Table 3.
Identification and analysis of EXT genes in Populus trichocarpa
| Locus Identifier 3.0 (ID 2.0)a | Name | Class | SP3/SP4/SP5/YXY Repeats | Amino Acids | Pfamb | SPc | GPI | Organ/issue-specific Expression11 | Arabidopsis HRGP BLAST Hits | Poplar HRGP BLAST Hitse |
|---|---|---|---|---|---|---|---|---|---|---|
| Potri.018G050100 (POPTR 0018 s05480) | PtEXT1 | Classical EXT | 1/6/4/5 | 190 | PF04554.11 | Y | N | Young leaf | AtEXT22, AtEXT21 | Potri.001G201800 |
| Potri.001G019700 (POPTR 0001 s05720) | PtEXT2 | Classical EXT | 1/21/0/11 | 213 | Y | N | AtEXT3/5 | PtEXT8 | ||
| Potri.001G122100 (POPTR_0001 s00420) | PtEXT3 | Classical EXT | 2/5/6/0 | 238 | PF14547.4 | Y | N | Male catkins | AtPRP16, AtPRP15, AtPRP14, AtHAE4 | Potri.013G128800, Potri.002G200100, Potri.018G025900, Potri.001G158400, Potri.014G059800 |
| Potri.001G259600 (POPTR 0001 s26690) | PtEXT4 | Classical EXT | 2/8/2/0 | 500 | Y | N | AtAGP51C | PtEXT7, AGP6C, AGP43P | ||
| Potri.001G020100 (POPTR 0001 s05740) | PtEXT5 | Classical EXT | 1/22/0/13 | 257 | Y | N | None | PtEXT6, PtEXT8 | ||
| Potri.001G019900 | PtEXT6 | Classical EXT | 1/25/0/14 | 259 | Y* | N | None | PtEXT8, PtEXT5 | ||
| Potri.001G260200 (POPTR_0001 s26680) | PtEXT7 | Classical EXT | 4/6/1/0 | 222 | Y | N | None | AGP43P, AGP6C, PtEXT4, Potri.003G074200 | ||
| Potri.001G020000 | PtEXT8 | Classical EXT | 1/23/0/16 | 267 | Y* | N | AtEXT3/5 | PtEXT6, PtEXT5 | ||
| Potri.010G001200 (POPTR_0010s003 50) | PtEXT9 | Short EXT | 1/6/0/3 | 174 | Y | Y | AtEXT37, AtEXT41 | PtEXT24, Potri.008G129200, Potri.010G128900, Potri.008G117500, FLA21 | ||
| Potri.010G113300 (POPTR_0010s12360) | PtEXT10 | Short EXT | 0/2/0/0 | 131 | Y | N | AtEXT31, AtEXT33 | PtEXT23, Potri.006G106800, Potri.005G033000, Potri.001G371600, PossiblePtEXT5 | ||
| Potri.T091000 | PtEXT11 | Short EXT | 1/1/0/0 | 106 | Y | N | None | PtEXT12, PtEXT19, Potri.005G079400 | ||
| Potri.013G045700 (POPTR 0013 s04290) | PtEXT12 | Short EXT | 1/1/0/0 | 111 | Y | N | None | PtEXT11, PtEXT19 | ||
| Potri.003G064900 (POPTR_0003 s063 50) | PtEXT13 | Short EXT | 1/1/3/0 | 167 | Y | N | AtEXT32, AtAGP57C, AtPERK5 | PtEXT26, Potri.009G013500, Potri.006G276200 | ||
| Potri.006G225400 (POPTR_0006s24190) | PtEXT14 | Short EXT | 2/0/1/3 | 186 | Y | Y | Male catkins, roots | AtEXT38, AtEXT7 | Potri.015G147200, Potri.008G168300, Potri.010G094700, Potri.012G144400, PtFH2 | |
| Potri.002G070100 | PtEXT15 | Short EXT | 0/1/2/2 | 102 | Y | N | AtEXT3/5, AtEXT1/4, AtEXT22 | PtEXT20, Potri.017G110900, PtEXT1, PtLRX3 | ||
| Potri.019G015900 (POPTR_0019s03210) | PtEXT16 | Short EXT | 0/2/0/0 | 108 | Y | N | None | PtEXT18, PtEXT33, PtEXT17, Potri.019G015700, Potri.T139100 | ||
