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
Vvi5g459 . . . . . . . . . . Cma06g01425 Cma14g01689 Car06g01228 Car14g01522 Sed12g0906 . Cpe03g01423 Bhi01g00838 Tan10g0866 Cmetu06g1993 . Hepe05g1534 . Lcy11g1521 . . . . . . . . . . . Lsi05g01440 . . Cme06g00628 . Blo07g00211 Bda11g00567 . . Bpe13g00617 . Bma06g01546 . Cmo06g01428 Cmo14g01733 . . . . . . . . . . . . . Cla05g00564 Cam05g0620 Cec05g0630 Cco05g0625 Clacu05g0616 Cmu05g0584 Cre05g0652 . Csa03g01353 Chy06g00598 .
Vvi5g460 . . . . . Bpe14g01173 . . Cmo08g01132 Cmo17g00241 . . . . . . . . . . . . . . Cla06g00562 Cam06g0602 Cec06g0602 Cco06g0607 Clacu06g0588 Cmu06g0583 Cre06g1349 . . . . . . . . Blo02g00553 . . Bda13g00140 . . Bma02g00859 . Sed09g0640 . . Cma08g01160 Cma17g00255 Car08g01037 Car17g00229 Cpe12g00211 Cpe17g00136 Bhi12g01822 Tan06g2636 Cmetu11g0294 Lac12g2383 Hepe03g0122 . Lcy13g0197 . . . . . . . Lsi09g01338 . . .
Vvi5g461 . . . . . Bpe14g01174 . . . . Cma06g01424 Cma14g01690 Car06g01227 Car14g01523 Sed02g1253 . Cpe03g01424 Bhi01g00837 Tan10g0865 Cmetu09g1642 . . . Lcy11g1522 . . . . . . . . . . . Lsi05g01438 . . Cme06g00627 . . . Bda13g00139 . . . . . Cmo06g01427 Cmo14g01734 . . . . . . . . . . . . . Cla05g00563 Cam05g0619 Cec05g0629 Cco05g0624 Clacu05g0615 Cmu05g0583 Cre05g0651 . Csa03g01352 Chy06g00597 .
Vvi5g462 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g463 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0835 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g464 . . . . . Bpe14g01175 . . . . Cma06g01423 Cma14g01691 Car06g01226 Car14g01525 Sed02g1251 Cpe08g00251 Cpe03g01425 Bhi01g00836 Tan10g0863 Cmetu06g0635 . . . Lcy11g1523 . . . . . . . . . Cone7ag0235 Cone4ag0225 Lsi05g01437 . . Cme06g00626 Blo02g00552 . . . . . . . . Cmo06g01425 Cmo14g01736 . . . . . . . . . . . . . Cla05g00562 Cam05g0618 Cec05g0628 Cco05g0623 Clacu05g0614 Cmu05g0582 Cre05g0650 . Csa03g01351 Chy06g00596 .
Vvi5g465 . . . . . Bpe14g01176 . . Cmo08g01131 . . . . . . . . . . . . . . . Cla06g00563 Cam06g0603 Cec06g0603 Cco06g0608 Clacu06g0589 Cmu06g0584 Cre06g1350 . . Cone7ag0236 Cone4ag0226 . . . . Blo02g00551 . . Bda13g00134 . . . . . . . Cma08g01159 . Car08g01036 . . Cpe17g00137 Bhi12g01823 . . . Hepe03g0115 . . . . . . . . . . . . .
Vvi5g466 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00565 Cam06g0605 Cec06g0605 Cco06g0610 Clacu06g0591 Cmu06g0586 Cre06g1352 . Cone15ag0822 . Cone4ag0228 . . . . . . . Bda13g00133 . . . . . . . . . . . Cpe12g00208 . Bhi12g01826 . . Lac12g1767 . . . . . . . . . . Lsi09g01336 . . .
