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
Vvi3g496 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g497 . . . . . Bpe12g00068 . . Cmo19g00646 Cmo11g01334 . . . . Sed10g2061 Cpe04g00258 Cpe15g00510 Bhi05g01161 Tan02g0868 Cmetu01g2091 . Hepe02g0557 . . Cla02g00569 Cam02g0599 Cec02g0599 Cco02g0610 Clacu02g0595 Cmu02g0593 Cre02g0922 Cone12ag1119 Cone8ag1164 . . . Csa07g00809 . Cme01g00016 . Blo13g00561 Bda15g00025 . . . . . . . . Cma11g01776 Cma19g00628 Car11g01075 Car19g00479 . . . . . . . . . . . . . . . . . . Chy01g00020 .
Vvi3g498 . . . Bda08g01358 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g499 . Blo15g00722 Bda06g01030 . . . . Bma12g00479 . . . Cma20g00886 . Car20g00763 . . . . . . . . . . . . . . . . . . . Cone3ag1120 . Lsi10g00319 . Chy11g00428 . . . . . . . . . . . Cmo20g00893 . . . . . . . . . . . . . Cla09g01727 Cam09g1821 Cec09g1881 Cco09g1974 . . Cre01g0687 . Csa02g01208 . Cme11g00499
Vvi3g500 . . . . . Bpe12g00069 . . Cmo19g00647 Cmo11g01333 . . . . . Cpe04g00257 Cpe15g00511 Bhi05g01163 . . . Hepe02g0556 . . Cla02g00568 Cam02g0598 Cec02g0598 Cco02g0609 Clacu02g0594 Cmu02g0592 Cre02g0921 Cone12ag1120 Cone8ag1165 . . . Csa07g00810 . Cme01g00015 . . Bda15g00024 . . . . . . . . Cma11g01777 Cma19g00630 Car11g01074 Car19g00481 . . . . . . . . . . . . . . . . Lsi11g01041 . Chy01g00019 .
Vvi3g501 . . . . . . . . . . Cma02g00432 . Car02g00287 . . . . . . . . . . . . . . . . . . . . . . Lsi10g00320 . Chy11g00426 . . . . . . . . . . Cmo02g00434 . . . . . . Cpe05g01230 . . . . . . . Cla09g01728 Cam09g1822 Cec09g1882 Cco09g1975 . . Cre01g0686 . Csa02g01209 . Cme11g00249
Vvi3g502 . . Bda06g01029 . Bpe07g00399 . . Bma12g00480 . . Cma02g00431 Cma20g00885 Car02g00286 Car20g00762 . . . . . . . . . . . . . . . . . . . . Cone10ag1129 Lsi10g00321 . Chy11g00425 . . . . . . . . . . Cmo02g00433 Cmo20g00892 . . . . . Cpe05g01231 . . . . . . . Cla09g01729 Cam09g1823 Cec09g1883 Cco09g1976 . . Cre01g0685 . Csa02g01210 . Cme11g00494
Vvi3g503 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g504 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g505 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 36168269 36169378 + Bda022774.1 Bda06g01029 1029
6 36186410 36187395 + Bda022775.1 Bda06g01030 1030
8 54032646 54033313 + Bda030408.1 Bda08g01358 1358
15 1644275 1656573 - Bda011778.2 Bda15g00024 24
15 1659368 1663159 + Bda011779.1 Bda15g00025 25
5 41579207 41584646 - XM_039032919.1 Bhi05g01161 1161
5 41630348 41645516 + XM_039032119.1 Bhi05g01163 1163
13 27619910 27624332 + BLOR19613 Blo13g00561 561
15 23924773 23926028 + BLOR07116 Blo15g00722 722
12 13941553 13942526 - Bma007511.1 Bma12g00479 479
12 13943701 13944809 - Bma007512.1 Bma12g00480 480
7 3789900 3790992 - Bpe021218.1 Bpe07g00399 399
