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
Vvi18g560 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g561 . . . . . . . . Cmo05g00590 . . . . . . . . Bhi04g00902 Tan02g2510 . . Hepe10g0403 . Lcy13g1453 Cla08g01185 Cam08g1650 Cec08g1226 Cco08g1345 Clacu08g1346 . Cre08g1132 Cone6ag1502 Cone9ag1428 . . . . . Cme03g01778 Blo17g00086 . . Bda13g01347 . . . . . . . . Cma05g00564 Car05g00510 . Cpe11g00495 . . . . . . . . . . . . . . . Lsi08g01048 Csa02g02232 Chy03g01285 .
Vvi18g562 Blo01g01789 . Bda01g00923 . Bpe02g00152 . . Bma01g02574 Cmo05g00592 . . . . . Sed04g0234 . . Bhi04g00900 Tan02g2512 Cmetu03g0168 . Hepe10g0402 . . Cla08g01186 Cam08g1651 Cec08g1227 Cco08g1346 Clacu08g1347 . Cre08g1133 . . Cone17ag1157 Cone20ag0572 . . . . Blo17g00085 Blo18g00728 . Bda13g01346 Bpe02g01168 Bpe14g00499 Bma01g01363 Bma02g00100 . . . . Cma05g00566 . . . . . . . . . . . . . . . . . . Lsi08g01049 Csa02g02233 Chy03g01284 .
Vvi18g563 . . Bda01g00924 . . . . . Cmo05g00593 . . . . . Sed04g0235 . . Bhi04g00899 Tan02g2513 Cmetu03g1732 . Hepe10g0401 . Lcy13g1452 Cla08g01187 Cam08g1652 Cec08g1228 Cco08g1347 Clacu08g1348 . Cre08g1134 Cone4ag1273 . Cone17ag1156 Cone20ag0573 . . . Cme03g01777 Blo17g00084 Blo18g00094 . Bda13g01345 Bpe02g01169 Bpe14g00500 Bma01g01362 Bma02g00099 . . . . Cma05g00567 Car05g00511 . Cpe11g00496 . . . . . . . . . . . . . . . Lsi08g01050 Csa02g02234 Chy03g01283 .
Vvi18g564 . . . . . . . . . . Cma01g01459 Cma09g00608 . . . Cpe06g00469 . . . . . . . . . . . . . . . Cone4ag1272 . Cone17ag1155 . Lsi04g02304 Csa03g04523 Chy04g00181 . Blo17g00083 Blo18g00093 . Bda13g01344 Bpe02g01170 Bpe14g00501 Bma01g01361 Bma02g00098 Sed13g1510 Cmo01g01511 Cmo09g00596 . . . . . Cpe02g00493 Bhi09g02539 Tan01g3886 Cmetu04g0192 . Hepe01g2194 Mch11g0739 . Cla11g01453 Cam11g1506 Cec11g1544 Cco11g1538 Clacu11g1671 Cmu11g1487 Cre11g1907 . . . Cme04g00209
Vvi18g565 Blo01g01788 . . . Bpe02g00153 . . Bma01g02573 . . Cma01g01458 . . . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00180 . . . Bda11g00813 . . . . . . Cmo01g01510 . . . . . . . Bhi09g02541 Tan01g3888 . . Hepe01g2195 Mch11g0740 . . . . . . . . . . . Cme04g00208
Vvi18g566 . . . . . . . . . . . Cma09g00609 . . . Cpe06g00470 . . . . . . . . . . . . . . . Cone4ag1271 . . . Lsi04g02305 Csa03g04524 . . . . . . . . . . . . Cmo09g00597 . . . Car09g00540 . Cpe02g00494 Bhi09g02542 Tan01g3889 . . . . . Cla11g01454 Cam11g1507 Cec11g1545 Cco11g1540 Clacu11g1672 Cmu11g1488 Cre11g1908 . . . .