Vvi5g467 . Blo12g00321 Bda03g00895 . Bpe04g00840 . Bma04g00793 . Cmo08g01129 Cmo17g00236 . . . . . . . . . . . . . . Cla06g00566 Cam06g0606 Cec06g0606 Cco06g0612 Clacu06g0592 Cmu06g0587 Cre06g1353 Cone14ag0837 . . . . . . . . . . . . . . . . . . Cma08g01155 Cma17g00251 Car08g01033 Car17g00225 Cpe12g00207 . Bhi12g01732 . . Lac12g2301 . . . . . . . . . . Lsi09g01335 . . .
Vvi5g468 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed04g1886 . . . Cma17g00250 . . . Cpe17g00140 Bhi12g01731 Tan06g2538 Cmetu05g0588 . Hepe03g0182 . Lcy13g0265 . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 7818692 7823995 - Bda016890.2 Bda03g00895 895
11 5861393 5864301 + Bda005305.1 Bda11g00567 567
13 1737549 1738424 + Bda000992.1 Bda13g00133 133
13 1743251 1746370 - Bda000993.1 Bda13g00134 134
13 1844218 1845228 + Bda000999.2 Bda13g00139 139
13 1845894 1852304 - Bda001000.1 Bda13g00140 140
1 15869290 15876373 + XM_039050765.1 Bhi01g00836 836
1 15878691 15881803 + XM_039050688.1 Bhi01g00837 837
1 15903577 15908698 - XM_039023687.1 Bhi01g00838 838
12 55945440 55953407 - XM_039018651.1 Bhi12g01731 1731
12 55946913 55953407 - XM_039018652.1 Bhi12g01732 1732
12 58140417 58147677 + XM_039018734.1 Bhi12g01822 1822
12 58153240 58157341 + XM_039020084.1 Bhi12g01823 1823
12 58248884 58250272 - XM_039020361.1 Bhi12g01826 1826
2 9704375 9708090 - BLOR10281 Blo02g00551 551
2 9721536 9731505 + BLOR10282 Blo02g00552 552
2 9732994 9739437 - BLOR10283 Blo02g00553 553
7 2682852 2685696 + BLOR18143 Blo07g00211 211
12 18671811 18677768 + BLOR04340 Blo12g00321 321
2 46252504 46258925 - Bma030910 Bma02g00859 859
4 9020235 9022090 - Bma019318.1 Bma04g00793 793
6 51807634 51810543 + Bma024663.1 Bma06g01546 1546
4 5529134 5534464 - Bpe015500.2 Bpe04g00840 840
13 13158170 13160955 - Bpe010316.1 Bpe13g00617 617
14 8776575 8788247 + Bpe014547.1 Bpe14g01173 1173
14 8788881 8790500 - Bpe014548.1 Bpe14g01174 1174
14 8792724 8798090 - Bpe014549.1 Bpe14g01175 1175
14 8803276 8806106 + Bpe014550.1 Bpe14g01176 1176
5 5371117 5376623 + CaPI482276_05g006180.1 Cam05g0618 618
5 5376777 5382394 + CaPI482276_05g006190.1 Cam05g0619 619
5 5384945 5389518 - CaPI482276_05g006200.1 Cam05g0620 620
6 8174479 8181493 + CaPI482276_06g006020.1 Cam06g0602 602
6 8184148 8188044 + CaPI482276_06g006030.1 Cam06g0603 603
6 8205876 8206910 - CaPI482276_06g006050.1 Cam06g0605 605
6 8217407 8228247 + CaPI482276_06g006060.1 Cam06g0606 606
6 8878969 8885199 + Carg17409-RA Car06g01226 1226
6 8886448 8888870 + Carg17408-RA Car06g01227 1227
6 8889283 8891601 - Carg17407-RA Car06g01228 1228
