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
Vvi5g489 . . . . . Bpe14g01183 . . . . Cma06g01415 . Car06g01220 . Sed02g1245 Cpe08g00256 . Bhi01g00819 Tan10g0850 Cmetu06g1818 . Hepe05g1545 . Lcy11g1540 . . . . . . . Cone14ag0845 . Cone7ag0246 Cone4ag0240 Lsi05g01598 . . Cme06g00614 Blo02g00543 Blo07g00215 Bda11g00573 . . Bpe13g00610 Bma02g00854 Bma06g01552 . Cmo06g01417 . . . . . . . . . . . . . . Cla05g00550 Cam05g0598 Cec05g0609 Cco05g0606 Clacu05g0596 Cmu05g0566 Cre05g0634 . Csa03g01337 Chy06g00584 .
Vvi5g490 . . . . . Bpe14g01184 . . . . Cma06g01414 . . . . . . . . . . . . . . . . . . . . . . . . Lsi05g01599 . . . Blo02g00542 . . Bda13g00129 . . . . . Cmo06g01416 Cmo14g01745 . . . . . . . . . . . . . Cla05g00549 . . . . . . . Csa03g01336 . .
Vvi5g491 . . . . . Bpe14g01185 . . . . Cma06g01413 Cma14g01704 Car06g01219 Car14g01539 Sed02g1242 Cpe08g00257 Cpe03g01432 Bhi01g00818 Tan10g0847 Cmetu06g1617 . Hepe05g1546 . Lcy11g1541 . . . . . . . . . . Cone4ag0241 Lsi05g01601 . . Cme06g00613 Blo02g00541 Blo07g00216 Bda11g00574 Bda13g00128 . Bpe13g00609 Bma02g00853 Bma06g01554 . Cmo06g01415 Cmo14g01747 . . . . . . . . . . . . . Cla05g00548 Cam05g0597 Cec05g0608 Cco05g0604 Clacu05g0594 Cmu05g0564 Cre05g0633 . Csa03g01334 . .
Vvi5g492 . Blo12g00329 Bda03g00889 . Bpe04g00833 . . . Cmo08g01121 Cmo17g00224 . . . . . . . . . . . . . . Cla06g00582 Cam06g0620 Cec06g0622 Cco06g0628 Clacu06g0607 Cmu06g0600 Cre06g1368 . . Cone7ag0248 Cone4ag0242 . . . . . . . . . . . . Sed08g1297 . . . Cma17g00238 Car08g01027 Car17g00216 Cpe12g00200 Cpe17g00146 Bhi12g01711 Tan06g2524 Cmetu02g1656 Lac12g2279 Hepe03g0197 . Lcy13g0281 . . . . . . . Lsi09g01322 . . Cme01g01561
Vvi5g493 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g494 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g495 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g496 . . . Bda08g00235 Bpe04g00832 . Bma04g00785 . Cmo08g01120 Cmo17g00223 . . . . . . . . . . . . . . Cla06g00583 Cam06g0621 Cec06g0623 Cco06g0629 Clacu06g0608 Cmu06g0601 Cre06g1369 Cone14ag0851 . . . . . . . . . . . Bpe05g00903 . . . Sed09g1123 . . Cma08g01143 Cma17g00236 Car08g01026 Car17g00215 Cpe12g00199 Cpe17g00147 Bhi12g01710 Tan06g0978 Cmetu01g0849 Lac12g2278 Hepe03g0198 . Lcy13g0282 . . . . . . . Lsi09g01321 . . Cme01g01562
Vvi5g497 Blo01g00125 Blo12g00330 Bda03g00887 Bda08g00236 Bpe04g00831 . Bma04g00784 Bma05g01109 . Cmo17g00222 . . . . . . . . . . . . . . Cla06g00584 Cam06g0622 Cec06g0624 Cco06g0630 Clacu06g0609 Cmu06g0602 Cre06g1370 . . . . . . . . . . . . Bpe05g00902 . . . Sed01g0119 . . . Cma17g00235 . Car17g00214 Cpe12g00198 . Bhi12g01709 Tan06g2522 Cmetu01g0197 . Hepe03g0199 . Lcy13g0283 . . . . . . . Lsi09g01320 . . Cme01g01564
