Doc-Alignment

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Cucurbitales genomes. We used V.vinifera as a reference, and by comparing homologous gene locus maps and Ks values between V.vinifera and other Cucurbitales, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created a hierarchical lists of homologous genes using V.vinifera as a reference.
  The relevant gene ids can be obtained from the Cucurbitales blast and match under the Tools module. This link is Cucurbitales blast and match.

Orthogroup analysis platform
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Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi5g749 . . . . . Bpe14g01271 . . . . . Cma14g01829 . Car14g01641 . . Cpe03g01532 Bhi01g00705 . . . . . . . . . . . . . Cone14ag0166 Cone15ag0176 . . . . . Cme06g00470 . . . Bda13g00047 . . Bma02g00759 . . . Cmo14g01870 . . . . . . . . . . . . . Cla05g00426 Cam05g0463 Cec05g0471 Cco05g0472 Clacu05g0460 Cmu05g0439 Cre05g0500 . Csa03g01188 Chy06g00452 .
Vvi5g750 Blo01g00297 . . . . . . Bma05g01247 Cmo08g01045 Cmo17g00150 . . . . . . . . . . . . . . Cla06g00680 Cam06g0733 Cec06g0740 Cco06g0749 Clacu06g0725 Cmu06g0709 Cre06g1483 . . . . . Csa02g01043 Chy05g00306 . . . . . Bpe05g01101 . . . Sed04g2009 . . Cma08g01072 Cma17g00150 Car08g00945 Car17g00132 Cpe12g00127 Cpe17g00206 Bhi12g01590 Tan06g2386 Cmetu05g1606 . . . Lcy13g0392 . . . . . . . Lsi09g01218 . . Cme05g00588
Vvi5g751 Blo01g00063 Blo12g00141 Bda03g01090 . Bpe04g00988 . Bma04g01015 Bma05g01248 . . Cma06g01306 Cma14g01830 Car06g01120 . . Cpe08g00349 Cpe03g01533 . . . . . . . . . . . . . . . . . . Lsi05g01752 . . Cme06g00469 . . . . Bpe05g01102 . . . . Cmo06g01313 Cmo14g01871 . . . . . . . . . . . . . Cla05g00425 Cam05g0462 Cec05g0470 Cco05g0471 Clacu05g0459 Cmu05g0438 Cre05g0499 . Csa03g01187 Chy06g00451 .
Vvi5g752 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g753 . . . . . . . . . . . Cma14g01831 . Car14g01642 Sed12g0452 . Cpe03g01534 Bhi01g00696 Tan10g0654 Cmetu06g1756 . Hepe05g1678 . . . . . . . . . . . . Cone4ag0351 Lsi05g01753 . . . . Blo07g00277 . . . . . Bma06g01611 . . Cmo14g01872 . . . . . . . . . . . . . . . . . . . . . Csa03g01186 Chy06g00450 .
Vvi5g754 . . . . . Bpe14g01272 . . Cmo08g01044 . . Cma14g01833 . . . Cpe08g00350 Cpe03g01535 Bhi01g00691 . . . . . Lcy11g1693 Cla06g00681 Cam06g0734 Cec06g0742 Cco06g0750 Clacu06g0727 Cmu06g0710 Cre06g1484 . Cone15ag0177 Cone7ag0340 Cone4ag0352 Lsi05g01758 Csa02g01042 . Cme06g00462 Blo02g00764 Blo07g00280 Bda11g00643 Bda13g00045 . Bpe13g00543 . Bma06g01612 . Cmo06g01312 Cmo14g01874 Cma08g01071 . Car08g00944 . . Cpe17g00207 Bhi12g01587 . . . . . Lcy13g0394 Cla05g00421 Cam05g0460 Cec05g0468 Cco05g0468 Clacu05g0457 Cmu05g0435 Cre05g0496 Lsi09g01216 Csa03g01183 Chy06g00445 Cme05g00591
Vvi5g755 . . . . . Bpe14g01273 . . . . Cma06g01302 Cma14g01835 Car06g01119 Car14g01643 Sed02g1443 Cpe08g00351 Cpe03g01536 Bhi01g00689 Tan10g0650 Cmetu06g2335 . Hepe05g1682 . Lcy11g1695 . . . . . . . Cone14ag0170 . . Cone4ag0354 Lsi05g01760 . . Cme06g00460 Blo02g00767 Blo07g00281 Bda11g00644 . . Bpe13g00542 Bma02g00757 Bma06g01613 . Cmo06g01311 Cmo14g01876 . . . . . . . . . . . . . Cla05g00419 Cam05g0457 Cec05g0464 Cco05g0466 Clacu05g0454 Cmu05g0432 Cre05g0493 . Csa03g01181 Chy06g00443 .