8 7066732 7074511 - Carg15912-RA Car08g01033 1033
8 7085789 7089805 - Carg15915-RA Car08g01036 1036
8 7091424 7099795 - Carg15916-RA Car08g01037 1037
14 12515457 12519786 + Carg23810-RA Car14g01522 1522
14 12521044 12522663 - Carg23809-RA Car14g01523 1523
14 12524367 12530171 - Carg23807-RA Car14g01525 1525
17 1385773 1393279 - Carg05429-RA Car17g00225 225
17 1408978 1415807 - Carg05434-RA Car17g00229 229
5 5065398 5071002 + CcPI632755_05g006230.1 Cco05g0623 623
5 5075259 5076881 + CcPI632755_05g006240.1 Cco05g0624 624
5 5079359 5083947 - CcPI632755_05g006250.1 Cco05g0625 625
6 6617304 6624249 + CcPI632755_06g006070.1 Cco06g0607 607
6 6626869 6631714 + CcPI632755_06g006080.1 Cco06g0608 608
6 6649565 6650608 - CcPI632755_06g006100.1 Cco06g0610 610
6 6668507 6678722 + CcPI632755_06g006120.1 Cco06g0612 612
5 5077021 5082526 + CePI673135_05g006280.1 Cec05g0628 628
5 5085534 5088323 + CePI673135_05g006290.1 Cec05g0629 629
5 5090874 5095463 - CePI673135_05g006300.1 Cec05g0630 630
6 6708928 6715800 + CePI673135_06g006020.1 Cec06g0602 602
6 6718395 6722288 + CePI673135_06g006030.1 Cec06g0603 603
6 6740384 6741421 - CePI673135_06g006050.1 Cec06g0605 605
6 6753606 6763555 + CePI673135_06g006060.1 Cec06g0606 606
6 4059622 4065101 + Chy6G111240.1 Chy06g00596 596
6 4068535 4070160 + Chy6G111250.1 Chy06g00597 597
6 4070566 4076133 - Chy6G111260.1 Chy06g00598 598
5 5087224 5092758 + ClG42_05g0061400.10 Clacu05g0614 614
5 5095765 5098558 + ClG42_05g0061500.10 Clacu05g0615 615
5 5101093 5105677 - ClG42_05g0061600.10 Clacu05g0616 616
6 6721537 6728528 + ClG42_06g0058800.10 Clacu06g0588 588
6 6731008 6734908 + ClG42_06g0058900.10 Clacu06g0589 589
6 6752712 6753737 - ClG42_06g0059100.10 Clacu06g0591 591
6 6766583 6775311 + ClG42_06g0059200.10 Clacu06g0592 592
5 5143405 5149457 + ClCG05G005280.1 Cla05g00562 562
5 5152815 5154870 + ClCG05G005290.2 Cla05g00563 563
5 5157047 5162046 - ClCG05G005300.1 Cla05g00564 564
6 6814928 6822328 + ClCG06G005980.1 Cla06g00562 562
6 6824405 6830172 + ClCG06G005990.2 Cla06g00563 563
6 6847752 6848777 - ClCG06G006020.1 Cla06g00565 565
6 6862280 6869298 + ClCG06G006030.2 Cla06g00566 566
6 9145973 9153039 + CmaCh06G014230.1 Cma06g01423 1423
6 9154854 9157799 + CmaCh06G014240.1 Cma06g01424 1424
6 9159640 9168340 - CmaCh06G014250.1 Cma06g01425 1425
8 7112833 7123299 - CmaCh08G011550.1 Cma08g01155 1155
8 7133693 7137336 - CmaCh08G011590.1 Cma08g01159 1159
8 7139017 7147391 - CmaCh08G011600.1 Cma08g01160 1160
14 12556473 12560666 + CmaCh14G016890.1 Cma14g01689 1689
14 12561638 12563257 - CmaCh14G016900.1 Cma14g01690 1690