| Potri.019G015800 (POPTR_0019s03200) | PtEXT17 | Short EXT | 0/2/0/0 | 107 | Y | N | Male catkins | None | PtEXT33, PtEXT18, PtEXT16, Potri.T139100, Potri.019G015700 | |
| Potri.019G016000 | PtEXT18 | Short EXT | 0/2/0/0 | 116 | Y | N | None | PtEXT16, PtEXT33, PtEXT17, Potri.019G015700, Potri.T139100 | ||
| Potri.019G017300 (POPTR_0019s03400) | PtEXT19 | Short EXT | 0/2/0/0 | 110 | Y* | N | Dark etiolated seedlings | AtPERK6, AtAGP45P | PtEXT11, PtEXT12, Potri.005G257000, Potri.010G244800, Potri.006G136900 | |
| Potri.005G190100 | PtEXT20 | Short EXT | 1/2/0/2 | 115 | Y | N | AtEXT3/5, AtEXT1/4, AtPRP3, AtPRP1 | Potri.019G083200, Potri.013G112500, PtLRX3, Potri.007G090300, Potri.005G077700 | ||
| Potri.014G124700 | PtEXT21 | Short EXT | 0/2/0/0 | 168 | Y | N | AtEXT34, AtEXT41, AtPERK3, AtPERK5 | Potri.015G147200, Potri.012G144400, Potri.001G371600, Potri.004G143700, PtFH2 | ||
| Potri.T082000 | PtEXT22 | Short EXT | 1/1/1/0 | 177 | Y* | N | None | PtAEH4, PtEXT28, PtEXT27, Potri.001G042100, Potri.008G043900 | ||
| Potri.008G129100 (POPTR_0008s12800) | PtEXT23 | Short EXT | 0/3/0/0 | 155 | Y | Y | Female catkins, xylem | AtEXT31, AtEXT33, AtPAG10 | PtEXT10, Potri.010G094700, Potri.015G147200, Potri.006G163700, Potri.018G086100 | |
| Potri.008G213600 (POPTR_0008s22980) | PtEXT24 | Short EXT | 0/1/1/2 | 172 | Y | Y | Male catkins | AtEXT37, AtPERK6, AtEXT41 | PtEXT9, Potri.008G129200, PossiblePtEXT15, Potri.010G094700, Potri.004G143700 | |
| Potri.008G125400 (POPTR_0008s12430) | PtEXT25 | Short EXT | 2/0/0/0 | 80 | Y* | N | None | Potri.005G239200, Potri.010G094700, Potri.010G006800, Potri.002G189300, Potri .005G239200 | ||
| Potri.001G169200 (POPTR 0001 s16930) | PtEXT26 | Short EXT | 0/0/2/0 | 147 | Y | N | None | PtEXT13, Potri.010G006800 | ||
| Potri.001G042200 (POPTR 0001 s03370) | PtEXT27 | Short EXT | 2/2/0/1 | 177 | Y | N | None | PtEXT28, PtEXT22, PtAEH4, Potri.001G042100, Potri.001G316500 | ||
| Potri.T179500 (POPTR_0523s00220) | PtEXT28 | Short EXT | 1/0/1/0 | 176 | Y* | N | None | PtAEH4, PtEXT22, PtEXT27, Potri.001G042100, Potri.005G030300 | ||
| Potri.T101300 (POPTR_0017 s06820) | PtEXT29 | Short EXT | 0/2/0/0 | 151 | Y* | N | AtAGP56C | Potri.007G120100, Potri.002G054100, Potri.001G371600, Potri.015G147200, Potri.002G235500 | ||
| Potri.T139000 | PtEXT33 | Short EXT | 0/1/0/0 | 107 | Y | N | None | PtEXT17, PtEXT18, PtEXT16, Potri.019G015700, Potri.T139100 | ||
| Potri.009G108100 (POPTR_0009s 11130) | PtLRX1 | Chimeric | 5/16/6/1 | 982 | PF13855.4 | Y | N | Female catkins | AtPEX3, AtPEX1, AtPEX4, AtPEX2, AtLRX4 | PtLRX2, PtLRX10, PtLRX3, PtLRX6, PtLRX7 |