Vvi5g756 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g757 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g758 Blo01g00298 . . . . . . Bma05g01249 . Cmo17g00148 . . . . . . . . . . . . . . Cla06g00686 Cam06g0737 Cec06g0744 Cco06g0754 Clacu06g0728 Cmu06g0712 Cre06g1487 . . . . . Csa02g01039 Chy05g00303 . . . . . . . . . . . . . Cma17g00149 . Car17g00131 Cpe12g00126 . Bhi12g01580 . . . . . . . . . . . . . Lsi09g01208 . . Cme05g00595
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 10966835 10968922 - Bda017134.1 Bda03g01090 1090
11 6412551 6414891 + Bda005389.1 Bda11g00643 643
11 6415127 6418510 - Bda005390.1 Bda11g00644 644
13 662878 665131 - Bda000887.3 Bda13g00045 45
13 680848 681126 + Bda000889.1 Bda13g00047 47
1 12831028 12834808 + XM_039018312.1 Bhi01g00689 689
1 12849636 12856466 - XM_039019817.1 Bhi01g00691 691
1 13015020 13017414 + XM_039023919.1 Bhi01g00696 696
1 13046164 13047124 - XM_039029125.1 Bhi01g00705 705
12 51126707 51138354 - XM_039050795.1 Bhi12g01580 1580
12 51489802 51498217 - XM_039018831.1 Bhi12g01587 1587
12 51780015 51790540 + XM_039050815.1 Bhi12g01590 1590
1 783770 787159 - BLOR00063 Blo01g00063 63
1 3689233 3699333 - BLOR00297 Blo01g00297 297
1 3701909 3708528 + BLOR00298 Blo01g00298 298
2 25702531 25704766 + BLOR10494 Blo02g00764 764
2 25765045 25768420 - BLOR10497 Blo02g00767 767
7 3256053 3257431 - BLOR18209 Blo07g00277 277
7 3274127 3280836 + BLOR18212 Blo07g00280 280
7 3281290 3283245 - BLOR18213 Blo07g00281 281
12 9913032 9916515 + BLOR04160 Blo12g00141 141
2 38882733 38886101 + Bma015462.1 Bma02g00757 757
2 39225251 39225986 + Bma015466.1 Bma02g00759 759
4 17787782 17789908 - Bma019631.1 Bma04g01015 1015
5 51816172 51825638 - Bma022438.2 Bma05g01247 1247
5 51828241 51830140 - Bma022439.1 Bma05g01248 1248
5 51831197 51838117 + Bma022440.1 Bma05g01249 1249
6 52272317 52273433 - Bma024726.1 Bma06g01611 1611
6 52274397 52276665 + Bma031339 Bma06g01612 1612
6 52276917 52280304 - Bma024727.2 Bma06g01613 1613
4 6858825 6859651 + Bpe015656.1 Bpe04g00988 988
5 23413146 23419904 - Bpe018517.1 Bpe05g01101 1101
5 23422426 23424345 - Bpe018518.1 Bpe05g01102 1102
13 12714666 12718053 + Bpe010246.1 Bpe13g00542 542
13 12718293 12720637 - Bpe010247.1 Bpe13g00543 543
14 9616165 9616903 - Bpe014629.1 Bpe14g01271 1271
14 9624095 9626346 + Bpe025551 Bpe14g01272 1272
14 9626526 9629893 - Bpe014630.3 Bpe14g01273 1273
5 4087762 4091225 + CaPI482276_05g004570.1 Cam05g0457 457
5 4103601 4108942 - CaPI482276_05g004600.1 Cam05g0460 460
5 4121971 4124123 + CaPI482276_05g004620.1 Cam05g0462 462
5 4126152 4132119 + CaPI482276_05g004630.1 Cam05g0463 463
6 9891640 9900100 - CaPI482276_06g007330.1 Cam06g0733 733