14 12565073 12570814 - CmaCh14G016910.1 Cma14g01691 1691
17 1284176 1285907 - CmaCh17G002500.1 Cma17g00250 250
17 1288119 1292518 - CmaCh17G002510.1 Cma17g00251 251
17 1309258 1316139 - CmaCh17G002550.1 Cma17g00255 255
6 4006478 4012667 + MELO3C006547.2.1 Cme06g00626 626
6 4014712 4017707 + MELO3C006548.2.1 Cme06g00627 627
6 4019000 4023697 - MELO3C006549.2.1 Cme06g00628 628
5 21196757 21197877 - PI0027209.1 Cmetu05g0588 588
6 4263515 4269682 + PI0027473.1 Cmetu06g0635 635
6 4275500 4280274 - PI0011604.1 Cmetu06g1993 1993
9 15595602 15616515 - PI0024261.2 Cmetu09g1642 1642
11 4383150 4390290 - PI0022863.1 Cmetu11g0294 294
6 10346583 10353549 + CmoCh06G014250.1 Cmo06g01425 1425
6 10355650 10357299 + CmoCh06G014270.1 Cmo06g01427 1427
6 10357769 10360583 - CmoCh06G014280.1 Cmo06g01428 1428
8 7210538 7214203 - CmoCh08G011290.1 Cmo08g01129 1129
8 7224396 7229304 - CmoCh08G011310.1 Cmo08g01131 1131
8 7230775 7239205 - CmoCh08G011320.1 Cmo08g01132 1132
14 13523496 13527729 + CmoCh14G017330.1 Cmo14g01733 1733
14 13529126 13530745 - CmoCh14G017340.1 Cmo14g01734 1734
14 13532414 13538265 - CmoCh14G017360.1 Cmo14g01736 1736
17 1397520 1404991 - CmoCh17G002360.1 Cmo17g00236 236
17 1421492 1428857 - CmoCh17G002410.1 Cmo17g00241 241
5 4930937 4936470 + CmPI595203_05g005820.1 Cmu05g0582 582
5 4939473 4942266 + CmPI595203_05g005830.1 Cmu05g0583 583
5 4944822 4949406 - CmPI595203_05g005840.1 Cmu05g0584 584
6 6528240 6535225 + CmPI595203_06g005830.1 Cmu06g0583 583
6 6535364 6542551 + CmPI595203_06g005840.1 Cmu06g0584 584
6 6559399 6560424 - CmPI595203_06g005860.1 Cmu06g0586 586
6 6570862 6581951 + CmPI595203_06g005870.1 Cmu06g0587 587
4 1031051 1036262 - Conep04aG0023400.1 Cone4ag0225 225
4 1037068 1040443 + Conep04aG0023500.1 Cone4ag0226 226
4 1045744 1047219 - Conep04aG0023700.1 Cone4ag0228 228
7 995223 1001373 - Conep07aG0024000.1 Cone7ag0235 235
7 1002589 1005932 + Conep07aG0024100.1 Cone7ag0236 236
14 5146680 5147867 - Conep14aG0085200.1 Cone14ag0835 835
14 5177667 5183941 + Conep14aG0085400.1 Cone14ag0837 837
15 5437604 5438978 + Conep15aG0083800.1 Cone15ag0822 822
3 11433739 11438402 + Cp4.1LG03g10910.1 Cpe03g01423 1423
3 11439981 11441600 - Cp4.1LG03g10850.1 Cpe03g01424 1424
3 11443441 11449319 - Cp4.1LG03g10830.1 Cpe03g01425 1425
8 1644011 1650434 - Cp4.1LG08g04230.1 Cpe08g00251 251
12 1352955 1359773 - Cp4.1LG12g02080.1 Cpe12g00207 207
12 1361176 1363002 + Cp4.1LG12g02010.1 Cpe12g00208 208
12 1377213 1384191 - Cp4.1LG12g02070.1 Cpe12g00211 211
17 847062 855460 + Cp4.1LG17g01340.1 Cpe17g00136 136
17 856939 864175 + Cp4.1LG17g01330.1 Cpe17g00137 137