| Potri.004G146400 (POPTR_0004s15360) | PtLRX2 | Chimeric | 2/19/1/1 | 603 | PF13855.4 | Y | N | Male catkins | AtPEX3, AtPEX4, AtPEX1, AtPEX2, AtLRX4 | PtLRX1, PtLRX10, PtLRX3, PtLRX4, PtLRX7 |
| Potri.006G081200 | PtLRX3 | Chimeric | 2/1/3/0 | 584 | PF13855.4 PF08263.10 | Y* | N | AtLRX2, AtLRX1, AtLRX4, AtLRX3, AtLRX5 | PtLRX7, PtLRX6, PtLRX4, PtLRX2, PtLRX10 | |
| Potri.006G245600 (POPTR_0006s26190) | PtLRX4 | Chimeric | 2/2/5/1 | 549 | PF08263.10 | Y | N | Xylem | AtLRX4, AtLRX3, AtLRX5, AtLRX7, AtLRX6 | PtLRX8, PtLRX5, PtLRX9, PtLRX6, PtLRX3 |
| Potri.006G162300 (POPTR_0024s00730) | PtLRX5 | Chimeric | 2/3/3/0 | 569 | PF13855.4 | Y | N | Male catkins | AtLRX4, AtLRX3, AtLRX2, AtLRX1, AtPEX4 | PtLRX9, PtLRX6, PtLRX4, PtLRX8, PtLRX3 |
| Potri.018G075900 (POPTR_0018s06150) | PtLRX6 | Chimeric | 1/2/5/0 | 509 | PF13855.4 | Y | N | Male catkins, young leaf, xylem | AtLRX3, AtLRX5, AtLRX2, AtLRX7, AtLRX1 | PtLRX5, PtLRX9, PtLRX4, PtLRX8, PtLRX3 |
| Potri.018G151000 (POPTR_0018s14790) | PtLRX7 | Chimeric | 1/6/1/0 | 481 | PF08263.10 PF13855.4 | Y | N | Male catkins | AtLRX2, AtLRX1, AtLRX4, AtLRX3, AtLRX5 | PtLRX3, PtLRX6, PtLRX5, PtLRX9, PtLRX4 |
| Potri.018G035100 (POPTR_0018s01010) | PtLRX8 | Chimeric | 0/3/2/1 | 496 | PF08263.10 | Y | N | Male catkins | AtLRX4, AtLRX3, AtLRX5, AtLRX7, AtLRX6 | PtLRX4, PtLRX6, Potri.010G083000, PtLRX3, PtLRX7 |
| Potri.T016600 (POPTR_0028s00200) | PtLRX9 | Chimeric | 2/3/4/0 | 573 | PF13855.4 | Y | N | Male catkins | AtLRX4, AtLRX3, AtLRX2, AtLRX1, AtPEX4 | PtLRX5, PtLRX6, PtLRX8, PtLRX3, PtLRX7 |
| Potri.014G036700 (POPTR_0014s03600) | PtLRX10 | Chimeric | 1/5/1/1 | 474 | PF13855.4 | Y | N | Male catkins | AtPEX3, AtPEX1, AtPEX4, AtPEX2, AtLRX4 | PtLRX2, PtLRX1, PtLRX3, PtLRX7, Potri.007G139200 |
| Potri.010G041400 (POPTR_0010s05110) | PtPERK1 | Chimeric | 5/0/2/1 | 700 | PF07714.15 | N | N | AtPERK13, AtPERK12, AtPERK11, AtPERK10, AtPERK8 | PtPERK11,PtPERK3, PtPERK6, PtPERK3, PtPERK12 | |
| Potri.010G132900 (POPTR_0010s14290) | PtPERK2 | Chimeric | 5/4/2/1 | 765 | PF00069.23 | N | N | AtPERK8, AtPERK13, AtPERK1, AtPERK15, AtPERK4 | PtPERK12, PtPERK11, PtPERK1, PtPERK8, PtPERK10 | |
| Potri.017G110400 (POPTR_0017s14140) | PtPERK3 | Chimeric | 5/5/0/1 | 724 | PF07714.15 | N | N | Dark etiolated and light-grown seedlings | AtPERK8, AtPERK10, AtPERK13, AtPERK12, AtPERK3 | PtPERK6, PtPERK12, PtPERK2, PtPERK1, PtPERK11 |
| Potri.009G115200 (POPTR_0009s 11810) | PtPERK4 | Chimeric | 1/6/2/1 | 649 | PF07714.15 | N | N | Male catkins | AtPERK5, AtPERK4, AtPERK15, AtPERK3, AtPERK13 | PtPERK10, PtPERK9, PtPERK8, Potri.001G183000, Potri.T140000 |