6 9942756 9951193 + CaPI482276_06g007340.1 Cam06g0734 734
6 9996502 10006836 + CaPI482276_06g007370.1 Cam06g0737 737
6 8361585 8364692 + Carg06238-RA Car06g01119 1119
6 8372857 8375183 + Carg06237-RA Car06g01120 1120
8 6308537 6312762 - Carg10979-RA Car08g00944 944
8 6317151 6326799 + Carg10978-RA Car08g00945 945
14 13143307 13144480 - Carg16546-RA Car14g01641 1641
14 13144713 13151401 - Carg16545-RA Car14g01642 1642
14 13167358 13170647 - Carg16544-RA Car14g01643 1643
17 785150 795508 - Carg10101-RA Car17g00131 131
17 799298 808414 + Carg10100-RA Car17g00132 132
5 3746937 3750399 + CcPI632755_05g004660.1 Cco05g0466 466
5 3764530 3770045 - CcPI632755_05g004680.1 Cco05g0468 468
5 3783063 3785220 + CcPI632755_05g004710.1 Cco05g0471 471
5 3787184 3793392 + CcPI632755_05g004720.1 Cco05g0472 472
6 8549445 8558359 - CcPI632755_06g007490.1 Cco06g0749 749
6 8611804 8620699 + CcPI632755_06g007500.1 Cco06g0750 750
6 8692633 8695027 + CcPI632755_06g007540.1 Cco06g0754 754
5 3739126 3742588 + CePI673135_05g004640.1 Cec05g0464 464
5 3756341 3761762 - CePI673135_05g004680.1 Cec05g0468 468
5 3774919 3777066 + CePI673135_05g004700.1 Cec05g0470 470
5 3779105 3784820 + CePI673135_05g004710.1 Cec05g0471 471
6 8603770 8612143 - CePI673135_06g007400.1 Cec06g0740 740
6 8657930 8666705 + CePI673135_06g007420.1 Cec06g0742 742
6 8706418 8711721 + CePI673135_06g007440.1 Cec06g0744 744
5 2944412 2963002 - Chy5G093490.1 Chy05g00303 303
5 3034305 3044690 + Chy5G093520.1 Chy05g00306 306
6 2974961 2978436 + Chy6G109710.1 Chy06g00443 443
6 2983731 2987414 - Chy6G109730.1 Chy06g00445 445
6 3012624 3015656 + Chy6G109780.1 Chy06g00450 450
6 3016006 3018264 + Chy6G109790.1 Chy06g00451 451
6 3019597 3020285 + Chy6G109800.1 Chy06g00452 452
5 3796531 3799994 + ClG42_05g0045400.10 Clacu05g0454 454
5 3813074 3818407 - ClG42_05g0045700.10 Clacu05g0457 457
5 3830206 3832353 + ClG42_05g0045900.10 Clacu05g0459 459
5 3834404 3839881 + ClG42_05g0046000.10 Clacu05g0460 460
6 8453029 8461500 - ClG42_06g0072500.10 Clacu06g0725 725
6 8508247 8516435 + ClG42_06g0072700.10 Clacu06g0727 727
6 8541742 8557682 + ClG42_06g0072800.10 Clacu06g0728 728
5 3769075 3772538 + ClCG05G004090.2 Cla05g00419 419
5 3774484 3792040 - ClCG05G004110.1 Cla05g00421 421
5 3805435 3812937 + ClCG05G004140.2 Cla05g00425 425
5 3814522 3815966 + ClCG05G004160.1 Cla05g00426 426
6 8657280 8666734 - ClCG06G007140.1 Cla06g00680 680
6 8713400 8721725 + ClCG06G007150.1 Cla06g00681 681
6 8780190 8787045 + ClCG06G007170.1 Cla06g00686 686
6 8625438 8628818 + CmaCh06G013020.1 Cma06g01302 1302
6 8637860 8639725 + CmaCh06G013060.1 Cma06g01306 1306
8 6667823 6672381 - CmaCh08G010710.1 Cma08g01071 1071
8 6677079 6686700 + CmaCh08G010720.1 Cma08g01072 1072