Vvi18g567 Blo01g01787 . . . Bpe02g00154 . . . . . Cma01g01457 Cma09g00610 . . . Cpe06g00471 . . . . . . . . . . . . . . . . . Cone17ag1154 Cone20ag0574 Lsi04g02306 Csa03g04525 Chy04g00179 . . . Bda11g00814 Bda01g01642 . . . . Sed05g1527 Cmo01g01509 Cmo09g00598 . . . Car09g00541 . Cpe02g00495 Bhi09g02544 Tan01g3891 Cmetu04g2820 . Hepe01g2196 Mch11g0742 . Cla11g01455 Cam11g1508 Cec11g1546 Cco11g1541 Clacu11g1673 Cmu11g1489 Cre11g1909 . . . Cme04g00207
Vvi18g568 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g569 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g00451 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 42460156 42463022 + Bda003070.2 Bda01g00923 923
1 42470038 42472340 - Bda003071.1 Bda01g00924 924
1 52409794 52411956 - Bda032968 Bda01g01642 1642
11 8052143 8061208 + Bda005564.1 Bda11g00813 813
11 8071905 8074118 - Bda005565.1 Bda11g00814 814
13 35802486 35804683 + Bda000159.1 Bda13g01344 1344
13 35806912 35809442 + Bda000160.1 Bda13g01345 1345
13 35816846 35819171 - Bda000161.1 Bda13g01346 1346
13 35829991 35831983 - Bda000162.1 Bda13g01347 1347
4 22599810 22602621 + XM_039029426.1 Bhi04g00899 899
4 22607353 22610428 - XM_039030203.1 Bhi04g00900 900
4 22702184 22706591 - XM_039028670.1 Bhi04g00902 902
9 68976211 68978083 - XM_039040820.1 Bhi09g02539 2539
9 69047125 69079912 + XM_039042524.1 Bhi09g02541 2541
9 69047125 69073059 + XM_039042526.1 Bhi09g02542 2542
9 69081583 69085500 - XM_039043674.1 Bhi09g02544 2544
1 57593969 57596204 + BLOR01787 Blo01g01787 1787
1 57597509 57619506 - BLOR01788 Blo01g01788 1788
1 57620563 57622887 - BLOR01789 Blo01g01789 1789
17 644525 646855 + BLOR15904 Blo17g00083 83
17 649081 651585 + BLOR15905 Blo17g00084 84
17 653072 655404 - BLOR15906 Blo17g00085 85
17 666765 668266 - BLOR15907 Blo17g00086 86
18 788600 790821 + BLOR08581 Blo18g00093 93
18 792664 794988 + BLOR08582 Blo18g00094 94
18 19129791 19132929 + BLOR09216 Blo18g00728 728
1 20535321 20537508 + Bma030249 Bma01g01361 1361
1 20539728 20542042 + Bma001693.1 Bma01g01362 1362
1 20563237 20565542 - Bma001694.1 Bma01g01363 1363
1 83344417 83347710 - Bma003455.1 Bma01g02573 2573
1 83348535 83350199 - Bma003456.1 Bma01g02574 2574
2 877705 880022 + Bma030854 Bma02g00098 98
2 881848 884397 + Bma014553.1 Bma02g00099 99
2 886548 888881 - Bma014554.1 Bma02g00100 100
2 1051491 1053809 + Bpe008003.1 Bpe02g00152 152
2 1054981 1073482 + Bpe008004.2 Bpe02g00153 153
2 1075115 1077257 - Bpe008005.1 Bpe02g00154 154
2 15363231 15365549 + Bpe009030.1 Bpe02g01168 1168
2 15366403 15368672 - Bpe025121 Bpe02g01169 1169
2 15370809 15373063 - Bpe009031.1 Bpe02g01170 1170
5 18886764 18889088 - Bpe017870.1 Bpe05g00451 451