| Potri.004G153600 (POPTR_0004s16100) | PtPERK5 | Chimeric | 3/3/3/1 | 656 | PF07714.15 | N | N | AtPERK5, AtPERK7, AtPERK4, AtPERK6, AtPERK15 | PtPERK4, PtPERK10, PtPERK9, PtPERK8, Potri.001G183000 | |
| Potri.004G105200 (POPTR_0004s10490) | PtPERK6 | Chimeric | 6/4/0/2 | 724 | PF07714.15 | N | N | Dark etiolated seedlings | AtPERK10, AtPERK12, AtPERK13, AtPERK3, AtPERK15 | PtPERK3, PtPERK2, PtPERK1, PtPERK11, PtPERK10 |
| Potri.006G242800 | PtPERK7 | Chimeric | 2/0/0/1 | 706 | PF07714.15 | N | N | AtPERK1, AtPERK5, AtPERK14, AtPERK15, AtPERK3 | PtPERK10, PtPERK9, Potri.001G183000, Potri.003G053300, Potri.T140000 | |
| Potri.018G081300 (POPTR_0018s08800) | PtPERK8 | Chimeric | 0/2/2/0 | 672 | PF07714.15 | N | N | Xylem | AtPERK1, AtPERK4, AtPERK5, AtPERK15, AtPERK6 | Potri.001G183000, PtPERK10, PtPERK9, Potri.003G053300, PtPERK5 |
| Potri.007G027000 (POPTR_0007s12680) | PtPERK9 | Chimeric | 2/3/5/1 | 639 | PF07714.15 | N | N | AtPERK5, AtPERK7, AtPERK6, AtPERK15, AtPERK13 | PtPERK10, PtPERK8, PtPERK5, Potri.003G053300, Potri.T140000 | |
| Potri.005G124400 (POPTR_0005s12590) | PtPERK10 | Chimeric | 2/1/5/0 | 592 | PF07714.15 | N | N | Female catkins, male catkins | AtPERK4, AtPERK5, AtPERK7, AtPERK6, AtPERK1 | PtPERK9, PtPERK8, PtPERK5, PtPERK4, Potri.001G183000 |
| Potri.008G189700 (POPTR_0008s19400) | PtPERK11 | Chimeric | 5/3/1/1 | 733 | PF07714.15 | N | N | Male catkins | AtPERK13, AtPERK11, AtPERK8, AtPERK10, AtPERK15 | PtPERK1, PtPERK3, PtPERK6, PtPERK12, PtPERK2 |
| Potri.008G111600 (POPTR_0008s11080) | PtPERK12 | Chimeric | 0/6/2/1 | 728 | PF07714.15 | N | N | AtPERK13, AtPERK1, AtPERK5, AtPERK15, AtPERK3 | PtPERK2, PtPERK1, PtPERK8, PtPERK11, Potri.001G183000 | |
| Potri.003G103800 (POPTR_0003 s10280) | PtFH1 | Chimeric | 1/0/2/0 | 1226 | PF02181.21 PF10409.7 | N | N | Female catkins, male catkins | None | Potri.018G019600, PtFH5, Potri.018G108000, Potri.006G263700, Potri.015G061000 |
| Potri.011G131700 (POPTR 0011 s13510) | PtFH2 | Chimeric | 1/0/2/0 | 987 | PF02181.21 | Y | N | Roots | None | Potri.001G416100, Potri.007G119900, Potri.007G054900, PtFH4, Potri.017G009900 |
| Potri.002G240200 (POPTR_0002s24130) | PtFH3 | Chimeric | 1/0/1/0 | 1066 | PF02181.21 | Y | N | Young leaf, male catkins | None | PtFH4, Potri.007G140200, Potri.017G009900, Potri.007G054900, Potri.013G017900 |
| Potri.014G174700 (POPTR_0014s17310) | PtFH4 | Chimeric | 0/0/2/0 | 1071 | PF02181.21 | Y | N | Roots, light-grown seedling | AtPERK5 | PtFH3, Potri.007G140200, Potri.017G009900, Potri.007G054900, Potri.013G017900 |
| Potri.012G067900 (POPTR_0012s06980) | PtFH5 | Chimeric | 0/0/2/0 | 1400 | PF10409.7 PF02181.21 | N | N | Xylem, male catkins | None | Potri.015G061000, Potri.018G019600, Potri.006G185500, Potri.018G108000, PtFH1 |
