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Table 4 Identification and analysis of PRP genes in Populus trichocarpa

From: Bioinformatic Identification and Analysis of Hydroxyproline-Rich Glycoproteins in Populus trichocarpa

Locus Identifier 3.0 (ID 2.0)a

Name

Class

% PVKCYT

PPV/PPLP/PELPK Repeats

Amino Acids

Pfamb

SPc

GPI

Organ/issue - Specific Expressiond

Arabidopsis HRGP BLAST Hits

Poplar HRGP BLAST Hitse

Potri.004G168600 (POPTR 0004 s17590)

PtPRP1

PRP

64 %

24/8/0

554

PF01190.15

Y

N

Dark etiolated seedlings

AtPRP2, AtPRP1, AtPRP11

PtPRP6, PtPRP32, PtPRP33, PtPRP143, Potri.016G006200

Potri.016G015500 (POPTR_0016s01720)

PtPRP2

PRP

70 %

13/0/0

449

PF14547.4

Y

N

Dark and +3 h light etiolated seedlings

AtPRP18, AtPEX4

Potri.012G076700, Potri.015G071500, Potri.019G083900, Potri.T155100, Potri.005G239100

Potri.014G126200 (POPTR 0014 s12100)

PtPRP3

PRP

51 %

0/0/0

372

PF01190.15

Y

N

 

AtPRP9, AtPRP10

PtPRP24, PtPRP22, PtPRP28, PtPRP26, PtPRP21

Potri.014G126500 (POPTR_0014s12120)

PtPRP4

PRP

52 %

0/0/0

366

PF01190.15

Y

N

 

AtPRP7, AtPRP3, AtPRP1, AtAGP30I, AtAGP31I

PtPRP35, PtPRP3, PtPRP4, Potri.014G126300, PtPRP39

Potri.018G126000 (POPTR 0018 s12630)

PtPRP5

PRP

62 %

15/9/0

310

PF14547.4

Y*

N

 

AtPRP9, AtPRP10, AtPERK15

PtPRP44, PtPRP42, PtPRP41, PtPRP43, Potri.011G060200

Potri.009G129900 (POPTR 0009 s13250)

PtPRP6

PRP

48 %

2/1/0

283

PF01190.15

Y*

N

 

AtPRP9, AtPRP10, AtPRP1

Potri.019G082700, PtPRP21, PtPRP26, PtPRP18, PtPRP28

Potri.003G111300 (POPTR 0003 s11060)

PtPRP7

PRP

46 %

4/1/0

234

PF14547.4

Y*

N

Male catkins

AtPRP9, AtPRP10, AtPRP15

PtPRP27, PtPRP30, PtPRP21, PtPRP26, PtPRP22

Potri.006G008300

PtPRP8

PRP

59 %

8/0/0

234

PF14547.4

Y

N

 

AtPRP9, AtPRP10

PtPRP49, PtPRP26, PtPRP22, PtPRP23, PtPRP24

Potri.T162800 (POPTR 0006 s01030)

PtPRP9

PRP

50 %

2/0/0

216

PF14547.4

Y

N

 

AtPRP9, AtPRP10

PtPRP48, PtPRP26, PtPRP22, PtPRP28, PtPRP23

Potri.006G008600

PtPRP10

PRP

53 %

4/0/0

214

PF14547.4

Y

N

Young leaf

AtPRP16, AtPRP14, AtPRP17, AtPRP15, AtHAE4

PtPRP15, PtPRP13, PtPRP5, PtPRP11, Potri.018G025900

Potri. 002G201800 (POPTR 0002 s20290)

PtPRP34

PRP

37 %

0/0/0

213

PF01190.15

Y

N

Young leaf, male catkins

AtPRP9, AtPRP10

PtPRP22, PtPRP23, PtPRP26, PtPRP24, PtPRP29

Potri. 017G145800 (POPTR 0017 s01230)

PtPRP35

PRP

42 %

0/0/0

272

PF01190.15

Y

N

 