14 13069123 13070926 - CmaCh14G018290.1 Cma14g01829 1829
14 13071254 13074197 - CmaCh14G018300.1 Cma14g01830 1830
14 13074538 13077164 - CmaCh14G018310.1 Cma14g01831 1831
14 13084711 13088458 + CmaCh14G018330.1 Cma14g01833 1833
14 13101363 13104844 - CmaCh14G018350.1 Cma14g01835 1835
17 730308 740129 - CmaCh17G001490.1 Cma17g00149 149
17 742914 752651 + CmaCh17G001500.1 Cma17g00150 150
5 5986935 5998336 - MELO3C023018.2.1 Cme05g00588 588
5 6065287 6070819 + MELO3C023022.2.1 Cme05g00591 591
5 6121655 6124603 + MELO3C027187.2.1 Cme05g00595 595
6 2916756 2923988 + MELO3C006388.2.1 Cme06g00460 460
6 2928224 2938164 - MELO3C006390.2.1 Cme06g00462 462
6 2958402 2965216 + MELO3C006399.2.1 Cme06g00469 469
6 2965890 2966895 + MELO3C006400.2.1 Cme06g00470 470
5 18017449 18027743 + PI0029158.1 Cmetu05g1606 1606
6 3186890 3189324 + PI0012777.1 Cmetu06g1756 1756
6 3145654 3150668 + PI0004856.1 Cmetu06g2335 2335
6 9809792 9812899 + CmoCh06G013110.1 Cmo06g01311 1311
6 9814897 9819653 - CmoCh06G013120.1 Cmo06g01312 1312
6 9822935 9825326 + CmoCh06G013130.1 Cmo06g01313 1313
8 6744568 6749135 - CmoCh08G010440.1 Cmo08g01044 1044
8 6753887 6763679 + CmoCh08G010450.1 Cmo08g01045 1045
14 14056535 14057777 - CmoCh14G018700.1 Cmo14g01870 1870
14 14058048 14062555 - CmoCh14G018710.1 Cmo14g01871 1871
14 14063304 14065580 - CmoCh14G018720.1 Cmo14g01872 1872
14 14073155 14076881 + CmoCh14G018740.1 Cmo14g01874 1874
14 14081631 14084920 - CmoCh14G018760.1 Cmo14g01876 1876
17 824156 831986 - CmoCh17G001480.1 Cmo17g00148 148
17 838374 847732 + CmoCh17G001500.1 Cmo17g00150 150
5 3632625 3636088 + CmPI595203_05g004320.1 Cmu05g0432 432
5 3641457 3646002 - CmPI595203_05g004350.1 Cmu05g0435 435
5 3666315 3668528 + CmPI595203_05g004380.1 Cmu05g0438 438
5 3670514 3676676 + CmPI595203_05g004390.1 Cmu05g0439 439
6 8265316 8273781 - CmPI595203_06g007090.1 Cmu06g0709 709
6 8320544 8328690 + CmPI595203_06g007100.1 Cmu06g0710 710
6 8386424 8393344 + CmPI595203_06g007120.1 Cmu06g0712 712
4 1606985 1608049 - Conep04aG0036300.1 Cone4ag0351 351
4 1610900 1614340 + Conep04aG0036400.1 Cone4ag0352 352
4 1618910 1622454 - Conep04aG0036600.1 Cone4ag0354 354
7 1484742 1487807 + Conep07aG0034800.1 Cone7ag0340 340
14 797492 798313 - Conep14aG0017000.1 Cone14ag0166 166
14 802003 805441 - Conep14aG0017400.1 Cone14ag0170 170
15 844326 845893 - Conep15aG0018000.1 Cone15ag0176 176
15 846241 848723 + Conep15aG0018100.1 Cone15ag0177 177
3 11955205 11956153 - Cp4.1LG03g09810.1 Cpe03g01532 1532
3 11956362 11960108 - Cp4.1LG03g09790.1 Cpe03g01533 1533
3 11960629 11963368 - Cp4.1LG03g09760.1 Cpe03g01534 1534
3 11965270 11980423 + Cp4.1LG03g09890.1 Cpe03g01535 1535
3 11979082 11983227 - Cp4.1LG03g09750.1 Cpe03g01536 1536
