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
Vvi4g52 Blo01g01476 Blo12g01007 Bda01g00610 Bda03g00150 . . . Bma01g02222 Cmo05g00112 Cmo12g00568 Cma01g01748 Cma05g00106 Car09g00277 Car12g00575 Sed08g1756 Cpe07g00548 Cpe06g00233 Bhi04g00489 Tan02g1657 Cmetu03g1033 . Hepe08g1378 . Lcy13g2173 Cla05g01816 Cam05g1940 Cec05g1953 . Clacu05g1932 Cmu05g1813 Cre05g1939 Cone4ag1648 . Cone17ag0915 Cone20ag0257 Lsi04g01438 . . . . . . . . Bpe04g00133 . . Sed11g1844 Cmo01g01761 Cmo09g00326 Cma09g00328 Cma12g00627 Car01g01360 Car05g00092 Cpe11g00086 Cpe02g00250 Bhi09g03175 Tan01g4647 Cmetu07g1833 . . . . . . . . . . . Lsi08g01570 Csa02g01850 Chy03g01633 Cme07g00240
Vvi4g53 . . . . Bpe02g01534 . . . Cmo05g00111 Cmo12g00569 . Cma05g00105 . Car12g00576 Sed08g1757 Cpe07g00549 . Bhi04g00491 Tan02g1654 Cmetu02g1720 . Hepe08g1379 . Lcy13g2174 . . . . . . . Cone4ag1649 Cone7ag1300 . Cone20ag0258 . . . . Blo17g00296 Blo18g00291 Bda01g01323 Bda13g01611 Bpe14g00254 . Bma01g00929 . . . . . Cma12g00628 . Car05g00091 Cpe11g00085 . . . . . . . . . . . . . . . Lsi08g01572 Csa02g01849 Chy03g01635 .
Vvi4g54 . . . . Bpe02g01535 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo18g00290 . . . . Bma01g00928 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g55 . . Bda01g00611 . . Bpe02g00479 . . . . Cma01g01746 . . . . . . . . . . . . . Cla05g01817 Cam05g1941 Cec05g1954 Cco05g2014 Clacu05g1933 Cmu05g1814 Cre05g1940 Cone4ag1650 . . . . . . . Blo17g00295 . . Bda13g01610 Bpe14g00255 . . . Sed13g1849 Cmo01g01764 . . . Car01g01358 . . Cpe02g00251 Bhi09g03173 Tan01g4645 Cmetu07g0228 . Hepe01g1867 Mch11g0402 . . . . . . . . . . . Cme07g00239
Vvi4g56 Blo01g01474 . . . . Bpe02g00480 . Bma01g02221 . . Cma01g01745 . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01437 . . . . . . . . . . . Sed13g1850 Cmo01g01765 . . . Car01g01357 . . Cpe02g00252 Bhi09g03172 Tan01g4644 Cmetu07g0123 . Hepe01g1868 Mch11g0403 . . . . . . . . . . . Cme07g00238
Vvi4g57 . . . . . . . . . . . Cma05g00104 . . Sed08g1758 . . Bhi04g00493 Tan02g1651 Cmetu03g0683 . Hepe08g1380 . Lcy13g2175 . . . . . . . . . . . . . . . Blo17g00294 . . Bda13g01609 Bpe14g00256 . . . . . . . . . Car05g00090 Cpe11g00084 . . . . . . . . . . . . . . . Lsi08g01573 Csa02g01848 Chy03g01636 .
Vvi4g58 . . . . . . . . . . . . . . Sed07g1476 Cpe07g00154 . Bhi04g00909 Tan02g2503 . . Hepe10g0407 . Lcy13g1458 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma12g00180 . . . . . . . . . . . Cla08g01180 Cam08g1645 Cec08g1219 Cco08g1340 Clacu08g1340 . Cre08g1126 . Csa02g02227 . .
Vvi4g59 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g60 . Blo12g01008 . . . . . . Cmo05g00110 Cmo12g00571 . Cma05g00103 . Car12g00578 Sed08g1759 Cpe07g00551 . Bhi04g00495 Tan02g1649 Cmetu03g0633 . Hepe08g1382 . Lcy13g2176 . . . . . . . Cone4ag1651 Cone7ag1299 . . . . . . . . . . . . . . . . . . Cma12g00630 . Car05g00089 Cpe11g00083 . . . . . . . . . . . . . . . Lsi08g01574 Csa02g01847 Chy03g01637 .
