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
Vvi17g136 . . . . . . . . Cmo13g00831 Cmo18g00210 . . . . . Cpe20g00312 . . . . . . . . . . . . . . . . Cone16ag0023 . . Lsi02g00497 Csa01g00957 Chy12g01175 Cme12g01597 . . . Bda14g01371 . Bpe15g00212 Bma03g01261 . Sed08g2443 . . Cma13g00799 Cma18g00324 Car13g00647 Car18g00224 Cpe09g00967 . Bhi08g01470 Tan05g2947 Cmetu12g1333 Lac10g0575 Hepe07g2100 . . Cla03g00349 Cam03g0366 Cec03g0354 Cco03g0368 Clacu03g0366 Cmu03g0972 Cre03g0664 . . . .
Vvi17g137 . . . . . . . . . Cmo18g00209 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma18g00325 . Car18g00223 . . Bhi08g01468 . . . Hepe07g2098 . . . . . . . . . . . . .
Vvi17g138 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00493 Csa01g00955 Chy12g01177 . . . . . . . . . Sed08g2444 . . . . . . Cpe09g00968 . Bhi08g01467 Tan05g2944 Cmetu07g1959 . . . . Cla03g00346 Cam03g0364 Cec03g0353 . . Cmu03g0970 Cre03g0662 . . . .
Vvi17g139 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g140 . . . . . . . Bma12g01077 Cmo13g00830 Cmo18g00206 . Cma11g00044 Car10g00059 Car11g00039 Sed08g2445 Cpe20g00313 Cpe04g01606 Bhi02g00535 Tan09g2357 Cmetu12g1017 . Hepe09g0059 . . Cla06g01732 Cam06g1923 Cec06g1973 Cco06g1977 Clacu06g1879 Cmu06g1821 Cre06g2636 Cone2ag0966 Cone16ag0026 . . Lsi02g00491 Csa01g00954 Chy12g01178 Cme12g01598 . Blo15g00214 . . . . . . . Cmo10g00068 Cmo11g00044 Cma13g00797 . Car13g00646 Car18g00222 Cpe09g00969 . . . . . . . . . . . . . . . Lsi06g01632 Csa01g00067 Chy02g02653 .
Vvi17g141 . . . Bda15g00609 Bpe12g00540 . . . Cmo13g00829 Cmo18g00204 . . . . . Cpe20g00314 . . . . . . . . . . . . . . . Cone2ag0965 Cone16ag0027 . . Lsi02g00490 Csa01g00953 Chy12g01179 Cme12g01599 . . . . . . . Bma08g00228 . . . Cma13g00795 . Car13g00644 Car18g00220 Cpe09g00970 . Bhi08g01464 . . . . . . Cla03g00345 . . . . . . . . . .
Vvi17g142 . . Bda06g00736 . . . . Bma12g01076 . . Cma10g00072 . Car10g00060 . . . . Bhi02g00536 . . . Hepe09g0060 . . Cla06g01731 Cam06g1922 Cec06g1972 Cco06g1976 Clacu06g1878 Cmu06g1820 Cre06g2635 . . Cone13ag0211 Cone19ag0200 . . . . . Blo15g00215 . . Bpe07g00883 . . . . Cmo10g00069 . . . . . . . . . . . . . . . . . . . . . Lsi06g01631 Csa01g00068 Chy02g02652 .
Vvi17g143 . . Bda06g00737 . . . . Bma12g01075 . Cmo18g00202 . . Car10g00061 . . . . Bhi02g00537 . . . Hepe09g0061 . . . . . . . . . Cone2ag0964 Cone16ag0028 . Cone19ag0199 Lsi02g00488 Csa01g00950 Chy12g01181 Cme12g01602 . Blo15g00217 Bda11g01817 . Bpe07g00882 . . . . . . . . . Car18g00219 Cpe09g00971 . Bhi08g01461 . . . . . . Cla03g00344 Cam03g0360 . Cco03g0365 Clacu03g0361 Cmu03g0966 Cre03g0659 . Csa01g00069 Chy02g02651 .
