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
Vvi19g404 . . . . . . . Bma13g00917 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma16g00832 . . Cpe14g00714 . . . . . . . . . . . . . . . Lsi05g00656 . . .
Vvi19g405 Blo03g00589 . Bda07g00332 . . . . . . . Cma01g01159 Cma09g00916 . Car09g00833 Sed07g2646 . Cpe02g00742 Bhi09g01957 Tan01g4496 Cmetu04g0683 . Hepe01g1320 Mch11g1144 . . . . . . . . . Cone9ag0110 . . Lsi04g01253 . Chy04g01026 . . . . . Bpe11g00518 . . Bma14g00364 . Cmo01g01214 Cmo09g00910 . . . Car16g00572 . . . . . . . . . Cla05g01549 . . Cco05g1701 Clacu05g1649 Cmu05g1543 Cre05g1656 . . . Cme04g00788
Vvi19g406 Blo03g00588 . Bda07g00333 . . . . . . . Cma01g01158 Cma09g00918 . Car09g00834 . Cpe06g00738 Cpe02g00744 Bhi09g01956 . . . . Mch11g1145 . . . . . . . . . Cone9ag0109 . . Lsi04g01252 . Chy04g01023 . . . . . Bpe11g00519 . . Bma14g00362 . Cmo01g01212 Cmo09g00912 Cma04g01014 . Car04g00865 Car16g00570 Cpe14g00713 Cpe01g00836 . . . . . . . Cla05g01548 . . . . . . . . . Cme04g00791
Vvi19g407 . . . . Bpe09g00201 . . Bma13g01020 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00800 . Bda12g00881 . . . . . . . . . . . Cpe14g00712 . . . . . . . . . . . . . . . . . . .
Vvi19g408 . . . . . . Bma10g00532 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1117 Cone15ag1133 . . . . . . Bda05g00741 . . Bpe03g00807 . . . . . . . . . Cpe14g00711 Cpe01g00793 . . . . . . . . . . . . . . . . . .
Vvi19g409 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g410 Blo03g00587 . Bda07g00334 . Bpe09g00200 . . Bma13g01021 . . Cma01g01157 Cma09g00919 . Car09g00835 Sed07g1906 . . Bhi09g01955 Tan01g4499 Cmetu04g0493 . Hepe01g1317 Mch11g1146 . . . . . . . . . Cone9ag0108 Cone14ag1118 Cone15ag1134 Lsi04g01251 . Chy04g01022 . . Blo10g00801 . Bda12g00882 Bpe11g00520 . . Bma14g00361 . Cmo01g01211 Cmo09g00914 . . Car04g00864 Car16g00569 . . . . . . . . . Cla05g01547 Cam05g1655 Cec05g1659 Cco05g1697 Clacu05g1646 Cmu05g1541 Cre05g1652 . . . Cme04g00792
Vvi19g411 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g412 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g413 Blo03g00586 Blo03g01432 Bda07g00335 Bda09g00381 Bpe09g00199 Bpe08g01144 . Bma13g01022 . . Cma01g01156 Cma09g00920 . Car09g00836 Sed07g2650 Cpe06g00739 Cpe02g00745 Bhi09g01954 Tan01g4500 Cmetu04g2314 . Hepe01g1316 Mch11g1147 . . . . . . . . . Cone9ag0107 . . Lsi04g01250 . Chy04g01021 . . Blo10g00802 Bda05g00738 . Bpe11g00521 . Bma07g01318 Bma14g00360 . Cmo01g01210 Cmo09g00916 . . . Car16g00568 Cpe14g00710 . . . . . . . . Cla05g01546 Cam05g1654 Cec05g1658 Cco05g1696 Clacu05g1645 Cmu05g1540 Cre05g1651 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55747283 55747790 - Bda021882.1 Bda05g00738 738