AtPRP9, AtPRP10

PtPRP22, PtPRP26, PtPRP21, PtPRP23, PtPRP24

Potri. 001G060500 (POPTR_0001s13450)

PtPRP38

PRP

39 %

0/7/0

332

PF01190.15

Y

N

Dark and +3 h light etiolated seedlings

AtPRP11, AtAGP31I, AtPRP1

PtPRP33, PtPRP36, Potri.001G326200, Potri.017G068400, PtPRP38

Potri. 003G167100 (POPTR_0003s16550)

PtPRP40

PRP

39 %

0/2/0

299

PF01190.15

Y

N

Female catkins

AtPRP7, AtPRP1, AtPRP3, AtAGP30I, AtAGP31I

PtPRP34, PtPRP4, PtPRP3, Potri.014G126300, PtPRP39

Potri.007G114400

PtPRP44

PRP

43 %

0/1/10

275

 

Y

N

Roots

AtPRP7, AtPRP3, AtPRP1, AtAGP30I, AtAGP31I

PtPRP34, PtPRP35, PtPRP4, PtPRP3, Potri.014G126300

Potri. 013 G111600 (POPTR 0013 s11600)

PtPRP46

PRP

39 %

0/4/0

216

 

Y

N

 

AtPRP9, AtPRP10, AtPERK5

PtPRP45, PtPRP44, PtPRP42, PtPRP43, PtPRP28

Potri.006G065500 (POPTR 0006 s06430)

PtPRP11

PR Peptide

56 %

5/2/0

198

PF14547.4

Y

N

Dark and +3 h light etiolated seedlings

AtPRP7, AtPRP3, AtPRP1, AtAGP30I, AtPRP9

PtPRP4, PossiblePtPRP6, Potri.002G201700, PtPRP34, PtPRP35

Potri.001G350600 (POPTR_0001s34750)

PtPRP12

PR Peptide

63 %

6/0/0

191

PF02704.12

Y

N

 

AtPRP7, AtPRP3, AtPRP1, AtPRP9, AtAGP30I

PtPRP3, PossiblePtPRP6, Potri.002G201700, PtPRP34, PtPRP35

Potri.T162900 (POPTR_0006s01020)

PtPRP13

PR Peptide

52 %

4/0/0

184

PF14547.4

Y

N

Young leaf

AtPRP15, AtPRP14, AtPRP17, AtPRP2, AtPRP1

PtPRP11, PtPRP7, PtPRP13, PtPRP15, PtPRP8

Potri.010G072200 (POPTR 0010 s08290)

PtPRP14

PR Peptide

50 %

6/0/0

179

PF02095.13

Y

N

Mature leaf

AtPRP2, AtPRP4, AtPRP11

PtPRP1.8, PtPRP32, PtPRP33, PtPRP36, Potri.005G041400

Potri.006G008500

PtPRP15

PR Peptide

53 %

4/0/0

179

PF14547.4

Y

N

Roots

AtPRP14, AtPRP15, AtPRP16, AtPRP17

PtPRP11, PtPRP5, PtPRP2, PtPRP13, PtPRP15

Potri.007G113900 (POPTR_0007s03420)

PtPRP16

PR Peptide

47 %

0/4/0

130

 

Y

N

 

AtPRP16, AtPRP17, AtPRP15, AtPRP14, AtHAE4

PtPRP15, PtPRP13, PtPRP9, PtPRP2, PtPRP11

Potri.007G114100 (POPTR_0007s03400)

PtPRP17

PR Peptide

46 %

0/3/0

119

 

Y

N

 

AtPRP16, AtPRP17, AtPRP14, AtPRP15, AtHAE4

PtPRP10, PtPRP13, PtPRP8, PtPRP2, PtPRP11

Potri.007G113700 (POPTR_0007s03440)

PtPRP18

PR Peptide

47 %

0/4/0

119

 

Y

N

 

AtPRP16, AtPRP17, AtPRP14, AtPRP15, AtAGP30I

PtPRP9, PtPRP13, PtPRP8, PtPRP2, PtPRP15

Potri.017G047400 (POPTR_0017s07470)