17 872038 880114 + Cp4.1LG17g01380.1 Cpe17g00140 140
5 5721682 5727186 + CrPI670011_05g006500.1 Cre05g0650 650
5 5730118 5732909 + CrPI670011_05g006510.1 Cre05g0651 651
5 5735454 5740022 - CrPI670011_05g006520.1 Cre05g0652 652
6 7582831 7589764 + CrPI670011_06g013490.1 Cre06g1349 1349
6 7592486 7596380 + CrPI670011_06g013500.1 Cre06g1350 1350
6 7614459 7615487 - CrPI670011_06g013520.1 Cre06g1352 1352
6 7628749 7639878 + CrPI670011_06g013530.1 Cre06g1353 1353
3 10190664 10196777 + CsaV3_3G013510.1 Csa03g01351 1351
3 10198744 10201842 + CsaV3_3G013520.1 Csa03g01352 1352
3 10202714 10207650 - CsaV3_3G013530.1 Csa03g01353 1353
3 1386548 1393567 - Hsped.03g01150.1 Hepe03g0115 115
3 1469160 1477243 - Hsped.03g01220.1 Hepe03g0122 122
3 2286626 2294714 + Hsped.03g01820.1 Hepe03g0182 182
5 64915239 64920781 + Hsped.05g15340.1 Hepe05g1534 1534
12 33776673 33780931 + Lag0016139.1 Lac12g1767 1767
12 40185094 40195269 - Lag0016673.1 Lac12g2301 2301
12 40940869 40948188 + Lag0016755.1 Lac12g2383 2383
11 39110478 39116245 + Maker00031310 Lcy11g1521 1521
11 39117957 39119573 - Maker00031373 Lcy11g1522 1522
11 39122912 39129233 - Maker00032094 Lcy11g1523 1523
13 2051521 2059373 - Maker00023816 Lcy13g0197 197
13 2785210 2793559 + Maker00023960 Lcy13g0265 265
5 22274060 22279736 + Lsi05G014370.1 Lsi05g01437 1437
5 22282618 22285176 + Lsi05G014380.1 Lsi05g01438 1438
5 22287298 22292079 - Lsi05G014400.1 Lsi05g01440 1440
9 21284033 21288571 - Lsi09G013350.1 Lsi09g01335 1335
9 21295561 21296598 + Lsi09G013360.1 Lsi09g01336 1336
9 21319700 21334697 - Lsi09G013380.1 Lsi09g01338 1338
2 49276590 49283099 + Sed0023903.1 Sed02g1251 1251
2 49286237 49289086 + Sed0014120.1 Sed02g1253 1253
4 33558701 33566814 + Sed0013212.1 Sed04g1886 1886
9 8056951 8065835 + Sed0025792.1 Sed09g0640 640
12 5669687 5675959 + Sed0010167.1 Sed12g0906 906
6 78077771 78086804 - Tan0017481.1 Tan06g2538 2538
6 78933084 78940905 + Tan0016930.1 Tan06g2636 2636
10 7242070 7248106 + Tan0014600.1 Tan10g0863 863
10 7251774 7254327 + Tan0020128.1 Tan10g0865 865
10 7256249 7261946 - Tan0021671.1 Tan10g0866 866
5 4695412 4703395 + Vvi5g459 Vvi5g459 459
5 4705769 4728522 + Vvi5g460 Vvi5g460 460
5 4728527 4730147 - Vvi5g461 Vvi5g461 461
5 4733970 4739497 - Vvi5g462 Vvi5g462 462
5 4744435 4746762 - Vvi5g463 Vvi5g463 463
5 4748333 4764341 - Vvi5g464 Vvi5g464 464
5 4768521 4774313 + Vvi5g465 Vvi5g465 465
5 4782868 4784874 - Vvi5g466 Vvi5g466 466
5 4794316 4798309 + Vvi5g467 Vvi5g467 467
5 4799946 4802669 + Vvi5g468 Vvi5g468 468
       

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