14 4437739 4439655 + Bpe007149.1 Bpe14g00499 499
14 4441330 4443864 - Bpe007150.1 Bpe14g00500 500
14 4446064 4448368 - Bpe007151.1 Bpe14g00501 501
8 22713097 22715947 + CaPI482276_08g016500.1 Cam08g1650 1650
8 22740163 22742504 + CaPI482276_08g016510.1 Cam08g1651 1651
8 22747217 22749515 - CaPI482276_08g016520.1 Cam08g1652 1652
11 27895075 27896498 - CaPI482276_11g015060.1 Cam11g1506 1506
11 27900038 27922938 + CaPI482276_11g015070.1 Cam11g1507 1507
11 27926151 27928529 - CaPI482276_11g015080.1 Cam11g1508 1508
5 2957437 2961928 + Carg08253-RA Car05g00510 510
5 2977210 2979918 - Carg08254-RA Car05g00511 511
9 3052985 3072235 + Carg03022-RA Car09g00540 540
9 3073246 3076395 - Carg03023-RA Car09g00541 541
8 25343826 25346622 + CcPI632755_08g013450.1 Cco08g1345 1345
8 25375982 25378324 + CcPI632755_08g013460.1 Cco08g1346 1346
8 25383203 25385501 - CcPI632755_08g013470.1 Cco08g1347 1347
11 28255827 28257698 - CcPI632755_11g015380.1 Cco11g1538 1538
11 28268554 28284642 + CcPI632755_11g015400.1 Cco11g1540 1540
11 28287481 28289845 - CcPI632755_11g015410.1 Cco11g1541 1541
8 24190441 24193156 + CePI673135_08g012260.1 Cec08g1226 1226
8 24217049 24219398 + CePI673135_08g012270.1 Cec08g1227 1227
8 24224100 24226402 - CePI673135_08g012280.1 Cec08g1228 1228
11 29702402 29704182 - CePI673135_11g015440.1 Cec11g1544 1544
11 29704246 29730811 + CePI673135_11g015450.1 Cec11g1545 1545
11 29733853 29736203 - CePI673135_11g015460.1 Cec11g1546 1546
3 15853851 15856228 + Chy3G062630.1 Chy03g01283 1283
3 15861472 15863816 - Chy3G062640.1 Chy03g01284 1284
3 15881864 15885209 - Chy3G062650.1 Chy03g01285 1285
4 1579880 1582243 + Chy4G068970.1 Chy04g00179 179
4 1584619 1609223 - Chy4G068980.1 Chy04g00180 180
4 1611190 1612624 + Chy4G068990.1 Chy04g00181 181
8 23486560 23489369 + ClG42_08g0134600.10 Clacu08g1346 1346
8 23514024 23516367 + ClG42_08g0134700.10 Clacu08g1347 1347
8 23521185 23523483 - ClG42_08g0134800.10 Clacu08g1348 1348
11 27924729 27926152 - ClG42_11g0167100.10 Clacu11g1671 1671
11 27926216 27952605 + ClG42_11g0167200.10 Clacu11g1672 1672
11 27955825 27958203 - ClG42_11g0167300.10 Clacu11g1673 1673
8 24753622 24756537 + ClCG08G011890.1 Cla08g01185 1185
8 24781530 24783899 + ClCG08G011900.1 Cla08g01186 1186
8 24788385 24791297 - ClCG08G011910.1 Cla08g01187 1187
11 28165154 28167295 - ClCG11G014860.1 Cla11g01453 1453
11 28167195 28195446 + ClCG11G014870.1 Cla11g01454 1454
11 28197769 28201171 - ClCG11G014880.1 Cla11g01455 1455
1 10236502 10240553 + CmaCh01G014570.1 Cma01g01457 1457
1 10240832 10263572 - CmaCh01G014580.1 Cma01g01458 1458
1 10263633 10265602 + CmaCh01G014590.1 Cma01g01459 1459
