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
Vvi17g506 Blo04g00759 . . . . . . . Cmo13g00959 Cmo18g00097 . . . . . Cpe20g00202 . . . . . . . . . . . . . . . . . . . Lsi02g00313 Csa01g00791 Chy12g01325 Cme12g01752 . . . . . Bpe15g00613 Bma03g00816 . Sed14g0733 . . Cma13g00930 Cma18g00127 Car13g00770 Car18g00117 . . Bhi08g01415 Tan05g2083 Cmetu08g1169 Lac10g0371 Hepe07g2284 . . Cla01g01425 Cam01g1492 Cec01g1532 Cco01g1578 Clacu01g1516 Cmu01g1408 Cre01g1326 . . . .
Vvi17g507 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g508 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0087 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g509 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g510 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g511 . Blo16g00243 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00312 Csa01g00790 Chy12g01326 . . . . Bda14g00790 . Bpe15g00661 . . . . . . Cma18g00126 . Car18g00116 Cpe09g01067 . Bhi08g01414 Tan05g2886 . Lac10g0530 . . . Cla01g01426 Cam01g1493 Cec01g1533 Cco01g1579 Clacu01g1517 Cmu01g1409 Cre01g1327 . . . .
Vvi17g512 . . . . . . . Bma12g01005 . . . Cma11g00162 . Car11g00138 Sed08g0198 . Cpe04g01514 Bhi02g00344 Tan09g2159 Cmetu02g0856 . Hepe09g0136 . . Cla06g01606 Cam06g1780 Cec06g1831 Cco06g1840 Clacu06g1742 Cmu06g1687 Cre06g2503 . . Cone13ag0086 . . . . . . . . . Bpe07g00794 . . . . . Cmo11g00148 . . . . . . . . . . . . . . . . . . . . Lsi06g01484 Csa01g00215 Chy02g02516 Cme02g01902
Vvi17g513 Blo04g00760 . . . . . . . . Cmo18g00096 . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00309 Csa01g00789 Chy12g01327 Cme12g01754 . . . Bda14g00840 . Bpe15g00612 Bma03g00817 . Sed08g2575 . . . Cma18g00125 . Car18g00114 Cpe09g01068 . Bhi08g01412 Tan05g2085 Cmetu12g1842 Lac10g0369 Hepe07g2285 . . Cla01g01427 Cam01g1494 Cec01g1534 Cco01g1580 Clacu01g1518 Cmu01g1410 Cre01g1328 . . . .
Vvi17g514 . . . . . . . Bma12g01004 . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0085 . . . . . . . . . Bpe07g00793 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g515 . . Bda06g00553 . . . . Bma12g01003 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0086 . . . . . . . . Bpe07g00792 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7806279 7815866 + Bda023813.1 Bda06g00553 553
14 6120551 6122066 + Bda027559.1 Bda14g00790 790
14 6461882 6468020 - Bda027614.3 Bda14g00840 840
2 6731776 6738007 + XM_039023712.1 Bhi02g00344 344
8 41871012 41878621 + XM_039038679.1 Bhi08g01412 1412
8 41879427 41884592 - XM_039038681.1 Bhi08g01414 1414
8 41889218 41892968 + XM_039038027.1 Bhi08g01415 1415
4 7203603 7206668 - BLOR13671 Blo04g00759 759
4 7209069 7215202 - BLOR13672 Blo04g00760 760
16 5643367 5644896 - BLOR07491 Blo16g00243 243