Vvi5g498 . Blo12g00331 Bda03g00886 . Bpe04g00830 . Bma04g00783 . . Cmo17g00221 . . . . . . . . . . . . . . Cla06g00585 Cam06g0623 Cec06g0625 Cco06g0631 Clacu06g0610 Cmu06g0603 Cre06g1371 . . Cone7ag0249 Cone4ag0243 . . . . . . . . . . . . Sed09g0756 . . . Cma17g00234 . Car17g00213 Cpe12g00197 . Bhi12g01708 Tan06g2521 Cmetu01g0541 . . . . . . . . . . . Lsi09g01319 . . Cme01g01565
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 7636440 7637098 + Bda016877.1 Bda03g00886 886
3 7637571 7639334 - Bda016878.1 Bda03g00887 887
3 7681203 7684008 - Bda016882.1 Bda03g00889 889
8 2359320 2362584 + Bda024650.1 Bda08g00235 235
8 2365290 2368987 + Bda024651.1 Bda08g00236 236
11 5901373 5903672 - Bda005312.1 Bda11g00573 573
11 5907753 5911409 - Bda005313.1 Bda11g00574 574
13 1663130 1666670 + Bda000987.1 Bda13g00128 128
13 1667936 1668508 - Bda000988.1 Bda13g00129 129
1 15265286 15270196 + XM_039020443.1 Bhi01g00818 818
1 15314731 15318825 + XM_039028131.1 Bhi01g00819 819
12 55273366 55275406 + XM_039019434.1 Bhi12g01708 1708
12 55275512 55278977 - XM_039019431.1 Bhi12g01709 1709
12 55287222 55298457 - XM_039018648.1 Bhi12g01710 1710
12 55317204 55320827 - XM_039019218.1 Bhi12g01711 1711
1 1690653 1705128 - BLOR00125 Blo01g00125 125
2 9217530 9221521 + BLOR10271 Blo02g00541 541
2 9222694 9223070 - BLOR10272 Blo02g00542 542
2 9238213 9240886 + BLOR10273 Blo02g00543 543
7 2718648 2720949 - BLOR18147 Blo07g00215 215
7 2728147 2731294 - BLOR18148 Blo07g00216 216
12 18887379 18898144 + BLOR04348 Blo12g00329 329
12 18906522 18921884 + BLOR04349 Blo12g00330 330
12 18913867 18914339 - BLOR04350 Blo12g00331 331
2 45738753 45740631 + Bma015607.1 Bma02g00853 853
2 45748059 45750113 + Bma015608.1 Bma02g00854 854
4 8510936 8511561 + Bma019306.1 Bma04g00783 783
4 8512040 8516056 - Bma019307.1 Bma04g00784 784
4 8517989 8525548 - Bma019308.1 Bma04g00785 785
5 49840680 49851073 - Bma031227 Bma05g01109 1109
6 51843163 51845476 - Bma024669.1 Bma06g01552 1552
6 51851351 51855132 - Bma024671.1 Bma06g01554 1554
4 5450437 5451096 + Bpe015490.2 Bpe04g00830 830
4 5451801 5455159 - Bpe015491.1 Bpe04g00831 831
4 5457092 5464238 - Bpe015492.1 Bpe04g00832 832
4 5464926 5471260 - Bpe015493.1 Bpe04g00833 833
5 22049178 22052614 - Bpe018313.1 Bpe05g00902 902
5 22054738 22059986 - Bpe018314.1 Bpe05g00903 903
13 13118149 13121781 + Bpe010307.1 Bpe13g00609 609
13 13125871 13128180 + Bpe010308.1 Bpe13g00610 610
14 8849639 8851708 - Bpe014556.1 Bpe14g01183 1183
14 8855146 8855718 + Bpe025535 Bpe14g01184 1184
14 8857019 8860904 - Bpe025536 Bpe14g01185 1185