12 477028 481581 - Bpe005306.1 Bpe12g00068 68
12 482836 494979 + Bpe005307.2 Bpe12g00069 69
2 6806360 6817006 - CaPI482276_02g005980.1 Cam02g0598 598
2 6825137 6830113 + CaPI482276_02g005990.1 Cam02g0599 599
9 32676121 32677117 - CaPI482276_09g018210.1 Cam09g1821 1821
9 32681778 32685785 + CaPI482276_09g018220.1 Cam09g1822 1822
9 32686401 32690113 - CaPI482276_09g018230.1 Cam09g1823 1823
2 1936163 1938704 + Carg22971-RA Car02g00286 286
2 1938459 1942154 - Carg22972-RA Car02g00287 287
11 8317364 8329475 - Carg20167-RA Car11g01074 1074
11 8354328 8359882 + Carg26379-RA Car11g01075 1075
19 6427430 6430891 - Carg22045-RA Car19g00479 479
19 6435601 6446143 + Carg22043-RA Car19g00481 481
20 4491150 4493535 + Carg23621-RA Car20g00762 762
20 4496185 4497421 + Carg23620-RA Car20g00763 763
2 5972108 5985058 - CcPI632755_02g006090.1 Cco02g0609 609
2 5991312 5996223 + CcPI632755_02g006100.1 Cco02g0610 610
9 33910180 33911192 - CcPI632755_09g019740.1 Cco09g1974 1974
9 33916327 33920221 + CcPI632755_09g019750.1 Cco09g1975 1975
9 33920792 33924401 - CcPI632755_09g019760.1 Cco09g1976 1976
2 5866488 5876556 - CePI673135_02g005980.1 Cec02g0598 598
2 5885437 5890455 + CePI673135_02g005990.1 Cec02g0599 599
9 35600644 35601634 - CePI673135_09g018810.1 Cec09g1881 1881
9 35606598 35610549 + CePI673135_09g018820.1 Cec09g1882 1882
9 35611171 35614910 - CePI673135_09g018830.1 Cec09g1883 1883
1 140008 150280 - Chy1G000190.1 Chy01g00019 19
1 154996 160123 + Chy1G000200.1 Chy01g00020 20
11 4119510 4121958 + Chy11G190050.1 Chy11g00425 425
11 4122483 4126309 - Chy11G190060.1 Chy11g00426 426
11 4129053 4130004 + Chy11G190080.1 Chy11g00428 428
2 5789777 5800380 - ClG42_02g0059400.10 Clacu02g0594 594
2 5808583 5813597 + ClG42_02g0059500.10 Clacu02g0595 595
2 6057836 6071212 - ClCG02G005570.2 Cla02g00568 568
2 6079266 6084888 + ClCG02G005580.2 Cla02g00569 569
9 34580572 34582287 - ClCG09G017640.1 Cla09g01727 1727
9 34587199 34591840 + ClCG09G017650.1 Cla09g01728 1728
9 34591171 34595612 - ClCG09G017660.2 Cla09g01729 1729
2 2183425 2184885 + CmaCh02G004310.1 Cma02g00431 431
2 2184341 2188533 - CmaCh02G004320.1 Cma02g00432 432
11 11872503 11877886 - CmaCh11G017760.1 Cma11g01776 1776
11 11883242 11896920 + CmaCh11G017770.1 Cma11g01777 1777
19 6765568 6770592 - CmaCh19G006280.1 Cma19g00628 628
19 6773296 6784615 + CmaCh19G006300.1 Cma19g00630 630
20 4251850 4254509 + CmaCh20G008850.1 Cma20g00885 885
20 4256785 4257989 + CmaCh20G008860.1 Cma20g00886 886
1 149854 160662 - MELO3C018420.2.1 Cme01g00015 15
1 161926 167373 + MELO3C018421.2.1 Cme01g00016 16
11 2812747 2815558 - MELO3C020926.2.1 Cme11g00249 249
11 4936161 4938748 + MELO3C021927.2.1 Cme11g00494 494
11 4973963 4975468 + MELO3C021923.2.1 Cme11g00499 499