Vvi4g61 . Blo12g01009 . Bda03g00149 . . Bma04g00131 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe04g00132 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33097151 33101714 - Bda002634.1 Bda01g00610 610
1 33108477 33110052 - Bda002635.1 Bda01g00611 611
1 48843677 48854162 - Bda003558.1 Bda01g01323 1323
3 1249304 1250029 + Bda016091.1 Bda03g00149 149
3 1260241 1264796 + Bda016092.2 Bda03g00150 150
13 39613789 39616440 - Bda000480.1 Bda13g01609 1609
13 39617835 39618985 + Bda000481.1 Bda13g01610 1610
13 39623697 39627486 + Bda000482.2 Bda13g01611 1611
4 12367505 12372103 - XM_039029750.1 Bhi04g00489 489
4 12380625 12385475 - XM_039028888.1 Bhi04g00491 491
4 12458828 12462651 - XM_039028179.1 Bhi04g00493 493
4 12466394 12470222 + XM_039028578.1 Bhi04g00495 495
4 22986396 22992179 - XM_039029569.1 Bhi04g00909 909
9 81013873 81016592 + XM_039042007.1 Bhi09g03172 3172
9 81018756 81021378 + XM_039043377.1 Bhi09g03173 3173
9 81144198 81148593 + XM_039042911.1 Bhi09g03175 3175
1 54002869 54009462 + BLOR01474 Blo01g01474 1474
1 54038030 54049212 + BLOR01476 Blo01g01476 1476
12 28053646 28058217 - BLOR05026 Blo12g01007 1007
12 28060629 28065117 + BLOR05027 Blo12g01008 1008
12 28065760 28066366 - BLOR05028 Blo12g01009 1009
17 3094095 3097000 - BLOR16115 Blo17g00294 294
17 3099904 3101372 + BLOR16116 Blo17g00295 295
17 3109681 3113239 + BLOR16117 Blo17g00296 296
18 3057043 3060430 - BLOR08778 Blo18g00290 290
18 3065103 3069320 + BLOR08779 Blo18g00291 291
1 9082037 9084851 - Bma001157.1 Bma01g00928 928
1 9085773 9089494 + Bma001158.1 Bma01g00929 929
1 79164676 79166260 + Bma003070.2 Bma01g02221 2221
1 79175758 79180162 + Bma003071.1 Bma01g02222 2222
4 1027957 1028680 + Bma018577.1 Bma04g00131 131
2 3107595 3109205 - Bpe008319.1 Bpe02g00479 479
2 3111882 3113447 - Bpe008320.1 Bpe02g00480 480
2 18458827 18462542 - Bpe009386.1 Bpe02g01534 1534
2 18463476 18466260 + Bpe009387.1 Bpe02g01535 1535
4 882677 883395 + Bpe014851.1 Bpe04g00132 132
4 893369 897818 + Bpe014852.2 Bpe04g00133 133
14 2659480 2663123 - Bpe006908.2 Bpe14g00254 254
14 2667138 2668611 - Bpe006909.1 Bpe14g00255 255
14 2669551 2672118 + Bpe006910.1 Bpe14g00256 256
5 28343031 28347715 - CaPI482276_05g019400.1 Cam05g1940 1940
5 28352637 28354447 - CaPI482276_05g019410.1 Cam05g1941 1941
8 22645424 22650707 + CaPI482276_08g016450.1 Cam08g1645 1645
1 11999996 12002652 + Carg10680-RA Car01g01357 1357
1 12004334 12006146 + Carg10679-RA Car01g01358 1358
1 12008352 12010473 + Carg10677-RA Car01g01360 1360
5 452534 456012 - Carg11916-RA Car05g00089 89
5 457705 460816 - Carg11915-RA Car05g00090 90
5 461592 465920 + Carg11914-RA Car05g00091 91
5 469963 472897 + Carg11913-RA Car05g00092 92
9 1504996 1508187 - Carg21744-RA Car09g00277 277
12 3849756 3850876 - Carg23973-RA Car12g00575 575
12 3852110 3856656 - Carg23972-RA Car12g00576 576
12 3864544 3867680 + Carg23970-RA Car12g00578 578
5 29263968 29275700 - CcPI632755_05g020140.1 Cco05g2014 2014
8 25276065 25281284 + CcPI632755_08g013400.1 Cco08g1340 1340
5 31613886 31618508 - CePI673135_05g019530.1 Cec05g1953 1953
5 31625478 31627442 - CePI673135_05g019540.1 Cec05g1954 1954
8 24113300 24118626 + CePI673135_08g012190.1 Cec08g1219 1219
