AT2g22500

6.13

0

contig9093*

 

Encodes a cell wall bound peroxidase

AT5g64120

3.76

4.46E-14

contig9094*

 

Encodes a cell wall bound peroxidase

AT5g64120

3.42

0

contig8534*

DMR6

Encodes a putative 2OG-Fe(II) oxygenase

AT5g24530

2.25

1.53E-06

contig1723*

 

Protein phosphatase 2C family protein

AT4g33920

3.07

7.56E-13

contig1722*

 

Protein phosphatase 2C family protein

AT4g33920

2.7

1.53E-14

contig1720*

 

Protein phosphatase 2C family protein

AT4g33920

2.32

4.51E-07

contig8378

 

Acyl-CoA N-acyltransferases (NAT) superfamily protein

AT2g32030

4.48

0

contig24379*

PLA/PLA2A

Encodes a lipid acyl hydrolase

AT2g26560

3.15

0

contig11992

 

Alpha/beta-Hydrolases superfamily protein

AT3g19970

3.13

1.89E-10

contig1674

TCH4

Encodes a cell wall-modifying enzyme

AT5g57560

5.84

9.62E-12

contig2539

TCH4

Encodes a cell wall-modifying enzyme

AT5g57560

5.57

0

contig1676

TCH4

Encodes a cell wall-modifying enzyme

AT5g57560

4.66

0

contig2101

TCH4

Encodes a cell wall-modifying enzyme

AT5g57560

4.63

0

contig2538

TCH4

Encodes a cell wall-modifying enzyme

AT5g57560

3.72

8.85E-13

contig2536

TCH4

Encodes a cell wall-modifying enzyme

AT5g57560

3.22

1.27E-13

contig4524

TCH4

Encodes a cell wall-modifying enzyme

AT5g57560

5.53

0

contig9042

RRTF1

Member of the ERF (ethylene response factor) of ERF/AP2 transcription factor family

AT4g34410

37.97

0

contig8299

RRTF1

Member of the ERF (ethylene response factor) of ERF/AP2 transcription factor family

AT4g34410

4.85

1.39E-13

contig8860

 

Member of the DREB subfamily A-5 of ERF/AP2 transcription factor family

AT1g19210

9.53

0

contig23571

 

Member of the DREB subfamily A-5 of ERF/AP2 transcription factor family

AT1g19210

7.29

0

contig24042

 

Member of the DREB subfamily A-5 of ERF/AP2 transcription factor family

AT1g19210

6.35

0

contig13134

 

Member of the DREB subfamily A-5 of ERF/AP2 transcription factor family

AT5g51190

5.25

0

contig19639

 

Member of the DREB subfamily A-5 of ERF/AP2 transcription factor family

AT1g19210

5.01

0

contig23741

ERF98

Member of the ERF (ethylene response factor)

AT3g23230

3.45

1.35E-09

contig5510

ERF-5

Member of the ERF (ethylene response factor)

AT5g47230

4.7

0

contig5512

ERF-5

Member of the ERF (ethylene response factor)

AT5g47230

4.47

0

contig5511

ERF-5

Member of the ERF (ethylene response factor)

AT5g47230

3.92

0

contig16446

ERF-5

Member of the ERF (ethylene response factor)

AT5g47230

3.72

0

contig22401

ERF-5

Member of the ERF (ethylene response factor)

AT5g47230

3.53

1.03E-10

contig5014

ERF-5

Member of the ERF (ethylene response factor)

AT5g47230

3.17

0

contig13018

ERF-5

Member of the ERF (ethylene response factor)

AT5g47230

2.85

4.47E-11

contig5559

ERF-4

Member of the ERF (ethylene response factor)

AT3g15210

3.05

0

contig6750

ERF-4

Member of the ERF (ethylene response factor)