| Potri.009G145700 (POPTR_0009s14810) | PtEXT30 | Chimeric | 5/0/0/0 | 467 | PF06830.9 | Y | N | Male catkins, roots | AtEXT51 | Potri.009G097400, Potri.012G145400, Potri.011G127900, Potri.009G012600, Potri.009G012500 |
| Potri.014G115700 (POPTR_0014s11110) | PtEXT31 | Chimeric | 8/0/0/0 | 526 | PF00295.15 | Y* | N | Roots | None | Potri.002G190600, Potri.005G005500, Potri.013G005000, Potri.010G152000, Potri.008G100500 |
| Potri.011G066900 (POPTR_0011s07300) | PtEXT32 | Chimeric | 0/1/2/2 | 498 | PF00112.21 PF00396.16 PF08246.10 | Y | N | Female catkins, male catkins | AtAGP4C | Potri.011G066800, Potri.004G057700, Potri.005G232900, Potri.014G024100, Potri.001G302100 |
| Potri.004G024500 | PtAEH1 | AGP EXT Hybrid | 0/1/1/1 | 673 | PF01657.15 PF07714.15 | Y | N | None | Potri.004G024600, PtAEH2, Potri.004G025800, Potri.011G028400, Potri.004G025900 | |
| Potri.004G024800 | PtAEH2 | AGP EXT Hybrid | 0/1/1/1 | 678 | PF01657.15 PF07714.15 | Y | N | None | Potri.004G024600, Potri.004G025800, PtAEH1, Potri.011G028400, Potri.004G025900 | |
| Potri.003G082300 (POPTR_0003 s08030) | PtAEH3 | AGP EXT Hybrid | 2/0/0/0 | 188 | Y* | Y | Dark and light-grown seedlings, young leaf | AtPRP1 | Potri.005G191900, Potri.016G025300, Potri.004G162500, PossibleHybrid2, Potri.015G147200 | |
| Potri.003G184500 | PtAEH4 | AGP EXT Hybrid | 1/1/1/0 | 177 | Y* | N | None | PtEXT22, PtEXT28, PtEXT27, Potri.001G042100, Potri.019G047600 |
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
b The domains indicated by the Pfam number are: PF04554.11, Extensin_2 domain (Extensin-like region); PF14547.4, Hydrophob_seed domain (Hydrophobic seed protein); PF13855.4, LRR_8 domain (Leucine rich repeat); PF08263.10, LRRNT_2 domain (Leucine rich repeat N-terminal domain); PF07714.15, Pkinase_Tyr domain (Protein tyrosine kinase); PF00069.23, Pkinase domain (Protein kinase domain); PF02181.21, FH2 domain (Formin Homology 2 Domain); PF10409.7, PTEN_C2 domain (C2 domain of PTEN tumour-suppressor protein); PF06830.9, Root_cap domain (Root cap); PF00295.15, Glyco_hydro_28 domain (Glycoside hydrolase family 28); PF00112.21, Peptidase_C1 domain (Papain family cysteine protease); PF00396.16, Granulin domain (Granulin); PF08246.10, Inhibitor_I29 domain (Cathepsin propeptide inhibitor domain); PF01657.15, Stress-antifung domain (Salt stress response/antifungal); PF07714.15, Pkinase_Tyr domain (Protein tyrosine kinase)
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
d Expression data are shown only when available at http://bar.utoronto.ca/efppop/cgi-bin/efpWeb.cgi
e A locus ID indicates that it is not identified as an HRGP