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
Vvi5g389 . . . . . Bpe14g01160 . . Cmo08g01163 Cmo17g00279 Cma06g01451 Cma14g01654 Car06g01253 . . Cpe08g00224 Cpe03g01399 Bhi01g00918 . . . . . . Cla06g00523 Cam06g0562 Cec06g0562 Cco06g0569 Clacu06g0550 Cmu06g0546 Cre06g1315 Cone14ag0801 Cone15ag0800 . . Lsi05g01486 . Chy11g01452 Cme06g00675 Blo02g00567 Blo07g00195 Bda11g00550 . . Bpe13g00639 . . . Cmo06g01452 Cmo14g01700 Cma08g01191 Cma17g00291 Car08g01068 Car17g00267 Cpe12g00243 Cpe17g00107 Bhi12g01764 . . . . . . . . . . . . . . Csa03g01400 Chy06g00643 Cme11g01957
Vvi5g390 . Blo12g00063 . . Bpe04g01182 . Bma04g01062 . Cmo08g01162 . . . . . . . . . . . . . . . Cla06g00524 . . . . . . . Cone15ag0801 Cone7ag0189 . . . Chy11g01451 . . . . . . . . . . . . Cma08g01190 Cma17g00290 Car08g01067 Car17g00266 Cpe12g00242 Cpe17g00108 Bhi12g01765 . . . . . . . . . . . . . Lsi09g01380 . . Cme11g01956
Vvi5g391 . . . . . . . . Cmo08g01161 Cmo17g00278 . . Car06g01252 . . Cpe08g00225 . . . . . . . . Cla06g00525 Cam06g0564 Cec06g0564 Cco06g0571 Clacu06g0552 Cmu06g0548 Cre06g1317 Cone14ag0802 Cone15ag0802 . . Lsi05g01484 . Chy11g01450 Cme06g00674 . . . . Bpe05g00758 . . . . Cmo06g01451 . Cma08g01189 Cma17g00289 Car08g01065 Car17g00265 Cpe12g00241 Cpe17g00109 Bhi12g01766 . . . . . . . . . . . . . Lsi09g01379 Csa03g01399 Chy06g00642 Cme11g01955
Vvi5g392 . . . . . . . . . . . . . . . . . Bhi01g00900 . . . Hepe05g1198 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g393 . . . Bda08g00350 . . . . . . . . . . . . . Bhi01g00899 . . . Hepe05g1199 . Lcy11g1468 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g394 . . . . . . . . . . Cma06g01450 Cma14g01656 Car06g01251 Car14g01490 . Cpe08g00226 Cpe03g01400 . . . . . . . . . . . . . . . . Cone7ag0191 Cone4ag0185 Lsi05g01481 . . Cme06g00671 . . . . . Bpe13g00637 . Bma06g01527 . Cmo06g01450 Cmo14g01701 . . . . . . . . . . . . . Cla05g00600 Cam05g0660 Cec05g0668 Cco05g0664 Clacu05g0654 Cmu05g0623 Cre05g0692 . Csa03g01397 Chy06g00640 .
Vvi5g395 . . . . . . . . . . . Cma14g01657 . Car14g01491 Sed02g1295 . Cpe03g01401 Bhi01g00893 Tan10g0919 Cmetu06g0465 . Hepe05g1499 . Lcy11g1475 . . . . . . . . . Cone7ag0192 . Lsi05g01479 . . Cme06g00670 . Blo07g00197 . . . Bpe13g00636 . Bma06g01528 . . Cmo14g01702 . . . . . . . . . . . . . Cla05g00599 Cam05g0659 Cec05g0666 . Clacu05g0652 Cmu05g0621 Cre05g0690 . Csa03g01396 Chy06g00639 .
Vvi5g396 . . . . . Bpe14g01162 . . . . Cma06g01447 . Car06g01250 . Sed02g1294 Cpe08g00227 . Bhi01g00892 Tan10g0918 Cmetu06g1283 . Hepe05g1500 . . . . . . . . . . . Cone7ag0193 Cone4ag0186 Lsi05g01478 . . Cme06g00669 Blo02g00565 . . . . . . . . Cmo06g01449 . . . . . . . . . . . . . . Cla05g00598 Cam05g0658 Cec05g0665 Cco05g0662 Clacu05g0651 Cmu05g0620 Cre05g0689 . Csa03g01394 Chy06g00637 .