AT3g15210

2.21

1.10E-10

contig8076*

GhWRKY40-like4

Pathogen-induced transcription factor

AT1g80840

4.98

0

contig1646*

GhWRKY40-like3

Pathogen-induced transcription factor

AT1g80840

4.29

0

contig4254*

GhWRKY40-like1

Pathogen-induced transcription factor

AT1g80840

2.45

6.95E-13

contig313*

GhWRKY40-like2

Pathogen-induced transcription factor

AT1g80840

2.27

1.60E-11

contig5359*

GhWRKY64-like1

Member of WRKY Transcription Factor; Group III

AT4g23810

5.37

0

contig9783*

GhWRKY70-like1

Member of WRKY Transcription Factor; Group III

AT3g56400

4.75

1.14E-13

contig3807*

GhWRKY70-like3

Member of WRKY Transcription Factor; Group III

AT3g56400

2.26

5.24E-11

contig3808*

GhWRKY70-like4

Member of WRKY Transcription Factor; Group III

AT3g56400

2.24

3.55E-06

contig4599*

GhWRKY70-like2

Member of WRKY Transcription Factor; Group III

AT3g56400

2.03

6.31E-05

contig4087

GhWRKY46-like1

Member of WRKY Transcription Factor; Group III

AT2g46400

4.37

1.77E-12

contig9296

GhWRKY46-like3

Member of WRKY Transcription Factor; Group III

AT2g46400

2.88

8.66E-14

contig4086

GhWRKY46-like2

Member of WRKY Transcription Factor; Group III

AT2g46400

3.5

0

contig2606*

GhWRKY33-like1

Member of the plant WRKY transcription factor family

AT2g38470

3.61

0

contig2605*

GhWRKY33-like2

Member of the plant WRKY transcription factor family

AT2g38470

3.36

0

contig1952

GhWRKY33-like3

Member of the plant WRKY transcription factor family

AT2g38470

2.56

3.01E-14

contig1953*

GhWRKY33-like4

Member of the plant WRKY transcription factor family

AT2g38470

2.43

2.46E-11

contig4409

GhWRKY22-like1

member of WRKY Transcription Factor; Group II-e

AT4g01250

2.56

1.57E-11

contig565

STZ

Related to Cys2/His2-type zinc-finger proteins

AT3g63380

5.4

0

contig6454

STZ

Related to Cys2/His2-type zinc-finger proteins

AT1g27730

5.22

0

contig561

STZ

Related to Cys2/His2-type zinc-finger proteins

AT1g27730

5.07

0

contig3187

STZ

RING-H2 protein induced after exposure to chitin

AT1g27730

3.64

0

contig1541*

ATL2

RING-H2 protein induced after exposure to chitin

AT3g16720

3.77

0

contig1540*

ATL2

RING-H2 protein induced after exposure to chitin

AT3g16720

3.71

0

contig3187

STZ

Related to Cys2/His2-type zinc-finger proteins found in higher plants

AT1g27730

3.64

0

contig567

STZ

Related to Cys2/His2-type zinc-finger proteins found in higher plants

AT1g27730

3.63

5.97E-12

contig563

STZ

Related to Cys2/His2-type zinc-finger proteins found in higher plants

AT1g27730

3.26

0

contig566

STZ

Related to Cys2/His2-type zinc-finger proteins found in higher plants

AT5g57560

3.2

5.90E-05

contig569

STZ

Related to Cys2/His2-type zinc-finger proteins found in higher plants

AT1g27730

2.41

9.60E-12

contig562

STZ

Related to Cys2/His2-type zinc-finger proteins found in higher plants

AT1g27730

3.38

0

contig5663

 

Related to Cys2/His2-type zinc-finger proteins found in higher plants

AT1g27730

3.63

0

contig564

ATSZF2

Domain Zinc finger, C3H-type

AT2g40140

2.95

4.46E-08

contig722*

ATSZF2

Domain Zinc finger, C3H-type

AT2g40140

3.54

0

contig729*

ATSZF2

Zinc finger, C3H-type

AT2g40140

2.95

0

contig719*

ATSZF2

Zinc finger, C3H-type

AT2g40140

2.79

0

contig717*

ATSZF2

Zinc finger, C3H-type

AT2g40140

2.59

2.08E-13

contig720

ATSZF1

Salt-inducible zinc finger 1 (SZF1)

AT3g55980

3.19

1.78E-08

contig728

ATSZF1

Salt-inducible zinc finger 1 (SZF1)