3 7571524 7574361 - Bma017130.1 Bma03g00816 816
3 7576666 7582807 - Bma017131.1 Bma03g00817 817
12 42134026 42135228 + Bma008351.1 Bma12g01003 1003
12 42135866 42138075 - Bma008352.1 Bma12g01004 1004
12 42140982 42143658 + Bma008353.1 Bma12g01005 1005
7 14331979 14333166 + Bpe021637.1 Bpe07g00792 792
7 14333799 14336082 - Bpe021638.1 Bpe07g00793 793
7 14338712 14341349 + Bpe021639.1 Bpe07g00794 794
15 17006379 17012473 + Bpe001545.1 Bpe15g00612 612
15 17014887 17017952 + Bpe001546.1 Bpe15g00613 613
15 17324303 17325815 - Bpe001594.1 Bpe15g00661 661
1 28461280 28464369 - CaPI482276_01g014920.1 Cam01g1492 1492
1 28470109 28471758 + CaPI482276_01g014930.1 Cam01g1493 1493
1 28472992 28480091 - CaPI482276_01g014940.1 Cam01g1494 1494
6 28964193 28972132 + CaPI482276_06g017800.1 Cam06g1780 1780
11 778347 782251 - Carg18175-RA Car11g00138 138
13 8614148 8616052 - Carg07720-RA Car13g00770 770
18 615003 621853 + Carg06679-RA Car18g00114 114
18 623998 626218 - Carg06681-RA Car18g00116 116
18 627762 633033 + Carg06682-RA Car18g00117 117
1 28478445 28481528 - CcPI632755_01g015780.1 Cco01g1578 1578
1 28487067 28488786 + CcPI632755_01g015790.1 Cco01g1579 1579
1 28490024 28497106 - CcPI632755_01g015800.1 Cco01g1580 1580
6 28672977 28680467 + CcPI632755_06g018400.1 Cco06g1840 1840
1 29906855 29909938 - CePI673135_01g015320.1 Cec01g1532 1532
1 29916046 29917730 + CePI673135_01g015330.1 Cec01g1533 1533
1 29918980 29926452 - CePI673135_01g015340.1 Cec01g1534 1534
6 31734592 31742339 + CePI673135_06g018310.1 Cec06g1831 1831
2 28549265 28554359 + Chy2G047830.1 Chy02g02516 2516
12 17599561 17604499 - Chy12G219250.1 Chy12g01325 1325
12 17608593 17610339 + Chy12G219260.1 Chy12g01326 1326
12 17611355 17618068 - Chy12G219270.1 Chy12g01327 1327
1 27243174 27246257 - ClG42_01g0151600.10 Clacu01g1516 1516
1 27251539 27253221 + ClG42_01g0151700.10 Clacu01g1517 1517
1 27254437 27261520 - ClG42_01g0151800.10 Clacu01g1518 1518
6 28018936 28025715 + ClG42_06g0174200.10 Clacu06g1742 1742
1 28734947 28738030 - ClCG01G014410.1 Cla01g01425 1425
1 28743312 28744994 + ClCG01G014420.1 Cla01g01426 1426
1 28745989 28753535 - ClCG01G014430.1 Cla01g01427 1427
6 29583470 29590249 + ClCG06G016360.2 Cla06g01606 1606
11 837375 841723 + CmaCh11G001620.1 Cma11g00162 162
13 7368623 7371709 - CmaCh13G009300.1 Cma13g00930 930
18 610631 614615 + CmaCh18G001250.1 Cma18g00125 125
18 615357 619017 - CmaCh18G001260.1 Cma18g00126 126
18 620442 623678 + CmaCh18G001270.1 Cma18g00127 127
2 25485178 25491493 + MELO3C017156.2.1 Cme02g01902 1902
12 24200802 24204099 - MELO3C002206.2.1 Cme12g01752 1752
12 24211690 24218654 - MELO3C002204.2.1 Cme12g01754 1754
2 23822202 23827926 + PI0007180.1 Cmetu02g0856 856
8 13021716 13024820 + PI0026160.1 Cmetu08g1169 1169
12 2074138 2081308 + PI0016432.1 Cmetu12g1842 1842