Vvi5g397 . . . . . Bpe14g01163 . . . . . Cma14g01661 Car06g01249 Car14g01494 . Cpe08g00228 Cpe03g01402 Bhi01g00890 . . . Hepe05g1501 . Lcy11g1476 . . . . . . . . . . . Lsi05g01477 . . Cme06g00668 . . . . . Bpe13g00635 . Bma06g01529 . . Cmo14g01705 . . . . . . . . . . . . . Cla05g00597 Cam05g0657 Cec05g0664 Cco05g0661 Clacu05g0650 Cmu05g0619 Cre05g0688 . Csa03g01393 Chy06g00636 .
Vvi5g398 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 3593878 3600322 + Bda024789.1 Bda08g00350 350
11 5719640 5739365 - Bda005286.2 Bda11g00550 550
1 16845179 16853226 + XM_039042950.1 Bhi01g00890 890
1 16854158 16856692 + XM_039021417.1 Bhi01g00892 892
1 16856828 16859248 + XM_039021414.1 Bhi01g00893 893
1 17010270 17022807 + XM_039023129.1 Bhi01g00899 899
1 17010270 17022807 + XM_039023146.1 Bhi01g00900 900
1 17108734 17111885 - XM_039047155.1 Bhi01g00918 918
12 56960405 56964384 - XM_039018655.1 Bhi12g01764 1764
12 56986514 56991578 - XM_039019708.1 Bhi12g01765 1765
12 57017932 57021766 - XM_039020179.1 Bhi12g01766 1766
2 10337223 10339763 + BLOR10295 Blo02g00565 565
2 10446984 10454879 + BLOR10297 Blo02g00567 567
7 2422363 2430739 - BLOR18127 Blo07g00195 195
7 2441795 2443465 - BLOR18129 Blo07g00197 197
12 4371072 4373066 - BLOR04082 Blo12g00063 63
4 19924181 19925700 - Bma019700.1 Bma04g01062 1062
6 51661059 51661619 + Bma024640.1 Bma06g01527 1527
6 51662052 51663730 - Bma024641.1 Bma06g01528 1528
6 51665417 51669017 - Bma024642.1 Bma06g01529 1529
4 13492975 13495049 + Bpe015878.1 Bpe04g01182 1182
5 20960231 20963294 - Bpe018172.1 Bpe05g00758 758
13 13254846 13259902 + Bpe010335.1 Bpe13g00635 635
13 13261194 13262876 + Bpe010336.1 Bpe13g00636 636
13 13263396 13263956 - Bpe010337.1 Bpe13g00637 637
13 13269496 13272478 + Bpe010339.1 Bpe13g00639 639
14 8641099 8643512 - Bpe014533.1 Bpe14g01160 1160
14 8650037 8652156 - Bpe014535.1 Bpe14g01162 1162
14 8653418 8658154 - Bpe014536.2 Bpe14g01163 1163
5 5683196 5692297 + CaPI482276_05g006570.1 Cam05g0657 657
5 5693766 5695794 + CaPI482276_05g006580.1 Cam05g0658 658
5 5695832 5699365 + CaPI482276_05g006590.1 Cam05g0659 659
5 5704154 5706622 + CaPI482276_05g006600.1 Cam05g0660 660
6 7692781 7696676 - CaPI482276_06g005620.1 Cam06g0562 562
6 7710729 7714832 - CaPI482276_06g005640.1 Cam06g0564 564
6 8997661 9001858 + Carg17386-RA Car06g01249 1249
6 9002492 9006665 + Carg17385-RA Car06g01250 1250
6 9007065 9007634 - Carg17384-RA Car06g01251 1251
6 9008993 9012282 + Carg17383-RA Car06g01252 1252
6 9013375 9016161 + Carg17382-RA Car06g01253 1253
8 7273941 7278816 + Carg15944-RA Car08g01065 1065
8 7280231 7285279 + Carg15946-RA Car08g01067 1067
8 7285977 7289589 + Carg15947-RA Car08g01068 1068
14 12364287 12364847 + Carg20154-RA Car14g01490 1490