Vvi17g144 . Blo16g00264 . . . . . . . . . Cma11g00045 . Car11g00040 . . Cpe04g01605 Bhi02g00539 . . . Hepe09g0063 . . Cla06g01730 Cam06g1921 Cec06g1971 Cco06g1975 Clacu06g1877 Cmu06g1819 Cre06g2634 . Cone16ag0029 . . . . . . . . . . . Bpe15g00210 Bma03g01265 . . . Cmo11g00046 . . . . . . . . . . . . . . . . . . . . Lsi06g01628 Csa01g00070 Chy02g02650 .
Vvi17g145 . . . . . . . . Cmo13g00827 . . . . . . Cpe20g00316 . . . . . . . . . . . . . . . Cone2ag0963 . . . . Csa01g00949 Chy12g01182 Cme12g01603 . . . Bda14g01373 . Bpe15g00209 Bma03g01266 . . . . Cma13g00794 . Car13g00643 . . . Bhi08g01460 . . . . . . Cla03g00343 Cam03g0359 . . Clacu03g0360 Cmu03g0965 Cre03g0658 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 10022621 10025633 + Bda024041.1 Bda06g00736 736
6 10027140 10030568 + Bda024042.1 Bda06g00737 737
11 53342819 53349303 - Bda008748.1 Bda11g01817 1817
14 16076482 16085333 - Bda011071.2 Bda14g01371 1371
14 16166007 16167968 + Bda011073.1 Bda14g01373 1373
15 9274797 9276650 - Bda012451.1 Bda15g00609 609
2 10161135 10164177 + XM_039023415.1 Bhi02g00535 535
2 10185995 10189725 + XM_039024159.1 Bhi02g00536 536
2 10190801 10193264 + XM_039022663.1 Bhi02g00537 537
2 10208367 10215422 - XM_039022956.1 Bhi02g00539 539
8 42887428 42890763 - XM_039037686.1 Bhi08g01460 1460
8 42891479 42894513 - XM_039037687.1 Bhi08g01461 1461
8 42959882 42964637 + XM_039038750.1 Bhi08g01464 1464
8 42989439 42992918 - XM_039038157.1 Bhi08g01467 1467
8 42989859 42992918 - XM_039038159.1 Bhi08g01468 1468
8 43068201 43071950 + XM_039037700.1 Bhi08g01470 1470
15 2195078 2207865 + BLOR06608 Blo15g00214 214
15 2214009 2217000 + BLOR06609 Blo15g00215 215
15 2229844 2238963 + BLOR06611 Blo15g00217 217
16 6198422 6206600 + BLOR07512 Blo16g00264 264
3 21353714 21357151 - Bma031021 Bma03g01261 1261
3 21669086 21673055 - Bma017730.1 Bma03g01265 1265
3 21716403 21718382 + Bma017731.1 Bma03g01266 1266
8 2796119 2797954 - Bma027237.1 Bma08g00228 228
12 43032914 43041858 - Bma008422.1 Bma12g01075 1075
12 43043268 43046169 - Bma030534 Bma12g01076 1076
12 43049951 43052497 - Bma008423.1 Bma12g01077 1077
7 14919750 14923049 - Bpe021725.1 Bpe07g00882 882
7 14924379 14927350 - Bpe021726.1 Bpe07g00883 883
12 11275015 11277621 + Bpe005806.1 Bpe12g00540 540
15 13180514 13182482 - Bpe001147.1 Bpe15g00209 209
15 13185342 13189477 + Bpe024548 Bpe15g00210 210
15 13229900 13233341 + Bpe001149.1 Bpe15g00212 212
3 4739047 4743861 - CaPI482276_03g003590.1 Cam03g0359 359
3 4745171 4747935 - CaPI482276_03g003600.1 Cam03g0360 360
3 4775037 4777894 - CaPI482276_03g003640.1 Cam03g0364 364
3 4792356 4796190 + CaPI482276_03g003660.1 Cam03g0366 366
6 30155155 30160287 + CaPI482276_06g019210.1 Cam06g1921 1921
6 30166868 30174717 - CaPI482276_06g019220.1 Cam06g1922 1922
6 30186084 30188790 - CaPI482276_06g019230.1 Cam06g1923 1923