3 18231033 18233675 - Chy3G066130.1 Chy03g01633 1633
3 18240026 18244312 - Chy3G066150.1 Chy03g01635 1635
3 18248676 18252260 + Chy3G066160.1 Chy03g01636 1636
3 18253994 18257029 + Chy3G066170.1 Chy03g01637 1637
5 28547109 28551744 - ClG42_05g0193200.10 Clacu05g1932 1932
5 28556357 28558196 - ClG42_05g0193300.10 Clacu05g1933 1933
8 23418908 23424192 + ClG42_08g0134000.10 Clacu08g1340 1340
5 30116958 30121896 - ClCG05G017720.2 Cla05g01816 1816
5 30126378 30128348 - ClCG05G017730.1 Cla05g01817 1817
8 24681996 24686241 + ClCG08G011840.2 Cla08g01180 1180
1 11794331 11796773 + CmaCh01G017450.1 Cma01g01745 1745
1 11798990 11800492 + CmaCh01G017460.1 Cma01g01746 1746
1 11802994 11805522 + CmaCh01G017480.1 Cma01g01748 1748
5 438953 442395 - CmaCh05G001030.1 Cma05g00103 103
5 443182 447142 - CmaCh05G001040.1 Cma05g00104 104
5 447963 456255 + CmaCh05G001050.1 Cma05g00105 105
5 456538 459640 + CmaCh05G001060.1 Cma05g00106 106
9 1350511 1356409 - CmaCh09G003280.1 Cma09g00328 328
12 820599 826265 - CmaCh12G001800.1 Cma12g00180 180
12 3327823 3329317 - CmaCh12G006270.1 Cma12g00627 627
12 3329955 3334965 - CmaCh12G006280.1 Cma12g00628 628
12 3341573 3344678 + CmaCh12G006300.1 Cma12g00630 630
7 1541188 1543937 + MELO3C016858.2.1 Cme07g00238 238
7 1546464 1548137 + MELO3C016857.2.1 Cme07g00239 239
7 1550763 1555813 + MELO3C016856.2.1 Cme07g00240 240
2 16269798 16274528 - PI0027772.1 Cmetu02g1720 1720
3 657947 661468 - PI0003634.1 Cmetu03g0633 633
3 662638 667075 - PI0001353.1 Cmetu03g0683 683
3 680802 685790 + PI0024640.2 Cmetu03g1033 1033
7 23256235 23259172 - PI0026473.1 Cmetu07g0123 123
7 23251527 23253489 - PI0013037.1 Cmetu07g0228 228
7 23241275 23246846 - PI0010627.1 Cmetu07g1833 1833
1 13081649 13084731 - CmoCh01G017610.1 Cmo01g01761 1761
1 13087240 13088759 - CmoCh01G017640.1 Cmo01g01764 1764
1 13090662 13094367 - CmoCh01G017650.1 Cmo01g01765 1765
5 448967 457245 - CmoCh05G001100.1 Cmo05g00110 110
5 458098 465889 + CmoCh05G001110.1 Cmo05g00111 111
5 466545 469392 + CmoCh05G001120.1 Cmo05g00112 112
9 1417600 1421835 - CmoCh09G003260.1 Cmo09g00326 326
12 3505830 3507434 - CmoCh12G005680.1 Cmo12g00568 568
12 3508587 3513199 - CmoCh12G005690.1 Cmo12g00569 569
12 3520853 3523881 + CmoCh12G005710.1 Cmo12g00571 571
5 28264716 28269354 - CmPI595203_05g018130.1 Cmu05g1813 1813
5 28273839 28277382 - CmPI595203_05g018140.1 Cmu05g1814 1814
4 12427714 12432251 - Conep04aG0170100.1 Cone4ag1648 1648
4 12432892 12435873 - Conep04aG0170200.1 Cone4ag1649 1649
4 12437128 12438443 - Conep04aG0170300.1 Cone4ag1650 1650
4 12441504 12444833 + Conep04aG0170400.1 Cone4ag1651 1651
7 9563612 9567003 - Conep07aG0133800.1 Cone7ag1299 1299
7 9571417 9580504 + Conep07aG0133900.1 Cone7ag1300 1300
17 7200642 7203729 - Conep17aG0094000.1 Cone17ag0915 915
20 1149991 1154966 - Conep20aG0026800.1 Cone20ag0257 257
20 1155359 1158008 - Conep20aG0026900.1 Cone20ag0258 258
2 1294736 1297196 - Cp4.1LG02g06240.1 Cpe02g00250 250
2 1299729 1301531 - Cp4.1LG02g06200.1 Cpe02g00251 251
2 1303229 1305919 - Cp4.1LG02g06170.1 Cpe02g00252 252
6 1235310 1240864 - Cp4.1LG06g02360.1 Cpe06g00233 233
7 875795 912269 - Cp4.1LG07g01650.1 Cpe07g00154 154