AT3g55980

2.38

0.01

contig5654

BRH1

Encodes a novel ring finger protein

AT3g61460

3.61

0

contig22866

ATMYB73

Member of the R2R3 factor gene family

AT3g16720

3.77

0

contig19903

ATMYB73

Member of the R2R3 factor gene family

AT4g37260

3.24

1.10E-09

contig5383

ATMYB73

Member of the R2R3 factor gene family

AT4g37260

2.78

0

contig11235

ATMYB73

Member of the R2R3 factor gene family

AT4g37260

2.73

1.10E-08

contig3507

GRAS

GRAS family transcription factor

AT3g46600

2.73

0

contig2875

ANAC002

Belongs to a large family of putative transcriptional activators with NAC domain

AT1g01720

3.04

0

contig718

ANAC002

Belongs to a large family of putative transcriptional activators with NAC domain

AT1g01720

2.82

0

contig725

ANAC002

Belongs to a large family of putative transcriptional activators with NAC domain

AT1g01720

2.05

1.37E-09

contig10852

ATL6

Encodes a putative RING-H2 zinc finger protein ATL6 (ATL6)

AT3g05200

2.27

1.63E-10

contig7248

RHL41

Encodes a zinc finger protein

AT5g59820

2.66

5.29E-06

contig1779

ATHSFA2

Member of Heat Stress Transcription Factor (Hsf) family

AT2g26150

−3.29

0

contig18462*

BETA

Encodes a beta carbonic anhydrase likely to be localized in the cytoplasm

AT5g14740

2.69

0

contig4843

 

Encodes an ABA- and drought-induced RING-DUF1117 gene

AT5g59550

2.09

1.56E-07

contig17118

AOS

Member of the cytochrome p450 CYP74 gene family that functions as an allene oxide synthase

AT5g42650

4.5

2.74E-09

contig3758

ACS

Encodes a a member of the 1-aminocyclopropane-1-carboxylate (ACC) synthase

AT4g11280

3.48

0

contig12553*

ACO

Encodes 1-aminocyclopropane-1-carboxylate oxidase

AT1g05010

3.1

0

contig1208*

ACO

Encodes 1-aminocyclopropane-1-carboxylate oxidase

AT1g05010

2.16

1.48E-10

contig1206*

ACO

Encodes 1-aminocyclopropane-1-carboxylate oxidase

AT1g05010

2.09

7.20E-10

contig1960

LOX

PLAT/LH2 domain-containing lipoxygenase family protein

AT1g72520

3.73

0

contig9217

CYP707A3

Encodes a protein with ABA 8′-hydroxylase activity

AT5g45340

3.19

0

contig4960*

JAZ1

JAZ1 is a nuclear-localized protein involved in jasmonate signaling

AT1g19180

2.26

5.01E-11

contig4959*

JAZ1

JAZ1 is a nuclear-localized protein involved in jasmonate signaling

AT1g19180

2.19

2.02E-09

contig15546

JAZ7

Jasmonate-zim-domain protein 7 (JAZ7)

AT2g34600

2.03

0

contig5978

ATCHITIV

Encodes an EP3 chitinase

AT3g54420

3.08

1.53E-14

contig21823

ATCHITIV

Encodes an EP3 chitinase

AT3g54420

2.57

2.26E-10

contig6127

AtCAF1a

Encodes one of the homologs of the yeast CCR4-associated factor 1

AT3g44260

2.94

0

contig1389

AT-SYR1

Encodes a syntaxin localized at the plasma membrane

AT3g11820

2.82

5.38E-12

contig1388

AT-SYR1

Encodes a syntaxin localized at the plasma membrane

AT3g11820

2.41

2.02E-12

contig5585

ATHSPRO2

Ortholog of sugar beet HS1 PRO-1 2 (HSPRO2)

AT2g40000

2.69

0

contig3792

ATHSPRO2

Ortholog of sugar beet HS1 PRO-1 2 (HSPRO2)

AT2g40000

2.16

6.93E-05

contig2278

 

Encodes an ABA- and drought-induced RING-DUF1117 gene

AT5g59550

2.61

1.53E-14

contig4842

 

Encodes an ABA- and drought-induced RING-DUF1117 gene

AT5g59550

2.41

8.61E-06

contig4022

ATNHL10

Encodes a protein whose sequence is similar to tobacco hairpin-induced gene (HIN1)

AT2g38470

2.56

8.82E-06

contig4024

ATNHL10

Encodes a protein whose sequence is similar to tobacco hairpin-induced gene (HIN1)

AT2g35980

2.26

1.06E-09

contig22620

 

Hs1pro-1 protein

AT3g55840

2.53

1.76E-09

contig3055

(AT)SRC2

Unknown protein

AT1g09070

2.38

6.49E-12

contig6505

 