1 194934 200266 + PI0018302.1 Cmetu01g2091 2091
2 2262900 2265473 + CmoCh02G004330.1 Cmo02g00433 433
2 2265534 2268959 - CmoCh02G004340.1 Cmo02g00434 434
11 9201538 9213679 - CmoCh11G013330.1 Cmo11g01333 1333
11 9242989 9248261 + CmoCh11G013340.1 Cmo11g01334 1334
19 6980027 6985610 - CmoCh19G006460.1 Cmo19g00646 646
19 6988487 6998833 + CmoCh19G006470.1 Cmo19g00647 647
20 4524047 4526379 + CmoCh20G008920.1 Cmo20g00892 892
20 4528768 4529967 + CmoCh20G008930.1 Cmo20g00893 893
2 5696567 5707171 - CmPI595203_02g005920.1 Cmu02g0592 592
2 5715344 5720358 + CmPI595203_02g005930.1 Cmu02g0593 593
3 29783802 29785270 - Conep03aG0162400.1 Cone3ag1120 1120
8 10076049 10079132 - Conep08aG0119600.1 Cone8ag1164 1164
8 10079695 10085298 + Conep08aG0119700.1 Cone8ag1165 1165
10 8127239 8128444 - Conep10aG0116100.1 Cone10ag1129 1129
12 9040626 9044023 - Conep12aG0115500.1 Cone12ag1119 1119
12 9044472 9050537 + Conep12aG0115600.1 Cone12ag1120 1120
4 3176829 3190859 - Cp4.1LG04g08230.1 Cpe04g00257 257
4 3197089 3202585 + Cp4.1LG04g08260.1 Cpe04g00258 258
5 8624018 8627794 + Cp4.1LG05g12220.1 Cpe05g01230 1230
5 8626948 8629211 - Cp4.1LG05g12320.1 Cpe05g01231 1231
15 6027484 6032745 - Cp4.1LG15g05070.1 Cpe15g00510 510
15 6035576 6047623 + Cp4.1LG15g05040.1 Cpe15g00511 511
1 6388948 6392636 + CrPI670011_01g006850.1 Cre01g0685 685
1 6393260 6397237 - CrPI670011_01g006860.1 Cre01g0686 686
1 6402455 6403442 + CrPI670011_01g006870.1 Cre01g0687 687
2 6296864 6307478 - CrPI670011_02g009210.1 Cre02g0921 921
2 6315826 6320802 + CrPI670011_02g009220.1 Cre02g0922 922
2 11894235 11895717 - CsaV3_2G014240.1 Csa02g01208 1208
2 11898407 11900822 + CsaV3_2G014250.1 Csa02g01209 1209
2 11901048 11903902 - CsaV3_2G014260.1 Csa02g01210 1210
7 5684567 5689467 - CsaV3_7G010070.1 Csa07g00809 809
7 5690610 5700684 + CsaV3_7G010080.1 Csa07g00810 810
2 5615388 5626334 - Hsped.02g05560.1 Hepe02g0556 556
2 5638198 5643331 + Hsped.02g05570.1 Hepe02g0557 557
10 5135357 5136557 - Lsi10G003190.1 Lsi10g00319 319
10 5140791 5145834 + Lsi10G003200.1 Lsi10g00320 320
10 5145194 5149487 - Lsi10G003210.1 Lsi10g00321 321
11 17942650 17952455 + Lsi11G010410.1 Lsi11g01041 1041
10 37108915 37113971 - Sed0008645.2 Sed10g2061 2061
2 9668223 9675019 + Tan0006988.4 Tan02g0868 868
3 4802388 4802910 - Vvi3g496 Vvi3g496 496
3 4804013 4809985 - Vvi3g497 Vvi3g497 497
3 4813763 4817457 - Vvi3g498 Vvi3g498 498
3 4819001 4820340 - Vvi3g499 Vvi3g499 499
3 4827171 4848481 + Vvi3g500 Vvi3g500 500
3 4854092 4857037 + Vvi3g501 Vvi3g501 501
3 4857381 4858281 - Vvi3g502 Vvi3g502 502
3 4866535 4866772 + Vvi3g503 Vvi3g503 503
3 4870221 4872315 - Vvi3g504 Vvi3g504 504
3 4874232 4875367 + Vvi3g505 Vvi3g505 505
       

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