10 265109 272312 + Carg10291-RA Car10g00059 59
10 273175 277255 + Carg10292-RA Car10g00060 60
10 277588 279847 + Carg10293-RA Car10g00061 61
11 204262 207192 + Carg20177-RA Car11g00039 39
11 208662 218631 - Carg20178-RA Car11g00040 40
13 8015520 8017612 - Carg07591-RA Car13g00643 643
13 8019928 8023779 + Carg07593-RA Car13g00644 644
13 8026408 8030774 - Carg07595-RA Car13g00646 646
13 8031795 8035550 + Carg07597-RA Car13g00647 647
18 1240704 1244581 + Carg06786-RA Car18g00219 219
18 1249364 1253374 + Carg06787-RA Car18g00220 220
18 1254439 1258487 - Carg06789-RA Car18g00222 222
18 1263930 1267215 - Carg06790-RA Car18g00223 223
18 1268421 1269350 + Carg06791-RA Car18g00224 224
3 3956472 3967501 - CcPI632755_03g003650.1 Cco03g0365 365
3 4012133 4015872 + CcPI632755_03g003680.1 Cco03g0368 368
6 29891186 29897722 + CcPI632755_06g019750.1 Cco06g1975 1975
6 29904947 29912736 - CcPI632755_06g019760.1 Cco06g1976 1976
6 29924032 29926703 - CcPI632755_06g019770.1 Cco06g1977 1977
3 3938126 3951206 - CePI673135_03g003530.1 Cec03g0353 353
3 3959193 3967196 + CePI673135_03g003540.1 Cec03g0354 354
6 32969783 32974871 + CePI673135_06g019710.1 Cec06g1971 1971
6 32981289 32988977 - CePI673135_06g019720.1 Cec06g1972 1972
6 33000306 33002467 - CePI673135_06g019730.1 Cec06g1973 1973
2 29536166 29540353 + Chy2G049170.1 Chy02g02650 2650
2 29545929 29547921 - Chy2G049180.1 Chy02g02651 2651
2 29547975 29552228 - Chy2G049190.1 Chy02g02652 2652
2 29562442 29565060 - Chy2G049200.1 Chy02g02653 2653
12 16617113 16623863 - Chy12G217750.1 Chy12g01175 1175
12 16628998 16631844 + Chy12G217770.1 Chy12g01177 1177
12 16633517 16636006 + Chy12G217780.1 Chy12g01178 1178
12 16636560 16640475 - Chy12G217790.1 Chy12g01179 1179
12 16654440 16656835 + Chy12G217810.1 Chy12g01181 1181
12 16658082 16660289 + Chy12G217820.1 Chy12g01182 1182
3 4055497 4060510 - ClG42_03g0036000.10 Clacu03g0360 360
3 4061733 4064457 - ClG42_03g0036100.10 Clacu03g0361 361
3 4108510 4114155 + ClG42_03g0036600.10 Clacu03g0366 366
6 29206006 29212550 + ClG42_06g0187700.10 Clacu06g1877 1877
6 29217719 29225568 - ClG42_06g0187800.10 Clacu06g1878 1878
6 29236939 29239551 - ClG42_06g0187900.10 Clacu06g1879 1879
3 3998132 4001236 - ClCG03G003630.2 Cla03g00343 343
3 4002244 4004968 - ClCG03G003640.2 Cla03g00344 344
3 4021525 4026023 + ClCG03G003650.1 Cla03g00345 345
3 4022547 4035588 - ClCG03G003660.1 Cla03g00346 346
3 4048657 4057775 + ClCG03G003690.2 Cla03g00349 349
6 30833760 30847083 + ClCG06G017750.1 Cla06g01730 1730
6 30851894 30861163 - ClCG06G017760.2 Cla06g01731 1731
6 30873877 30877001 - ClCG06G017780.2 Cla06g01732 1732
10 283159 291286 + CmaCh10G000720.1 Cma10g00072 72
11 193856 196822 + CmaCh11G000440.1 Cma11g00044 44
11 199106 209339 - CmaCh11G000450.1 Cma11g00045 45
13 6771945 6774028 - CmaCh13G007940.1 Cma13g00794 794