11 744678 748905 - CmoCh11G001480.1 Cmo11g00148 148
13 8312927 8316013 - CmoCh13G009590.1 Cmo13g00959 959
18 655275 662057 + CmoCh18G000960.1 Cmo18g00096 96
18 668777 674169 + CmoCh18G000970.1 Cmo18g00097 97
1 27586908 27589997 - CmPI595203_01g014080.1 Cmu01g1408 1408
1 27595283 27596965 + CmPI595203_01g014090.1 Cmu01g1409 1409
1 27598181 27605267 - CmPI595203_01g014100.1 Cmu01g1410 1410
6 27927303 27934675 + CmPI595203_06g016870.1 Cmu06g1687 1687
13 536648 539443 - Conep13aG0008900.1 Cone13ag0085 85
13 539682 543692 + Conep13aG0009000.1 Cone13ag0086 86
19 504896 506493 + Conep19aG0009200.1 Cone19ag0086 86
19 508835 509618 + Conep19aG0009300.1 Cone19ag0087 87
4 11935412 11940595 + Cp4.1LG04g15070.1 Cpe04g01514 1514
9 9286487 9290502 + Cp4.1LG09g10630.1 Cpe09g01067 1067
9 9291247 9298011 - Cp4.1LG09g10750.1 Cpe09g01068 1068
20 1163679 1167701 + Cp4.1LG20g01970.1 Cpe20g00202 202
1 26463474 26466557 - CrPI670011_01g013260.1 Cre01g1326 1326
1 26471749 26473429 + CrPI670011_01g013270.1 Cre01g1327 1327
1 26474438 26481539 - CrPI670011_01g013280.1 Cre01g1328 1328
6 32741647 32749151 + CrPI670011_06g025030.1 Cre06g2503 2503
1 1392804 1402108 - CsaV3_1G002150.1 Csa01g00215 215
1 4997015 5004043 + CsaV3_1G007890.1 Csa01g00789 789
1 5004584 5006591 - CsaV3_1G007900.1 Csa01g00790 790
1 5010170 5016708 + CsaV3_1G007910.1 Csa01g00791 791
7 67151965 67155036 - Hsped.07g22840.1 Hepe07g2284 2284
7 67160582 67167179 - Hsped.07g22850.1 Hepe07g2285 2285
9 1084229 1089860 + Hsped.09g01360.1 Hepe09g0136 136
10 2895219 2903203 + Lag0024414.1 Lac10g0369 369
10 2911554 2914637 + Lag0024416.1 Lac10g0371 371
10 4115298 4116805 - Lag0024575.1 Lac10g0530 530
2 2670675 2685961 + Lsi02G003090.1 Lsi02g00309 309
2 2687334 2689511 - Lsi02G003120.1 Lsi02g00312 312
2 2697484 2700567 + Lsi02G003130.1 Lsi02g00313 313
6 25320379 25327597 + Lsi06G014840.1 Lsi06g01484 1484
8 1116298 1122029 - Sed0007559.1 Sed08g0198 198
8 38242116 38248767 - Sed0028137.1 Sed08g2575 2575
14 7557725 7562501 - Sed0003697.1 Sed14g0733 733
5 71255332 71260187 - Tan0013761.1 Tan05g2083 2083
5 71269316 71277471 - Tan0001575.1 Tan05g2085 2085
5 81256955 81259028 - Tan0006837.2 Tan05g2886 2886
9 71694241 71701013 + Tan0014563.1 Tan09g2159 2159
17 6173380 6176410 - Vvi17g506 Vvi17g506 506
17 6176483 6176741 + Vvi17g507 Vvi17g507 507
17 6180588 6181177 - Vvi17g508 Vvi17g508 508
17 6187382 6189951 - Vvi17g509 Vvi17g509 509
17 6211392 6213589 - Vvi17g510 Vvi17g510 510
17 6215991 6217587 + Vvi17g511 Vvi17g511 511
17 6218346 6227878 - Vvi17g512 Vvi17g512 512
17 6230027 6253619 - Vvi17g513 Vvi17g513 513
17 6265858 6279294 + Vvi17g514 Vvi17g514 514
17 6280174 6283955 - Vvi17g515 Vvi17g515 515
       

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