5 5226965 5232187 + CaPI482276_05g005970.1 Cam05g0597 597
5 5251606 5254845 + CaPI482276_05g005980.1 Cam05g0598 598
6 8446147 8448945 + CaPI482276_06g006200.1 Cam06g0620 620
6 8452808 8463389 + CaPI482276_06g006210.1 Cam06g0621 621
6 8464871 8468618 + CaPI482276_06g006220.1 Cam06g0622 622
6 8469101 8470359 - CaPI482276_06g006230.1 Cam06g0623 623
6 8832177 8837600 + Carg17416-RA Car06g01219 1219
6 8845870 8848358 + Carg17415-RA Car06g01220 1220
8 6999023 7005602 - Carg15905-RA Car08g01026 1026
8 7007254 7010863 - Carg15906-RA Car08g01027 1027
14 12692247 12696234 - Carg23525-RA Car14g01539 1539
17 1292935 1294702 + Carg05417-RA Car17g00213 213
17 1294787 1298091 - Carg05418-RA Car17g00214 214
17 1299510 1306595 - Carg05419-RA Car17g00215 215
17 1308498 1311675 - Carg05420-RA Car17g00216 216
5 4901156 4905089 + CcPI632755_05g006040.1 Cco05g0604 604
5 4926261 4929473 + CcPI632755_05g006060.1 Cco05g0606 606
6 6951084 6953873 + CcPI632755_06g006280.1 Cco06g0628 628
6 6957720 6973917 + CcPI632755_06g006290.1 Cco06g0629 629
6 6975584 6979275 + CcPI632755_06g006300.1 Cco06g0630 630
6 6979815 6981060 - CcPI632755_06g006310.1 Cco06g0631 631
5 4929418 4934584 + CePI673135_05g006080.1 Cec05g0608 608
5 4954187 4957429 + CePI673135_05g006090.1 Cec05g0609 609
6 7000913 7003720 + CePI673135_06g006220.1 Cec06g0622 622
6 7007543 7018313 + CePI673135_06g006230.1 Cec06g0623 623
6 7019554 7023564 + CePI673135_06g006240.1 Cec06g0624 624
6 7023741 7024936 - CePI673135_06g006250.1 Cec06g0625 625
6 3978029 3981608 + Chy6G111120.1 Chy06g00584 584
5 4937709 4946241 + ClG42_05g0059400.10 Clacu05g0594 594
5 4966814 4970038 + ClG42_05g0059600.10 Clacu05g0596 596
6 7007267 7010084 + ClG42_06g0060700.10 Clacu06g0607 607
6 7013823 7024540 + ClG42_06g0060800.10 Clacu06g0608 608
6 7025916 7029658 + ClG42_06g0060900.10 Clacu06g0609 609
6 7030140 7031389 - ClG42_06g0061000.10 Clacu06g0610 610
5 4990251 4995829 + ClCG05G005180.2 Cla05g00548 548
5 4997094 4997484 - ClCG05G005185.1 Cla05g00549 549
5 5017772 5020996 + ClCG05G005190.2 Cla05g00550 550
6 7111152 7114501 + ClCG06G006190.1 Cla06g00582 582
6 7117484 7127203 + ClCG06G006200.1 Cla06g00583 583
6 7131943 7135685 + ClCG06G006210.2 Cla06g00584 584
6 7135998 7137937 - ClCG06G006220.1 Cla06g00585 585
6 9092187 9100688 + CmaCh06G014130.1 Cma06g01413 1413
6 9101111 9101767 - CmaCh06G014140.1 Cma06g01414 1414
6 9111414 9114070 + CmaCh06G014150.1 Cma06g01415 1415
8 7048416 7055617 - CmaCh08G011430.1 Cma08g01143 1143
14 12619565 12623137 - CmaCh14G017040.1 Cma14g01704 1704
17 1189888 1196294 + CmaCh17G002340.1 Cma17g00234 234
17 1196557 1199764 - CmaCh17G002350.1 Cma17g00235 235