PtPRP19

PR Peptide

46 %

0/3/0

113

 

Y

N

Dark etiolated seedlings, light-grown seedling

AtPRP15, AtPRP14, AtPRP17, AtPRP2

PtPRP5, PtPRP7, PtPRP13, PtPRP15, PtPRP8

Potri.019G082600 (POPTR_0019s11220)

PtPRP20

PR Peptide

45 %

0/4/0

112

 

Y

N

light-grown seedling

AtPRP16, AtPRP17, AtPRP14, AtPRP15, AtHAE4,

PtPRP15, PtPRP8, PtPRP10, PtPRP9, PtPRP11

Potri.017G047200 (POPTR_0017s07450)

PtPRP21

PR Peptide

43 %

0/3/0

130

 

Y

N

Young leaf, male catkins

AtPRP1, AtPRP2, AtPEX4

Potri.004G110100, Potri.010G211100, Potri.004G109000, Potri.T018900, Potri.004G109900

Potri.017G045800 (POPTR_0017 s07310)

PtPRP22

PR Peptide

43 %

0/3/0

116

 

Y

N

 

AtPRP16, AtPRP17, AtPRP14, AtPRP15, AtHAE4, AtPERK5

PtPRP13, PtPRP10, PtPRP2, PtPRP9, PtPRP11

Potri.017G046700 (POPTR 0017 s07400)

PtPRP23

PR Peptide

40 %

0/3/0

116

 

Y

N

 

AtPRP9, AtPRP10, AtPRP15

PtPRP21, PtPRP26, PtPRP31, Potri.017G046800, PtPRP27

Potri.017G046400 (POPTR 0017 s07370)

PtPRP24

PR Peptide

43 %

0/3/0

116

 

Y

N

Roots

AtPRP9, AtPRP10

PtPRP21, PtPRP30, PtPRP27, Potri.017G046800, PtPRP18

Potri.017G045900 (POPTR 0017 s07320)

PtPRP25

PR Peptide

43 %

0/3/0

116

 

Y

N

 

AtPRP9, AtPRP10, AtPRP15

PtPRP19, PtPRP21, PtPRP27, PtPRP30, Potri.017G046800

Potri.017G047000 (POPTR_0017 s07430)

PtPRP26

PR Peptide

42 %

0/3/0

116

 

Y

N

 

AtPRP9, AtPRP10

PtPRP18, PtPRP21, Potri.017G046800, PtPRP27, PtPRP30

Potri.017G047100

PtPRP27

PR Peptide

44 %

0/4/0

134

 

Y

N

Female catkins

AtPRP9, AtPRP10, AtPRP15

PtPRP21, PtPRP18, PtPRP26, PtPRP37, PtPRP19

Potri.017G045600 (POPTR 0017 s07290)

PtPRP28

PR Peptide

44 %

0/3/0

126

 

Y

N

Roots

AtPRP9, AtPRP10

PtPRP30, Potri.017G046800, PtPRP27, PtPRP18, PtPRP17

Potri.017G046100 (POPTR 0017 s07340)

PtPRP29

PR Peptide

42 %

0/3/0

116

 

Y

N

 

AtPRP9, AtPRP10

PtPRP26, PtPRP25, PtPRP24, PtPRP23, PtPRP29

Potri.T178800 (POPTR 2000 s00200)

PtPRP30

PR Peptide

42 %

0/4/0

135

 

Y

N

Xylem

AtPRP9, AtPRP10

PtPRP22, PtPRP23, PtPRP26, PtPRP21, PtPRP28

Potri.007G114200 (POPTR 0007 s03390)

PtPRP31

PR Peptide

44 %

0/4/0

121

 

Y

N

 

AtPRP9, AtPRP10

PtPRP22, PtPRP26, PtPRP21, PtPRP23, PtPRP28

Potri. 017G045000

PtPRP37

PR Peptide

40 %

0/3/0

105

 