5 55758203 55760377 - Bda021885.1 Bda05g00741 741
7 4419946 4421667 - Bda025418.1 Bda07g00332 332
7 4430724 4433552 + Bda025419.1 Bda07g00333 333
7 4435105 4436768 - Bda025420.1 Bda07g00334 334
7 4439531 4440196 + Bda025421.1 Bda07g00335 335
9 4882579 4883187 + Bda034089 Bda09g00381 381
12 39550628 39552822 + Bda033187 Bda12g00881 881
12 39556224 39557660 - Bda009413.1 Bda12g00882 882
9 54443091 54444097 - XM_039040881.1 Bhi09g01954 1954
9 54479029 54481454 + XM_039043708.1 Bhi09g01955 1955
9 54482504 54486485 - XM_039040385.1 Bhi09g01956 1956
9 54565368 54568124 + XM_039043191.1 Bhi09g01957 1957
3 22959623 22960286 - BLOR11767 Blo03g00586 586
3 23006884 23008506 + BLOR11768 Blo03g00587 587
3 23009892 23012761 - BLOR11769 Blo03g00588 588
3 23047572 23049293 + BLOR11770 Blo03g00589 589
3 40915096 40919470 + BLOR12613 Blo03g01432 1432
10 25375794 25376871 + BLOR02590 Blo10g00800 800
10 25382475 25384004 - BLOR02591 Blo10g00801 801
10 25386486 25387053 + BLOR02592 Blo10g00802 802
7 48715208 48715816 - Bma031405 Bma07g01318 1318
10 6466135 6467991 + Bma030357 Bma10g00532 532
13 39585436 39587814 + Bma009994.1 Bma13g00917 917
13 42780750 42782925 + Bma010148.2 Bma13g01020 1020
13 42785489 42786935 - Bma010149.1 Bma13g01021 1021
13 42794183 42794780 + Bma010150.1 Bma13g01022 1022
14 4375190 4375857 - Bma030659 Bma14g00360 360
14 4387186 4388854 + Bma010781.1 Bma14g00361 361
14 4390302 4393023 - Bma010782.1 Bma14g00362 362
14 4406307 4408028 + Bma010784.1 Bma14g00364 364
3 27997879 28000022 - Bpe012716.1 Bpe03g00807 807
8 13284869 13285468 - Bpe023269.1 Bpe08g01144 1144
9 1392936 1393521 - Bpe026213 Bpe09g00199 199
9 1397029 1398471 + Bpe023866.1 Bpe09g00200 200
9 1400758 1402894 - Bpe023867.1 Bpe09g00201 201
11 4035595 4037316 - Bpe003886.1 Bpe11g00518 518
11 4047241 4049954 + Bpe003887.1 Bpe11g00519 519
11 4051556 4053220 - Bpe003888.1 Bpe11g00520 520
11 4058222 4058892 + Bpe024762 Bpe11g00521 521
5 24386223 24386822 - CaPI482276_05g016540.1 Cam05g1654 1654
5 24411273 24412894 + CaPI482276_05g016550.1 Cam05g1655 1655
4 4978981 4980614 - Carg00039-RA Car04g00864 864
4 4982848 4985351 - Carg00040-RA Car04g00865 865
9 5076543 5078276 - Carg12787-RA Car09g00833 833
9 5090037 5093601 + Carg12788-RA Car09g00834 834
9 5096028 5097651 - Carg12789-RA Car09g00835 835
9 5100382 5101342 + Carg12790-RA Car09g00836 836
16 3594288 3595245 - Carg05653-RA Car16g00568 568
16 3597167 3598716 + Carg05654-RA Car16g00569 569