17 1199775 1208480 - CmaCh17G002360.1 Cma17g00236 236
17 1210638 1213864 - CmaCh17G002380.1 Cma17g00238 238
1 20725952 20729747 + MELO3C012645.2.1 Cme01g01561 1561
1 20733835 20742990 + MELO3C012646.2.1 Cme01g01562 1562
1 20762669 20766920 + MELO3C012647.2.1 Cme01g01564 1564
1 20765806 20767970 - MELO3C012648.2.1 Cme01g01565 1565
6 3905897 3911290 + MELO3C006534.2.1 Cme06g00613 613
6 3930901 3934378 + MELO3C006535.2.1 Cme06g00614 614
1 7749611 7752786 + PI0015912.1 Cmetu01g0197 197
1 7752923 7754454 - PI0026592.1 Cmetu01g0541 541
1 7734659 7743855 + PI0028101.1 Cmetu01g0849 849
2 14605150 14608424 + PI0028304.2 Cmetu02g1656 1656
6 4145546 4150870 + PI0026820.2 Cmetu06g1617 1617
6 4170616 4175103 + PI0017949.1 Cmetu06g1818 1818
6 10298102 10304136 + CmoCh06G014150.1 Cmo06g01415 1415
6 10304488 10305219 - CmoCh06G014160.1 Cmo06g01416 1416
6 10312442 10315641 + CmoCh06G014170.1 Cmo06g01417 1417
8 7135406 7143395 - CmoCh08G011200.1 Cmo08g01120 1120
8 7145129 7148452 - CmoCh08G011210.1 Cmo08g01121 1121
14 13588104 13588847 + CmoCh14G017450.1 Cmo14g01745 1745
14 13590206 13593988 - CmoCh14G017470.1 Cmo14g01747 1747
17 1304261 1305999 + CmoCh17G002210.1 Cmo17g00221 221
17 1306357 1310639 - CmoCh17G002220.1 Cmo17g00222 222
17 1310846 1318161 - CmoCh17G002230.1 Cmo17g00223 223
17 1320289 1323729 - CmoCh17G002240.1 Cmo17g00224 224
5 4781343 4789874 + CmPI595203_05g005640.1 Cmu05g0564 564
5 4810488 4813713 + CmPI595203_05g005660.1 Cmu05g0566 566
6 6813534 6816343 + CmPI595203_06g006000.1 Cmu06g0600 600
6 6820148 6830868 + CmPI595203_06g006010.1 Cmu06g0601 601
6 6832256 6836303 + CmPI595203_06g006020.1 Cmu06g0602 602
6 6836480 6837729 - CmPI595203_06g006030.1 Cmu06g0603 603
4 1082181 1085285 - Conep04aG0024900.1 Cone4ag0240 240
4 1090308 1093351 - Conep04aG0025000.1 Cone4ag0241 241
4 1093750 1095435 + Conep04aG0025100.1 Cone4ag0242 242
4 1094797 1097342 - Conep04aG0025200.1 Cone4ag0243 243
7 1033953 1037049 - Conep07aG0025100.1 Cone7ag0246 246
7 1045463 1047990 + Conep07aG0025300.1 Cone7ag0248 248
7 1047132 1049381 - Conep07aG0025400.1 Cone7ag0249 249
14 5338143 5341499 - Conep14aG0086200.1 Cone14ag0845 845
14 5399179 5407279 + Conep14aG0086800.1 Cone14ag0851 851
3 11501095 11506083 - Cp4.1LG03g10650.1 Cpe03g01432 1432
8 1681290 1684025 - Cp4.1LG08g04250.1 Cpe08g00256 256
8 1691242 1697649 - Cp4.1LG08g04060.1 Cpe08g00257 257
12 1259286 1260844 + Cp4.1LG12g01880.1 Cpe12g00197 197
12 1261412 1264564 - Cp4.1LG12g01930.1 Cpe12g00198 198
12 1264968 1272681 - Cp4.1LG12g01940.1 Cpe12g00199 199
12 1274157 1277375 - Cp4.1LG12g01970.1 Cpe12g00200 200
17 934227 937168 + Cp4.1LG17g01500.1 Cpe17g00146 146
17 939351 947509 + Cp4.1LG17g01460.1 Cpe17g00147 147