5 2772489 2776728 + CmaCh05G005640.1 Cma05g00564 564
5 2786674 2789489 + CmaCh05G005660.1 Cma05g00566 566
5 2791803 2794638 - CmaCh05G005670.1 Cma05g00567 567
9 2858630 2861090 - CmaCh09G006080.1 Cma09g00608 608
9 2861808 2881280 + CmaCh09G006090.1 Cma09g00609 609
9 2881725 2885916 - CmaCh09G006100.1 Cma09g00610 610
3 26244783 26247902 + MELO3C011113.2.1 Cme03g01777 1777
3 26272540 26278690 - MELO3C011111.2.1 Cme03g01778 1778
4 1536708 1540325 + MELO3C003488.2.1 Cme04g00207 207
4 1542821 1566193 - MELO3C003489.2.1 Cme04g00208 208
4 1567654 1569809 + MELO3C003490.2.1 Cme04g00209 209
3 3168009 3171114 + PI0005188.1 Cmetu03g0168 168
3 3175531 3178407 - PI0025446.1 Cmetu03g1732 1732
4 31796438 31798367 - PI0025905.1 Cmetu04g0192 192
4 31825546 31829386 - PI0007672.1 Cmetu04g2820 2820
1 11653855 11658008 + CmoCh01G015090.1 Cmo01g01509 1509
1 11658415 11679767 - CmoCh01G015100.1 Cmo01g01510 1510
1 11679958 11681948 + CmoCh01G015110.1 Cmo01g01511 1511
5 2923936 2926796 + CmoCh05G005900.1 Cmo05g00590 590
5 2936853 2942213 + CmoCh05G005920.1 Cmo05g00592 592
5 2941846 2944553 - CmoCh05G005930.1 Cmo05g00593 593
9 2943897 2946345 - CmoCh09G005960.1 Cmo09g00596 596
9 2946885 2966549 + CmoCh09G005970.1 Cmo09g00597 597
9 2967281 2970858 - CmoCh09G005980.1 Cmo09g00598 598
11 27176805 27178227 - CmPI595203_11g014870.1 Cmu11g1487 1487
11 27181344 27204715 + CmPI595203_11g014880.1 Cmu11g1488 1488
11 27207935 27210314 - CmPI595203_11g014890.1 Cmu11g1489 1489
4 10444764 10458787 - Conep04aG0131700.1 Cone4ag1271 1271
4 10463628 10465190 + Conep04aG0131800.1 Cone4ag1272 1272
4 10466429 10469231 + Conep04aG0131900.1 Cone4ag1273 1273
6 11902934 11905978 - Conep06aG0156100.1 Cone6ag1502 1502
9 10612327 10615243 - Conep09aG0147100.1 Cone9ag1428 1428
17 8524709 8527337 + Conep17aG0118300.1 Cone17ag1154 1154
17 8527988 8529554 + Conep17aG0118400.1 Cone17ag1155 1155
17 8530428 8533265 + Conep17aG0118500.1 Cone17ag1156 1156
17 8536106 8538948 - Conep17aG0118600.1 Cone17ag1157 1157
20 3269715 3272921 + Conep20aG0058900.1 Cone20ag0572 572
20 3275911 3278539 - Conep20aG0059000.1 Cone20ag0573 573
20 3281919 3284672 - Conep20aG0059100.1 Cone20ag0574 574
2 2854494 2856342 - Cp4.1LG02g03730.1 Cpe02g00493 493
2 2856489 2878517 + Cp4.1LG02g03820.1 Cpe02g00494 494
2 2879151 2883246 - Cp4.1LG02g03720.1 Cpe02g00495 495
6 2755381 2759070 - Cp4.1LG06g03910.1 Cpe06g00469 469
6 2759655 2779542 + Cp4.1LG06g03950.1 Cpe06g00470 470
6 2780044 2783784 - Cp4.1LG06g03880.1 Cpe06g00471 471
11 2872806 2874273 + Cp4.1LG11g04910.1 Cpe11g00495 495
11 2891388 2894414 - Cp4.1LG11g05040.1 Cpe11g00496 496
8 24512589 24515359 + CrPI670011_08g011320.1 Cre08g1132 1132