ARM repeat superfamily protein

AT4g27280

4.04

0

contig17616*

PUB23

Encodes a cytoplasmically localized U-box domain containing E3 ubiquitin ligase

AT2g35930

4.21

4.10E-12

contig2098

ATPUB29

E3 ubiquitin ligase activity

AT3g18710

3.95

0

contig6504

ATCMPG1

Ubiquitin-protein ligase activity

AT1g66160

3.9

0

contig8776

 

Ubiquitin-protein ligase activity

AT5g37490

2.31

2.24E-07

GO:0016265 - Death

contig10876

RLK1

Encodes a receptor-like protein kinase

AT5g60900

2.56

5.07E-05

contig15035

RLK1

Encodes a receptor-like protein kinase

AT5g60900

2.28

8.92E-06

contig6958

RIPK

Encodes a receptor-like cytoplasmic kinase

AT2g05940

2.13

1.14E-09

contig5615

EVR

Encodes a putative leucine rich repeat transmembrane protein kinase

AT2g31880

2.21

7.45E-09

contig12017

CCR3

CRINKLY4 related 3 (CCR3); kinase activity

AT3g55950

2.24

3.33E-07

contig7179

NA

Protein kinase family protein with leucine-rich repeat domain

AT5g25930

2.02

5.33E-09

contig10122

ATPP2-A1

Encodes a phloem lectin

AT4g19840

2.79

0

contig7573

GRX480

Encodes GRX480, a member of the glutaredoxin family that regulates protein redox state

AT1g28480

2.35

2.97E-12

contig8179

ATRBOHD

NADPH/respiratory burst oxidase protein D (RbohD)

AT5g47910

2.64

1.53E-14

contig9014

ATRBOHD

NADPH/respiratory burst oxidase protein D (RbohD)

AT5g47910

2.48

7.49E-11

contig9015

ATRBOHD

NADPH/respiratory burst oxidase protein D (RbohD)

AT5g47910

2.65

1.57E-09

contig4745

ATMC1

Metacaspase AtMCP1b

AT1g02170

2.24

1.02E-09

contig5579

ATGATL1

The PARVUS/GLZ1 gene encodes a putative family 8 glycosyl transferase

AT1g19300

2.66

0

contig2607

ATWRKY33

Member of the plant WRKY transcription factor family

AT2g38470

3.14

1.00E-13

contig2076

ATEBP

Encodes a member of the ERF (ethylene response factor)

AT3g16770

2.23

5.79E-11

contig14400

ANAC083

Encodes a NAC domain transcription factor

AT5g13180

2.26

1.93E-07

contig12668

JMT

Encodes a S-adenosyl-L-methionine:jasmonic acid carboxyl methyltransferase

AT1g19640

3.4

0

contig13244

AtLEA5

Encodes AtLEA5, also known as Senescence-associated gene 21 (SAG21). Has a role on oxidative stress tolerance

AT4g02380

2.34

7.06E-12

contig4041

AtLEA5

Encodes AtLEA5, also known as Senescence-associated gene 21 (SAG21). Has a role on oxidative stress tolerance

AT4g02380

2.76

0

contig4042

AtLEA5

Encodes AtLEA5, also known as Senescence-associated gene 21 (SAG21). Has a role on oxidative stress tolerance

AT4g02380

2.37

2.58E-09

contig4022

ATNHL10

Encodes a protein non-race specific disease resistance gene (NDR1)

AT2g35980

2.56

8.82E-06

contig4024

ATNHL10

Encodes a protein non-race specific disease resistance gene (NDR1)

AT2g35980

2.26

1.06E-09

contig3055

(AT)SRC2

SRC2 specifically binds the peptide PIEPPPHH

AT1g09070

2.38

6.49E-12

contig1388

AT-SYR1

Encodes a syntaxin

AT3g11820

2.41

2.02E-12

contig1389

AT-SYR1

Encodes a syntaxin

AT3g11820

2.82

5.38E-12

contig21823

ATCHITIV

Encodes an EP3 chitinase

AT3g54420

2.57

2.26E-10

contig5978

ATCHITIV

Encodes an EP3 chitinase

AT3g54420

3.08

1.53E-14

  1. Only DEG with the GO term for the biological process “response to chitin” (GO:0010200) and/or “death” (GO:0016265) are shown. The complete list of DEG is shown in Additional file 2.
  2. *Genes present in both biological processes: response to chitin and death.
  3. Genes in bold were tested by qPCR.