13 6776915 6781207 + CmaCh13G007950.1 Cma13g00795 795
13 6783771 6786442 - CmaCh13G007970.1 Cma13g00797 797
13 6788771 6792500 + CmaCh13G007990.1 Cma13g00799 799
18 1735188 1738353 - CmaCh18G003240.1 Cma18g00324 324
18 1739327 1742687 + CmaCh18G003250.1 Cma18g00325 325
12 23251481 23256098 - MELO3C002354.2.1 Cme12g01597 1597
12 23258212 23271184 + MELO3C002352.2.1 Cme12g01598 1598
12 23271355 23276012 - MELO3C002351.2.1 Cme12g01599 1599
12 23290838 23292883 + MELO3C002349.2.1 Cme12g01602 1602
12 23293852 23296369 + MELO3C002348.2.1 Cme12g01603 1603
7 7568425 7569753 - PI0001459.1 Cmetu07g1959 1959
12 3071884 3082223 - PI0023703.1 Cmetu12g1017 1017
12 3088278 3092192 + PI0015551.1 Cmetu12g1333 1333
10 311766 314728 + CmoCh10G000680.1 Cmo10g00068 68
10 314987 318998 + CmoCh10G000690.1 Cmo10g00069 69
11 190225 193346 + CmoCh11G000440.1 Cmo11g00044 44
11 201401 205317 - CmoCh11G000460.1 Cmo11g00046 46
13 7700823 7702919 - CmoCh13G008270.1 Cmo13g00827 827
13 7705571 7709807 + CmoCh13G008290.1 Cmo13g00829 829
13 7712313 7716309 - CmoCh13G008300.1 Cmo13g00830 830
13 7717543 7721166 + CmoCh13G008310.1 Cmo13g00831 831
18 1355141 1359321 + CmoCh18G002020.1 Cmo18g00202 202
18 1364231 1368330 + CmoCh18G002040.1 Cmo18g00204 204
18 1370222 1371753 - CmoCh18G002060.1 Cmo18g00206 206
18 1379538 1383069 - CmoCh18G002090.1 Cmo18g00209 209
18 1384431 1387913 + CmoCh18G002100.1 Cmo18g00210 210
3 4269382 4274395 - CmPI595203_03g009650.1 Cmu03g0965 965
3 4275618 4278342 - CmPI595203_03g009660.1 Cmu03g0966 966
3 4305595 4308421 - CmPI595203_03g009700.1 Cmu03g0970 970
3 4322270 4326112 + CmPI595203_03g009720.1 Cmu03g0972 972
6 29109409 29114334 + CmPI595203_06g018190.1 Cmu06g1819 1819
6 29119712 29128747 - CmPI595203_06g018200.1 Cmu06g1820 1820
6 29140239 29142933 - CmPI595203_06g018210.1 Cmu06g1821 1821
2 35197630 35199806 + Conep02aG0199700.1 Cone2ag0963 963
2 35200753 35203039 - Conep02aG0199800.1 Cone2ag0964 964
2 35206773 35207926 + Conep02aG0199900.1 Cone2ag0965 965
2 35208130 35211318 - Conep02aG0200000.1 Cone2ag0966 966
13 1365182 1368436 - Conep13aG0021600.1 Cone13ag0211 211
16 154312 160773 - Conep16aG0002300.1 Cone16ag0023 23
16 172963 175841 + Conep16aG0002600.1 Cone16ag0026 26
16 176072 179215 - Conep16aG0002700.1 Cone16ag0027 27
16 180341 184902 + Conep16aG0002800.1 Cone16ag0028 28
16 186684 189967 + Conep16aG0002900.1 Cone16ag0029 29
19 1247532 1250001 - Conep19aG0020500.1 Cone19ag0199 199
19 1250617 1253505 - Conep19aG0020600.1 Cone19ag0200 200
4 12488152 12499147 + Cp4.1LG04g16070.1 Cpe04g01605 1605
4 12501655 12504431 - Cp4.1LG04g16170.1 Cpe04g01606 1606
9 8628061 8630546 - Cp4.1LG09g09700.1 Cpe09g00967 967
9 8632537 8636689 + Cp4.1LG09g09590.1 Cpe09g00968 968
9 8645045 8649324 + Cp4.1LG09g09620.1 Cpe09g00969 969
9 8651204 8655075 - Cp4.1LG09g09670.1 Cpe09g00970 970