14 12368171 12372507 - Carg20155-RA Car14g01491 1491
14 12386132 12390106 - Carg20158-RA Car14g01494 1494
17 1638674 1644152 + Carg05471-RA Car17g00265 265
17 1646580 1650970 + Carg05472-RA Car17g00266 266
17 1652000 1654883 + Carg05473-RA Car17g00267 267
5 5378928 5387857 + CcPI632755_05g006610.1 Cco05g0661 661
5 5389319 5394241 + CcPI632755_05g006620.1 Cco05g0662 662
5 5401771 5402355 + CcPI632755_05g006640.1 Cco05g0664 664
6 6132616 6136503 - CcPI632755_06g005690.1 Cco06g0569 569
6 6150607 6154682 - CcPI632755_06g005710.1 Cco06g0571 571
5 5383870 5399489 + CePI673135_05g006640.1 Cec05g0664 664
5 5400952 5402990 + CePI673135_05g006650.1 Cec05g0665 665
5 5403612 5406622 + CePI673135_05g006660.1 Cec05g0666 666
5 5413385 5413954 + CePI673135_05g006680.1 Cec05g0668 668
6 6229488 6233313 - CePI673135_06g005620.1 Cec06g0562 562
6 6247412 6251476 - CePI673135_06g005640.1 Cec06g0564 564
6 4322295 4329814 + Chy6G111640.1 Chy06g00636 636
6 4331180 4333007 + Chy6G111650.1 Chy06g00637 637
6 4334105 4335870 + Chy6G111670.1 Chy06g00639 639
6 4338977 4341456 + Chy6G111680.1 Chy06g00640 640
6 4351888 4354579 + Chy6G111700.1 Chy06g00642 642
6 4356238 4359058 + Chy6G111710.1 Chy06g00643 643
11 21285075 21313437 + Chy11G200300.1 Chy11g01450 1450
11 21314192 21317567 + Chy11G200310.1 Chy11g01451 1451
11 21320142 21322820 + Chy11G200320.1 Chy11g01452 1452
5 5408134 5417240 + ClG42_05g0065000.10 Clacu05g0650 650
5 5418753 5420779 + ClG42_05g0065100.10 Clacu05g0651 651
5 5421388 5424349 + ClG42_05g0065200.10 Clacu05g0652 652
5 5431084 5431653 + ClG42_05g0065400.10 Clacu05g0654 654
6 6240933 6244808 - ClG42_06g0055000.10 Clacu06g0550 550
6 6258840 6262887 - ClG42_06g0055200.10 Clacu06g0552 552
5 5470607 5479711 + ClCG05G005590.2 Cla05g00597 597
5 5481024 5483601 + ClCG05G005600.1 Cla05g00598 598
5 5483846 5486200 + ClCG05G005610.2 Cla05g00599 599
5 5491597 5494491 + ClCG05G005630.1 Cla05g00600 600
6 6308472 6312735 - ClCG06G005580.1 Cla06g00523 523
6 6315553 6319413 - ClCG06G005590.1 Cla06g00524 524
6 6326332 6330791 - ClCG06G005600.2 Cla06g00525 525
6 9269337 9278211 + CmaCh06G014470.1 Cma06g01447 1447
6 9281135 9281704 - CmaCh06G014500.1 Cma06g01450 1450
6 9282589 9289802 + CmaCh06G014510.1 Cma06g01451 1451
8 7312596 7317429 + CmaCh08G011890.1 Cma08g01189 1189
8 7318469 7323698 + CmaCh08G011900.1 Cma08g01190 1190
8 7324299 7329589 + CmaCh08G011910.1 Cma08g01191 1191
14 12395828 12403613 - CmaCh14G016540.1 Cma14g01654 1654
14 12405840 12406400 + CmaCh14G016560.1 Cma14g01656 1656
14 12408830 12410918 - CmaCh14G016570.1 Cma14g01657 1657
14 12428989 12433426 - CmaCh14G016610.1 Cma14g01661 1661
17 1539268 1544863 + CmaCh17G002890.1 Cma17g00289 289