5 5575093 5580318 + CrPI670011_05g006330.1 Cre05g0633 633
5 5600773 5604077 + CrPI670011_05g006340.1 Cre05g0634 634
6 7881587 7884416 + CrPI670011_06g013680.1 Cre06g1368 1368
6 7888291 7898831 + CrPI670011_06g013690.1 Cre06g1369 1369
6 7900534 7904289 + CrPI670011_06g013700.1 Cre06g1370 1370
6 7904772 7906928 - CrPI670011_06g013710.1 Cre06g1371 1371
3 10089482 10093765 + CsaV3_3G013340.1 Csa03g01334 1334
3 10096137 10096536 - CsaV3_3G013360.1 Csa03g01336 1336
3 10111015 10115208 + CsaV3_3G013370.1 Csa03g01337 1337
3 2532869 2536461 + Hsped.03g01970.1 Hepe03g0197 197
3 2541351 2550161 + Hsped.03g01980.1 Hepe03g0198 198
3 2551897 2556232 + Hsped.03g01990.1 Hepe03g0199 199
5 65070520 65074950 - Hsped.05g15450.1 Hepe05g1545 1545
5 65101244 65105704 - Hsped.05g15460.1 Hepe05g1546 1546
12 39906929 39914800 - Lag0016650.1 Lac12g2278 2278
12 39919600 39922362 - Lag0016651.1 Lac12g2279 2279
11 39269428 39273587 - Maker00031876 Lcy11g1540 1540
11 39296787 39303562 - Maker00031335 Lcy11g1541 1541
13 3072507 3075472 + Maker00023394 Lcy13g0281 281
13 3080714 3089713 + Maker00024012 Lcy13g0282 282
13 3091631 3095593 + Maker00023480 Lcy13g0283 283
5 23717290 23723189 - Lsi05G015980.1 Lsi05g01598 1598
5 23742883 23743597 + Lsi05G015990.1 Lsi05g01599 1599
5 23746186 23750022 - Lsi05G016010.1 Lsi05g01601 1601
9 21050761 21052666 + Lsi09G013190.1 Lsi09g01319 1319
9 21051594 21055905 - Lsi09G013200.1 Lsi09g01320 1320
9 21057745 21067961 - Lsi09G013210.1 Lsi09g01321 1321
9 21071199 21074090 - Lsi09G013220.1 Lsi09g01322 1322
1 1070621 1074998 - Sed0017770.5 Sed01g0119 119
2 49204964 49210677 + Sed0011568.2 Sed02g1242 1242
2 49226887 49230432 + Sed0007259.2 Sed02g1245 1245
8 26904542 26907672 - Sed0016060.1 Sed08g1297 1297
9 14160728 14163612 + Sed0002009.4 Sed09g0756 756
9 35312114 35323663 - Sed0016378.2 Sed09g1123 1123
6 8594590 8608187 + Tan0018120.1 Tan06g0978 978
6 77832699 77833632 + Tan0013603.1 Tan06g2521 2521
6 77834292 77837428 - Tan0013032.1 Tan06g2522 2522
6 77851752 77855322 - Tan0018108.1 Tan06g2524 2524
10 7017712 7022966 + Tan0019662.1 Tan10g0847 847
10 7058473 7062619 + Tan0000735.1 Tan10g0850 850
5 5108615 5111341 - Vvi5g489 Vvi5g489 489
5 5119009 5120096 + Vvi5g490 Vvi5g490 490
5 5127092 5134133 - Vvi5g491 Vvi5g491 491
5 5145292 5148759 + Vvi5g492 Vvi5g492 492
5 5162319 5164612 - Vvi5g493 Vvi5g493 493
5 5165689 5166307 + Vvi5g494 Vvi5g494 494
5 5173996 5183773 - Vvi5g495 Vvi5g495 495
5 5188838 5200736 + Vvi5g496 Vvi5g496 496
5 5203550 5209684 + Vvi5g497 Vvi5g497 497
5 5209749 5212723 - Vvi5g498 Vvi5g498 498
       

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