16 3599664 3602484 - Carg05655-RA Car16g00570 570
16 3613089 3614837 + Carg05657-RA Car16g00572 572
5 24889612 24890211 - CcPI632755_05g016960.1 Cco05g1696 1696
5 24934045 24935672 + CcPI632755_05g016970.1 Cco05g1697 1697
5 25051197 25053690 + CcPI632755_05g017010.1 Cco05g1701 1701
5 27282257 27282856 - CePI673135_05g016580.1 Cec05g1658 1658
5 27332078 27333750 + CePI673135_05g016590.1 Cec05g1659 1659
4 15132412 15133036 - Chy4G077390.1 Chy04g01021 1021
4 15163880 15165504 + Chy4G077400.1 Chy04g01022 1022
4 15167067 15169711 - Chy4G077410.1 Chy04g01023 1023
4 15263883 15265670 + Chy4G077440.1 Chy04g01026 1026
5 24460904 24461503 - ClG42_05g0164500.10 Clacu05g1645 1645
5 24515990 24517608 + ClG42_05g0164600.10 Clacu05g1646 1646
5 24584293 24584631 - ClG42_05g0164900.10 Clacu05g1649 1649
5 25838194 25839387 - ClCG05G014880.1 Cla05g01546 1546
5 25896322 25897940 + ClCG05G014890.2 Cla05g01547 1547
5 25899733 25902609 - ClCG05G014900.1 Cla05g01548 1548
5 25965162 25973493 - ClCG05G014910.1 Cla05g01549 1549
1 8447288 8448364 - CmaCh01G011560.1 Cma01g01156 1156
1 8450329 8451898 + CmaCh01G011570.1 Cma01g01157 1157
1 8452702 8456351 - CmaCh01G011580.1 Cma01g01158 1158
1 8466405 8468144 + CmaCh01G011590.1 Cma01g01159 1159
4 5266210 5270073 + CmaCh04G010140.1 Cma04g01014 1014
9 4566670 4568403 - CmaCh09G009160.1 Cma09g00916 916
9 4577607 4580778 + CmaCh09G009180.1 Cma09g00918 918
9 4582915 4584503 - CmaCh09G009190.1 Cma09g00919 919
9 4587252 4587961 + CmaCh09G009200.1 Cma09g00920 920
16 4716753 4719688 + CmaCh16G008320.1 Cma16g00832 832
4 9540036 9542595 - MELO3C018144.2.1 Cme04g00788 788
4 9670850 9674544 + MELO3C018139.2.1 Cme04g00791 791
4 9675644 9677476 - MELO3C018138.2.1 Cme04g00792 792
4 2538512 2539657 - PI0027804.1 Cmetu04g0493 493
4 25184744 25187381 + PI0005302.1 Cmetu04g0683 683
4 25078251 25079552 - PI0018344.1 Cmetu04g2314 2314
1 9778729 9779418 - CmoCh01G012100.1 Cmo01g01210 1210
1 9781096 9782597 + CmoCh01G012110.1 Cmo01g01211 1211
1 9783257 9787103 - CmoCh01G012120.1 Cmo01g01212 1212
1 9797559 9799307 + CmoCh01G012140.1 Cmo01g01214 1214
9 4762310 4764043 - CmoCh09G009100.1 Cmo09g00910 910
9 4776770 4779760 + CmoCh09G009120.1 Cmo09g00912 912
9 4781899 4783463 - CmoCh09G009140.1 Cmo09g00914 914
9 4785535 4786780 + CmoCh09G009160.1 Cmo09g00916 916
5 24180790 24181389 - CmPI595203_05g015400.1 Cmu05g1540 1540
5 24235898 24237516 + CmPI595203_05g015410.1 Cmu05g1541 1541
5 24298091 24298429 - CmPI595203_05g015430.1 Cmu05g1543 1543
9 467804 468801 - Conep09aG0010700.1 Cone9ag0107 107
9 469629 471300 + Conep09aG0010800.1 Cone9ag0108 108
9 472426 475620 - Conep09aG0010900.1 Cone9ag0109 109