17 1551954 1556596 + CmaCh17G002900.1 Cma17g00290 290
17 1557781 1562010 + CmaCh17G002910.1 Cma17g00291 291
6 4312257 4319267 + MELO3C006585.2.1 Cme06g00668 668
6 4319910 4322011 + MELO3C006586.2.1 Cme06g00669 669
6 4323113 4325071 + MELO3C006587.2.1 Cme06g00670 670
6 4327607 4328286 + MELO3C006588.2.1 Cme06g00671 671
6 4341982 4345288 + MELO3C006591.2.1 Cme06g00674 674
6 4346427 4349726 + MELO3C006592.2.1 Cme06g00675 675
11 27604997 27609022 + MELO3C021382.2.1 Cme11g01955 1955
11 27612220 27616906 + MELO3C021381.2.1 Cme11g01956 1956
11 27620618 27624718 + MELO3C021380.2.1 Cme11g01957 1957
6 4558749 4560529 + PI0021221.1 Cmetu06g0465 465
6 4555760 4557645 + PI0019625.1 Cmetu06g1283 1283
6 10471969 10481752 + CmoCh06G014490.1 Cmo06g01449 1449
6 10482700 10483266 - CmoCh06G014500.1 Cmo06g01450 1450
6 10484471 10488249 + CmoCh06G014510.1 Cmo06g01451 1451
6 10488986 10491900 + CmoCh06G014520.1 Cmo06g01452 1452
8 7408621 7413368 + CmoCh08G011610.1 Cmo08g01161 1161
8 7414969 7420024 + CmoCh08G011620.1 Cmo08g01162 1162
8 7420604 7424756 + CmoCh08G011630.1 Cmo08g01163 1163
14 13352861 13359242 - CmoCh14G017000.1 Cmo14g01700 1700
14 13361364 13361924 + CmoCh14G017010.1 Cmo14g01701 1701
14 13363430 13367224 - CmoCh14G017020.1 Cmo14g01702 1702
14 13384774 13389546 - CmoCh14G017050.1 Cmo14g01705 1705
17 1663183 1675024 + CmoCh17G002780.1 Cmo17g00278 278
17 1676125 1680515 + CmoCh17G002790.1 Cmo17g00279 279
5 5251655 5260774 + CmPI595203_05g006190.1 Cmu05g0619 619
5 5262276 5264302 + CmPI595203_05g006200.1 Cmu05g0620 620
5 5264910 5267866 + CmPI595203_05g006210.1 Cmu05g0621 621
5 5274562 5275131 + CmPI595203_05g006230.1 Cmu05g0623 623
6 6048133 6052008 - CmPI595203_06g005460.1 Cmu06g0546 546
6 6066081 6070128 - CmPI595203_06g005480.1 Cmu06g0548 548
4 864409 867125 + Conep04aG0019400.1 Cone4ag0185 185
4 868923 870796 - Conep04aG0019500.1 Cone4ag0186 186
7 805881 808092 - Conep07aG0019400.1 Cone7ag0189 189
7 813590 814195 + Conep07aG0019600.1 Cone7ag0191 191
7 815737 817539 - Conep07aG0019700.1 Cone7ag0192 192
7 818481 819719 - Conep07aG0019800.1 Cone7ag0193 193
14 4731069 4734016 - Conep14aG0081800.1 Cone14ag0801 801
14 4737697 4740741 - Conep14aG0081900.1 Cone14ag0802 802
15 4904500 4907891 - Conep15aG0081500.1 Cone15ag0800 800
15 4913510 4917362 - Conep15aG0081600.1 Cone15ag0801 801
15 4928201 4931166 - Conep15aG0081700.1 Cone15ag0802 802
3 11279303 11282866 - Cp4.1LG03g11130.1 Cpe03g01399 1399
3 11284973 11285533 + Cp4.1LG03g11060.1 Cpe03g01400 1400
3 11286393 11302579 - Cp4.1LG03g11000.1 Cpe03g01401 1401
3 11305170 11310145 - Cp4.1LG03g10980.1 Cpe03g01402 1402
8 1499807 1502953 - Cp4.1LG08g04410.1 Cpe08g00224 224
8 1503524 1507325 - Cp4.1LG08g04390.1 Cpe08g00225 225