9 8659270 8663354 - Cp4.1LG09g09830.1 Cpe09g00971 971
20 1766030 1769565 - Cp4.1LG20g03090.1 Cpe20g00312 312
20 1770929 1778629 + Cp4.1LG20g03050.1 Cpe20g00313 313
20 1780998 1785144 - Cp4.1LG20g03330.1 Cpe20g00314 314
20 1787403 1790468 + Cp4.1LG20g03150.1 Cpe20g00316 316
3 5471179 5482962 - CrPI670011_03g006580.1 Cre03g0658 658
3 5484274 5487009 - CrPI670011_03g006590.1 Cre03g0659 659
3 5514178 5517039 - CrPI670011_03g006620.1 Cre03g0662 662
3 5531628 5535462 + CrPI670011_03g006640.1 Cre03g0664 664
6 33935947 33947566 + CrPI670011_06g026340.1 Cre06g2634 2634
6 33947611 33955186 - CrPI670011_06g026350.1 Cre06g2635 2635
6 33966608 33969324 - CrPI670011_06g026360.1 Cre06g2636 2636
1 394824 398213 + CsaV3_1G000670.1 Csa01g00067 67
1 407157 411061 + CsaV3_1G000680.1 Csa01g00068 68
1 411387 414207 + CsaV3_1G000690.1 Csa01g00069 69
1 417967 422027 - CsaV3_1G000700.1 Csa01g00070 70
1 5894881 5897558 - CsaV3_1G009490.1 Csa01g00949 949
1 5897638 5901075 - CsaV3_1G009500.1 Csa01g00950 950
1 5912729 5917563 + CsaV3_1G009530.1 Csa01g00953 953
1 5917890 5920245 - CsaV3_1G009540.1 Csa01g00954 954
1 5921925 5924721 - CsaV3_1G009550.1 Csa01g00955 955
1 5932912 5937386 + CsaV3_1G009570.1 Csa01g00957 957
7 65267694 65273242 - Hsped.07g20980.1 Hepe07g2098 2098
7 65292953 65296568 + Hsped.07g21000.1 Hepe07g2100 2100
9 496522 498707 + Hsped.09g00590.1 Hepe09g0059 59
9 513618 517200 + Hsped.09g00600.1 Hepe09g0060 60
9 518691 521216 + Hsped.09g00610.1 Hepe09g0061 61
9 533556 538209 - Hsped.09g00630.1 Hepe09g0063 63
10 4411636 4415362 + Lag0024620.1 Lac10g0575 575
2 4130925 4136743 - Lsi02G004880.1 Lsi02g00488 488
2 4155714 4160340 + Lsi02G004900.1 Lsi02g00490 490
2 4160345 4168292 - Lsi02G004910.1 Lsi02g00491 491
2 4196860 4198937 - Lsi02G004930.1 Lsi02g00493 493
2 4214106 4217356 + Lsi02G004970.1 Lsi02g00497 497
6 26584536 26589844 + Lsi06G016280.1 Lsi06g01628 1628
6 26603737 26611286 - Lsi06G016310.1 Lsi06g01631 1631
6 26619792 26625298 - Lsi06G016320.1 Lsi06g01632 1632
8 37447295 37450984 - Sed0001462.1 Sed08g2443 2443
8 37451537 37454645 + Sed0011561.1 Sed08g2444 2444
8 37456130 37461440 + Sed0014346.1 Sed08g2445 2445
5 81621135 81623975 - Tan0005363.1 Tan05g2944 2944
5 81637682 81640175 + Tan0002356.1 Tan05g2947 2947
9 73322250 73325574 - Tan0009339.1 Tan09g2357 2357
17 1231701 1237709 - Vvi17g136 Vvi17g136 136
17 1238486 1241306 + Vvi17g137 Vvi17g137 137
17 1241791 1242459 + Vvi17g138 Vvi17g138 138
17 1243375 1246011 - Vvi17g139 Vvi17g139 139
17 1246491 1250567 - Vvi17g140 Vvi17g140 140
17 1252339 1260721 - Vvi17g141 Vvi17g141 141
17 1274810 1279340 + Vvi17g142 Vvi17g142 142
17 1280790 1285398 + Vvi17g143 Vvi17g143 143
17 1287129 1293354 - Vvi17g144 Vvi17g144 144
17 1305276 1307598 + Vvi17g145 Vvi17g145 145
       

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