9 478390 481250 + Conep09aG0011000.1 Cone9ag0110 110
14 9309525 9311034 + Conep14aG0113900.1 Cone14ag1117 1117
14 9313725 9315485 - Conep14aG0114000.1 Cone14ag1118 1118
15 9224364 9226943 + Conep15aG0115900.1 Cone15ag1133 1133
15 9227314 9228633 - Conep15aG0116000.1 Cone15ag1134 1134
1 4677585 4680423 - Cp4.1LG01g08760.1 Cpe01g00793 793
1 4957749 4960592 - Cp4.1LG01g08380.1 Cpe01g00836 836
2 4722576 4724321 - Cp4.1LG02g01340.1 Cpe02g00742 742
2 4735010 4738946 + Cp4.1LG02g01290.1 Cpe02g00744 744
2 4743190 4744471 + Cp4.1LG02g01240.1 Cpe02g00745 745
6 4636267 4639682 + Cp4.1LG06g07330.1 Cpe06g00738 738
6 4644688 4645788 + Cp4.1LG06g07260.1 Cpe06g00739 739
14 4684114 4685195 - Cp4.1LG14g00050.1 Cpe14g00710 710
14 4692992 4695651 - Cp4.1LG14g00070.1 Cpe14g00711 711
14 4717569 4720356 - Cp4.1LG14g00040.1 Cpe14g00712 712
14 4720960 4726198 - Cp4.1LG14g00060.1 Cpe14g00713 713
14 4728483 4729419 + Cp4.1LG14g00090.1 Cpe14g00714 714
5 27315770 27316369 - CrPI670011_05g016510.1 Cre05g1651 1651
5 27364797 27366418 + CrPI670011_05g016520.1 Cre05g1652 1652
5 27522011 27523072 + CrPI670011_05g016560.1 Cre05g1656 1656
1 78369332 78369917 - Hsped.01g13160.1 Hepe01g1316 1316
1 78378817 78380455 + Hsped.01g13170.1 Hepe01g1317 1317
1 78408881 78411179 + Hsped.01g13200.1 Hepe01g1320 1320
4 19477750 19479040 - Lsi04G012500.1 Lsi04g01250 1250
4 19487967 19490104 + Lsi04G012510.1 Lsi04g01251 1251
4 19491354 19494823 - Lsi04G012520.1 Lsi04g01252 1252
4 19527943 19530358 + Lsi04G012530.1 Lsi04g01253 1253
5 8410960 8415720 + Lsi05G006560.1 Lsi05g00656 656
11 8022143 8023897 - MC11g0943 Mch11g1144 1144
11 8045229 8047987 + MC11g0944 Mch11g1145 1145
11 8049517 8051116 - MC11g0945 Mch11g1146 1146
11 8054504 8055119 + MC11g0946 Mch11g1147 1147
7 32919466 32922317 + Sed0017155.1 Sed07g1906 1906
7 41913935 41916955 - Sed0027942.1 Sed07g2646 2646
7 41950908 41951848 + Sed0022896.1 Sed07g2650 2650
1 110541079 110543851 - Tan0014132.1 Tan01g4496 4496
1 110613449 110615413 - Tan0013865.1 Tan01g4499 4499
1 110634767 110635853 + Tan0022396.1 Tan01g4500 4500
19 5254956 5257674 + Vvi19g404 Vvi19g404 404
19 5275676 5279667 - Vvi19g405 Vvi19g405 405
19 5304036 5310414 + Vvi19g406 Vvi19g406 406
19 5311061 5315097 + Vvi19g407 Vvi19g407 407
19 5318041 5326891 + Vvi19g408 Vvi19g408 408
19 5327582 5327979 + Vvi19g409 Vvi19g409 409
19 5329127 5331056 - Vvi19g410 Vvi19g410 410
19 5331069 5331677 - Vvi19g411 Vvi19g411 411
19 5339583 5342567 + Vvi19g412 Vvi19g412 412
19 5356451 5357337 + Vvi19g413 Vvi19g413 413
       

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