8 1508381 1509016 + Cp4.1LG08g04460.1 Cpe08g00226 226
8 1509651 1513006 - Cp4.1LG08g04360.1 Cpe08g00227 227
8 1514081 1518511 - Cp4.1LG08g04370.1 Cpe08g00228 228
12 1620346 1626026 + Cp4.1LG12g02380.1 Cpe12g00241 241
12 1630007 1633262 + Cp4.1LG12g02420.1 Cpe12g00242 242
12 1634093 1639100 + Cp4.1LG12g02390.1 Cpe12g00243 243
17 654655 659261 - Cp4.1LG17g01080.1 Cpe17g00107 107
17 659671 665084 - Cp4.1LG17g01140.1 Cpe17g00108 108
17 666567 671311 - Cp4.1LG17g01100.1 Cpe17g00109 109
5 6037030 6046215 + CrPI670011_05g006880.1 Cre05g0688 688
5 6047689 6049716 + CrPI670011_05g006890.1 Cre05g0689 689
5 6050820 6053276 + CrPI670011_05g006900.1 Cre05g0690 690
5 6060058 6060627 + CrPI670011_05g006920.1 Cre05g0692 692
6 7094723 7098642 - CrPI670011_06g013150.1 Cre06g1315 1315
6 7112896 7116943 - CrPI670011_06g013170.1 Cre06g1317 1317
3 10441908 10450058 + CsaV3_3G013930.1 Csa03g01393 1393
3 10450616 10452483 + CsaV3_3G013940.1 Csa03g01394 1394
3 10453578 10455343 + CsaV3_3G013960.1 Csa03g01396 1396
3 10457950 10460390 + CsaV3_3G013970.1 Csa03g01397 1397
3 10466785 10470155 + CsaV3_3G013990.1 Csa03g01399 1399
3 10471230 10474681 + CsaV3_3G014000.1 Csa03g01400 1400
5 58191495 58193391 + Hsped.05g11980.1 Hepe05g1198 1198
5 58238735 58240627 + Hsped.05g11990.1 Hepe05g1199 1199
5 64471202 64472988 - Hsped.05g14990.1 Hepe05g1499 1499
5 64473454 64476445 - Hsped.05g15000.1 Hepe05g1500 1500
5 64484003 64492442 - Hsped.05g15010.1 Hepe05g1501 1501
11 38603012 38613158 + Maker00031510 Lcy11g1468 1468
11 38679522 38685658 - Maker00031376 Lcy11g1475 1475
11 38687538 38694556 - Maker00031334 Lcy11g1476 1476
5 22588154 22597981 + Lsi05G014770.1 Lsi05g01477 1477
5 22599199 22601238 + Lsi05G014780.1 Lsi05g01478 1478
5 22602319 22604076 + Lsi05G014790.1 Lsi05g01479 1479
5 22617740 22618303 + Lsi05G014810.1 Lsi05g01481 1481
5 22632002 22633627 + Lsi05G014840.1 Lsi05g01484 1484
5 22640816 22641825 + Lsi05G014860.1 Lsi05g01486 1486
9 21815510 21820577 + Lsi09G013790.1 Lsi09g01379 1379
9 21820796 21830825 + Lsi09G013800.1 Lsi09g01380 1380
2 49546798 49550745 + Sed0005422.1 Sed02g1294 1294
2 49551762 49553550 + Sed0003590.1 Sed02g1295 1295
10 7707443 7709796 + Tan0021024.1 Tan10g0918 918
10 7710899 7712682 + Tan0009230.1 Tan10g0919 919
5 3947363 3955722 - Vvi5g389 Vvi5g389 389
5 3956952 3960217 - Vvi5g390 Vvi5g390 390
5 3961006 3965332 - Vvi5g391 Vvi5g391 391
5 3968916 3972344 + Vvi5g392 Vvi5g392 392
5 3978961 3984862 + Vvi5g393 Vvi5g393 393
5 3998888 3999706 + Vvi5g394 Vvi5g394 394
5 3999814 4002525 - Vvi5g395 Vvi5g395 395
5 4003639 4006971 - Vvi5g396 Vvi5g396 396
5 4007202 4024721 - Vvi5g397 Vvi5g397 397
5 4030153 4031701 + Vvi5g398 Vvi5g398 398
       

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