Y

N

Roots

AtPRP9, AtPRP10, AtPRP15

PtPRP16, PtPRP21, PtPRP26, Potri.017G046800, PtPRP27

Potri. 002G201900 (POPTR_0002s20300)

PtPRP39

PR Peptide

33 %

0/0/0

179

PF01190.15

Y

N

 

AtPRP11, AtAGP31I, AtPRP1

PtPRP32, PtPRP36, Potri.001G326200, Potri.017G068400, PtPRP38

Potri. 017G044800 (POPTR_0017s07230)

PtPRP41

PR Peptide

34 %

0/1/3

112

 

Y

N

Young leaf, male catkins

AtPRP11, AtPRP1, AtAGP31I, AtPRP2

PtPRP32, Potri .001G326200, Potri.017G068400, PtPRP38, PtPRP40

Potri. 017G044900

PtPRP42

PR Peptide

39 %

0/0/5

109

 

Y

N

 

AtPRP9, AtPRP10

PtPRP26, PtPRP21, PtPRP22, PtPRP28, PtPRP23

Potri. 018G146200

PtPRP43

PR Peptide

42 %

0/1/2

114

 

Y

N

Young leaf

AtPRP9

PtPRP40, Potri.017G068400, Potri.001G326200, PtPRP32, PtPRP33

Potri.007G114700 (P0PTR_0007s03340)

PtPRP45

PR Peptide

38 %

0/0/4

107

 

Y

N

 

AtPRP11

PtPRP38, Potri.017G068400, Potri.001G326200, PtPRP33, PtPRP32

Potri. 017G046800 (POPTR 0017 s07440)

PtPRP47

PR Peptide

41 %

0/5/0

174

 

Y*

N

 

AtPRP9, AtPRP10, AtPEX2

PtPRP45, PtPRP44, PtPRP43, PtPRP41, PtPRP18

Potri. 017G045700 (POPTR 0017 s07300)

PtPRP48

PR Peptide

38 %

0/2/0

97

 

Y

N

 

AtPRP9, AtPRP10

PtPRP44, PtPRP45, PtPRP42, PtPRP41, PtPRP37

Potri. 017G046500 (POPTR 0017 s07380)

PtPRP49

PR Peptide

38 %

0/3/0

97

 

Y*

N

 

AtPRP10, AtPRP9, AtPEX2

PtPRP45, PtPRP43, PtPRP42, PtPRP41, Potri.017G052100

Potri. 004G114300 (POPTR 0004 s11300)

PtPRP32I

Chimeric

41 %

2/5/0

319

PF01190.15

Y

N

 

AtPRP9, AtPRP10

PtPRP22, PtPRP21, PtPRP23, PtPRP28, PtPRP24

Potri. 004G114400

PtPRP33I

Chimeric

41 %

0/6/0

365

PF01190.15

Y

N

 

AtPRP9, AtPRP10

PtPRP30, Potri.017G046800, PtPRP21, PtPRP17, PtPRP18

Potri. 017G100600 (POPTR_0017s13490)

PtPRP36I

Chimeric

43 %

0/5/0

410

PF01190.15

Y

N

 

AtPRP9, AtPRP10

PtPRP27, PtPRP21, Potri.017G046800, PtPRP17, PtPRP18

  1. a Protein identifiers of the version 2.0 are shown in the parenthesis. Italics indicates a protein that was identified only by a BLAST search
  2. b The domains indicated by the Pfam number are: PF01190.15, Pollen_Ole_e_I domain (Pollen proteins Ole e I like); PF14547.4, Hydrophob_seed domain (Hydrophobic seed protein); PF02704.12, GASA domain (Gibberellin regulated protein); PF02095.13, Extensin_1 domain (Extensin-like protein repeat)
  3. c Asterisk indicates a protein that is predicted to have a signal peptide either using the sensitive mode in the SignalP website or only if amino acids at the N terminus are discarded
  4. d Expression data are shown only when available at http://bar.utoronto.ca/efppop/cgi-bin/efpWeb.cgi
  5. e A locus ID indicates that it is not identified as an HRGP