8 2175593 2177917 - Cp4.1LG08g03290.1 Cpe08g00349 349
8 2179623 2185333 + Cp4.1LG08g03390.1 Cpe08g00350 350
8 2185862 2188869 - Cp4.1LG08g03280.1 Cpe08g00351 351
12 781821 792222 - Cp4.1LG12g01350.1 Cpe12g00126 126
12 797810 810152 + Cp4.1LG12g01280.1 Cpe12g00127 127
17 1329896 1340024 - Cp4.1LG17g02200.1 Cpe17g00206 206
17 1344180 1354565 + Cp4.1LG17g02130.1 Cpe17g00207 207
5 4425668 4429130 + CrPI670011_05g004930.1 Cre05g0493 493
5 4431907 4438632 - CrPI670011_05g004960.1 Cre05g0496 496
5 4461709 4463855 + CrPI670011_05g004990.1 Cre05g0499 499
5 4465924 4472191 + CrPI670011_05g005000.1 Cre05g0500 500
6 9395672 9404600 - CrPI670011_06g014830.1 Cre06g1483 1483
6 9460341 9469084 + CrPI670011_06g014840.1 Cre06g1484 1484
6 9520301 9527424 + CrPI670011_06g014870.1 Cre06g1487 1487
2 10062411 10072395 - CsaV3_2G012550.1 Csa02g01039 1039
2 10109561 10115707 - CsaV3_2G012580.1 Csa02g01042 1042
2 10136203 10146416 + CsaV3_2G012590.1 Csa02g01043 1043
3 9167708 9173981 + CsaV3_3G011810.1 Csa03g01181 1181
3 9176507 9179954 - CsaV3_3G011830.1 Csa03g01183 1183
3 9196609 9199022 + CsaV3_3G011860.1 Csa03g01186 1186
3 9199590 9202682 + CsaV3_3G011870.1 Csa03g01187 1187
3 9203196 9204483 + CsaV3_3G011880.1 Csa03g01188 1188
5 66689424 66692734 - Hsped.05g16780.1 Hepe05g1678 1678
5 66754764 66758199 - Hsped.05g16820.1 Hepe05g1682 1682
11 40828262 40833909 + Maker00031688 Lcy11g1693 1693
11 40851242 40855519 - Maker00031363 Lcy11g1695 1695
13 4482725 4492990 - Maker00023718 Lcy13g0392 392
13 4530843 4539255 + Maker00023583 Lcy13g0394 394
5 24917126 24924890 - Lsi05G017520.1 Lsi05g01752 1752
5 24925962 24928508 - Lsi05G017530.1 Lsi05g01753 1753
5 24961181 24966102 + Lsi05G017580.1 Lsi05g01758 1758
5 24972303 24976345 - Lsi05G017600.1 Lsi05g01760 1760
9 19330717 19346536 - Lsi09G012080.1 Lsi09g01208 1208
9 19553087 19562920 - Lsi09G012160.1 Lsi09g01216 1216
9 19597787 19603277 + Lsi09G012180.1 Lsi09g01218 1218
2 50496716 50500116 + Sed0021634.1 Sed02g1443 1443
4 34553017 34569491 - Sed0025551.1 Sed04g2009 2009
12 2726588 2729206 + Sed0021014.1 Sed12g0452 452
6 76039547 76051111 + Tan0002285.1 Tan06g2386 2386
10 5227136 5230590 + Tan0014079.1 Tan10g0650 650
10 5301202 5303745 + Tan0004709.1 Tan10g0654 654
5 8803755 8806188 - Vvi5g749 Vvi5g749 749
5 8809254 8847176 - Vvi5g750 Vvi5g750 750
5 8866526 8872218 + Vvi5g751 Vvi5g751 751
5 8872246 8872642 - Vvi5g752 Vvi5g752 752
5 8874202 8882011 - Vvi5g753 Vvi5g753 753
5 8924446 8929184 + Vvi5g754 Vvi5g754 754
5 8930078 8934179 - Vvi5g755 Vvi5g755 755
5 8958784 8963415 - Vvi5g756 Vvi5g756 756
5 8963422 8963617 + Vvi5g757 Vvi5g757 757
5 9032939 9048206 + Vvi5g758 Vvi5g758 758
       

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