8 24539225 24541568 + CrPI670011_08g011330.1 Cre08g1133 1133
8 24546293 24548591 - CrPI670011_08g011340.1 Cre08g1134 1134
11 30810598 30812021 - CrPI670011_11g019070.1 Cre11g1907 1907
11 30812130 30838663 + CrPI670011_11g019080.1 Cre11g1908 1908
11 30841904 30844282 - CrPI670011_11g019090.1 Cre11g1909 1909
2 20037726 20045362 + CsaV3_2G030510.1 Csa02g02232 2232
2 20059330 20062317 + CsaV3_2G030520.1 Csa02g02233 2233
2 20066943 20070145 - CsaV3_2G030530.1 Csa02g02234 2234
3 39416125 39419215 - CsaV3_3G048290.1 Csa03g04523 4523
3 39420103 39445687 + CsaV3_3G048300.1 Csa03g04524 4524
3 39446304 39450303 - CsaV3_3G048310.1 Csa03g04525 4525
1 86630914 86633109 - Hsped.01g21940.1 Hepe01g2194 2194
1 86635449 86659709 + Hsped.01g21950.1 Hepe01g2195 2195
1 86664179 86668772 - Hsped.01g21960.1 Hepe01g2196 2196
10 4434005 4436990 + Hsped.10g04010.1 Hepe10g0401 401
10 4445089 4446702 - Hsped.10g04020.1 Hepe10g0402 402
10 4474657 4478935 - Hsped.10g04030.1 Hepe10g0403 403
13 33036348 33039485 + Maker00033993 Lcy13g1452 1452
13 33063420 33070088 - Maker00033935 Lcy13g1453 1453
4 30201800 30203422 - Lsi04G023040.1 Lsi04g02304 2304
4 30205706 30232907 + Lsi04G023050.1 Lsi04g02305 2305
4 30233981 30237507 - Lsi04G023060.1 Lsi04g02306 2306
8 19070604 19076128 + Lsi08G010480.1 Lsi08g01048 1048
8 19098073 19101087 + Lsi08G010490.1 Lsi08g01049 1049
8 19105248 19108289 - Lsi08G010500.1 Lsi08g01050 1050
11 4964297 4966029 - MC11g0619 Mch11g0739 739
11 4968092 4991171 + MC11g0620 Mch11g0740 740
11 4996821 5000763 - MC11g0622 Mch11g0742 742
4 1746904 1749508 + Sed0011559.1 Sed04g0234 234
4 1752407 1755583 - Sed0012926.1 Sed04g0235 235
5 29016174 29019971 + Sed0013268.1 Sed05g1527 1527
13 20312400 20314693 + Sed0023469.1 Sed13g1510 1510
1 103804470 103806501 - Tan0014267.1 Tan01g3886 3886
1 103809888 103837274 + Tan0007587.2 Tan01g3888 3888
1 103809888 103837274 + Tan0007587.3 Tan01g3889 3889
1 103840029 103843689 - Tan0005965.2 Tan01g3891 3891
2 93697041 93702702 + Tan0020171.1 Tan02g2510 2510
2 93726830 93730077 + Tan0021237.1 Tan02g2512 2512
2 93735641 93738707 - Tan0021540.1 Tan02g2513 2513
18 6511945 6512743 + Vvi18g560 Vvi18g560 560
18 6526890 6532321 + Vvi18g561 Vvi18g561 561
18 6547018 6549993 + Vvi18g562 Vvi18g562 562
18 6555819 6559893 - Vvi18g563 Vvi18g563 563
18 6561401 6573040 - Vvi18g564 Vvi18g564 564
18 6574840 6580376 + Vvi18g565 Vvi18g565 565
18 6580896 6634655 + Vvi18g566 Vvi18g566 566
18 6636210 6638672 - Vvi18g567 Vvi18g567 567
18 6643140 6643646 + Vvi18g568 Vvi18g568 568
18 6644092 6648772 - Vvi18g569 Vvi18g569 569
       

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