7 3639166 3640593 - Cp4.1LG07g06220.1 Cpe07g00548 548
7 3642378 3647375 - Cp4.1LG07g06140.1 Cpe07g00549 549
7 3654793 3657834 + Cp4.1LG07g06260.1 Cpe07g00551 551
11 438704 446132 - Cp4.1LG11g00020.1 Cpe11g00083 83
11 447137 451089 - Cp4.1LG11g00060.1 Cpe11g00084 84
11 451782 456089 + Cp4.1LG11g00090.1 Cpe11g00085 85
11 458802 463568 + Cp4.1LG11g00100.1 Cpe11g00086 86
5 31574047 31578673 - CrPI670011_05g019390.1 Cre05g1939 1939
5 31583701 31585700 - CrPI670011_05g019400.1 Cre05g1940 1940
8 24444218 24449451 + CrPI670011_08g011260.1 Cre08g1126 1126
2 17633288 17636761 - CsaV3_2G025670.1 Csa02g01847 1847
2 17637715 17642035 - CsaV3_2G025680.1 Csa02g01848 1848
2 17644905 17650120 + CsaV3_2G025690.1 Csa02g01849 1849
2 17653621 17658289 + CsaV3_2G025700.1 Csa02g01850 1850
2 19996377 20002016 + CsaV3_2G030460.1 Csa02g02227 2227
1 83600673 83603966 - Hsped.01g18670.1 Hepe01g1867 1867
1 83606487 83608851 - Hsped.01g18680.1 Hepe01g1868 1868
8 16165259 16170278 - Hsped.08g13780.1 Hepe08g1378 1378
8 16195661 16200757 - Hsped.08g13790.1 Hepe08g1379 1379
8 16216890 16221371 + Hsped.08g13800.1 Hepe08g1380 1380
8 16238818 16242395 + Hsped.08g13820.1 Hepe08g1382 1382
10 4549691 4557805 - Hsped.10g04070.1 Hepe10g0407 407
13 33143775 33149101 - Maker00034113 Lcy13g1458 1458
13 40668818 40673666 - Maker00025363 Lcy13g2173 2173
13 40681843 40687070 - Maker00025382 Lcy13g2174 2174
13 40695931 40699811 + Maker00025209 Lcy13g2175 2175
13 40701842 40705808 + Maker00025386 Lcy13g2176 2176
4 22091024 22101481 + Lsi04G014370.1 Lsi04g01437 1437
4 22109527 22114602 + Lsi04G014380.1 Lsi04g01438 1438
8 23734336 23735600 - Lsi08G015700.1 Lsi08g01570 1570
8 23746727 23761344 - Lsi08G015720.1 Lsi08g01572 1572
8 23761152 23765390 + Lsi08G015730.1 Lsi08g01573 1573
8 23767001 23770645 + Lsi08G015740.1 Lsi08g01574 1574
11 2536674 2538794 - MC11g0322 Mch11g0402 402
11 2540617 2543407 - MC11g0323 Mch11g0403 403
7 11388757 11400608 - Sed0015171.2 Sed07g1476 1476
8 32416281 32421722 - Sed0000349.1 Sed08g1756 1756
8 32429836 32435514 - Sed0000684.1 Sed08g1757 1757
8 32449938 32455168 + Sed0008959.1 Sed08g1758 1758
8 32456276 32460137 + Sed0001417.1 Sed08g1759 1759
11 33193281 33197537 + Sed0022728.1 Sed11g1844 1844
13 23460053 23464034 - Sed0011630.1 Sed13g1849 1849
13 23468672 23472304 - Sed0025565.1 Sed13g1850 1850
1 112312672 112315626 + Tan0008369.1 Tan01g4644 4644
1 112317390 112320371 + Tan0020530.1 Tan01g4645 4645
1 112324779 112328552 + Tan0006548.1 Tan01g4647 4647
2 77170214 77173904 - Tan0012164.1 Tan02g1649 1649
2 77176723 77185375 - Tan0006671.1 Tan02g1651 1651
2 77291516 77298282 + Tan0005370.1 Tan02g1654 1654
2 77429868 77435408 + Tan0012561.1 Tan02g1657 1657
2 93617206 93624686 + Tan0008094.1 Tan02g2503 2503
4 632642 638222 - Vvi4g52 Vvi4g52 52
4 641164 646899 - Vvi4g53 Vvi4g53 53
4 653634 659952 + Vvi4g54 Vvi4g54 54
4 660327 662113 - Vvi4g55 Vvi4g55 55
4 663812 668638 - Vvi4g56 Vvi4g56 56
4 669069 674844 + Vvi4g57 Vvi4g57 57
4 676238 680999 + Vvi4g58 Vvi4g58 58
4 684293 687056 - Vvi4g59 Vvi4g59 59
4 690535 694940 + Vvi4g60 Vvi4g60 60
4 695312 698914 - Vvi4g61 Vvi4g61 61
       

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