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
Vvi17g586 . . . . . . . . . . . . . Car11g00166 . . Cpe04g01485 . . . . . . . . . . . . . . . . . . Lsi02g00088 . Chy12g01526 Cme12g01975 . . . . . . . . Sed08g2087 . Cmo11g00182 . . . . . . Bhi08g01139 Tan05g2421 Cmetu12g2014 Lac10g0096 Hepe07g2494 . . Cla04g01184 . . . . . . . . . .
Vvi17g587 . . . . . . . Bma12g00984 . . . . . . . . . . . . . . . . . . . . . . . . Cone16ag0184 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g588 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g589 . . . . . Bpe13g00309 . . . . Cma10g00206 Cma11g00128 . Car11g00168 Sed08g0498 . Cpe04g01484 Bhi02g00742 Tan09g1708 Cmetu05g1231 . Hepe09g0469 . . Cla06g01576 Cam06g1743 Cec06g1802 Cco06g1803 Clacu06g1709 Cmu06g1654 Cre06g2466 . . . . . . . . Blo13g00001 . . . . . . . . Cmo10g00224 Cmo11g00184 . . . . . Cpe18g00781 . . . . . . . . . . . . . . Lsi06g01449 Csa01g00255 Chy02g02480 Cme02g01866
Vvi17g590 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g591 . . . . . . . . . . . Cma11g00126 . Car11g00169 Sed08g1458 . Cpe04g01483 Bhi02g00296 Tan09g2092 Cmetu06g0079 . . . . Cla06g01573 . . . . . . Cone2ag0829 Cone16ag0186 Cone13ag0056 Cone19ag0059 . . . . . . . . . . . . . . Cmo11g00185 . . . . . . . . . . . . . . . . . . . . Lsi06g01447 Csa01g00256 Chy02g02479 Cme02g01864
Vvi17g592 Blo04g00779 Blo16g00180 . . . Bpe13g00300 Bma06g00166 . . . Cma10g00209 Cma11g00123 Car10g00196 Car11g00171 . Cpe20g00055 Cpe04g01480 Bhi02g00293 Tan09g2089 . . Hepe09g0095 . . Cla06g01570 Cam06g1735 Cec06g1796 Cco06g1795 Clacu06g1702 Cmu06g1648 Cre06g2459 Cone2ag0827 Cone16ag0189 Cone13ag0054 . Lsi02g00091 Csa01g00571 Chy12g01523 Cme12g01971 . . Bda11g01706 Bda14g00861 . Bpe15g00594 Bma03g00847 . Sed08g0241 Cmo10g00227 Cmo11g00187 Cma13g01093 . Car13g00929 . . Cpe18g00780 Bhi08g01136 Tan05g2418 Cmetu02g1238 Lac10g0118 Hepe07g2490 . . Cla04g01181 Cam04g1237 Cec01g1748 Cco01g1794 Clacu04g1265 Cmu04g1244 Cre01g1538 Lsi06g01445 Csa01g00260 Chy02g02475 Cme02g01861
Vvi17g593 Blo04g00781 Blo16g00179 . . . Bpe13g00301 Bma06g00165 . Cmo13g01141 . . . . . . Cpe20g00057 . . . . . . . . . . . . . . . Cone2ag0826 Cone16ag0190 . . Lsi02g00092 Csa01g00572 . Cme12g01970 . . . . . . . . . . . Cma13g01092 . . . . . Bhi08g01135 . . . . . . Cla04g01180 . . . . . . . . . .
Vvi17g594 . . Bda06g00533 . . . . Bma12g00979 . . . Cma11g00122 . . Sed08g0243 . Cpe04g01478 Bhi02g00292 Tan09g2087 Cmetu02g1591 . Hepe09g0094 . . Cla06g01568 Cam06g1734 Cec06g1794 Cco06g1794 Clacu06g1701 Cmu06g1647 Cre06g2458 . . Cone13ag0067 Cone19ag0068 . . . . . Blo15g00324 . . Bpe07g00769 . . Bma08g00281 . . Cmo11g00190 . . . . . . . . . . . . . . . . . . . . Lsi06g01443 Csa01g00261 Chy02g02474 Cme02g01860
Vvi17g595 Blo04g00782 Blo16g00178 . . . Bpe13g00302 Bma06g00164 . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0825 Cone16ag0191 . . . . . . . . Bda11g01710 Bda14g00862 . Bpe15g00593 Bma03g00840 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7618545 7620268 + Bda023791.1 Bda06g00533 533
11 51303533 51305928 - Bda033163 Bda11g01706 1706
11 51423275 51425143 - Bda033164 Bda11g01710 1710
14 6618208 6641581 - Bda027636.2 Bda14g00861 861
14 6643844 6646214 - Bda027637.1 Bda14g00862 862
2 5455096 5457650 + XM_039022325.1 Bhi02g00292 292
2 5505982 5524216 + XM_039023346.1 Bhi02g00293 293
2 5544309 5553924 - XM_039022755.1 Bhi02g00296 296
2 14891238 14899482 - XM_039022358.1 Bhi02g00742 742
8 35922322 35927785 + XM_039039659.1 Bhi08g01135 1135
8 35933432 35944377 + XM_039039227.1 Bhi08g01136 1136
8 36015238 36020658 - XM_039038134.1 Bhi08g01139 1139
4 7722084 7730529 - BLOR13691 Blo04g00779 779
4 7742880 7758707 - BLOR13693 Blo04g00781 781
4 7763372 7765502 - BLOR13694 Blo04g00782 782
13 17451 18934 + BLOR05282 Blo13g00001 1
15 3755862 3758067 - BLOR06718 Blo15g00324 324
16 3985046 3986882 + BLOR07426 Blo16g00178 178
16 3997830 4012820 + BLOR07427 Blo16g00179 179
16 4013756 4020794 + BLOR07428 Blo16g00180 180
3 8035180 8037307 - Bma017155.1 Bma03g00840 840
3 8104314 8147357 + Bma017163.1 Bma03g00847 847
6 2095754 2097486 + Bma031272 Bma06g00164 164
6 2106363 2110335 + Bma031273 Bma06g00165 165
6 2113391 2152997 + Bma022781.4 Bma06g00166 166
8 3817640 3818482 - Bma027303.1 Bma08g00281 281
12 41853365 41855031 + Bma008323.1 Bma12g00979 979
12 41886543 41889987 + Bma008328.1 Bma12g00984 984
7 14199860 14201568 + Bpe021614.1 Bpe07g00769 769
13 10830282 10841722 - Bpe024935 Bpe13g00300 300
13 10845873 10849914 - Bpe006427.1 Bpe13g00301 301
13 10857672 10859522 - Bpe006428.1 Bpe13g00302 302
13 10931093 10965682 - Bpe006436.1 Bpe13g00309 309
15 16847999 16850153 + Bpe001527.1 Bpe15g00593 593
15 16852546 16884151 + Bpe001528.1 Bpe15g00594 594
4 26396716 26406433 + CaPI482276_04g012370.1 Cam04g1237 1237
6 28626125 28628427 + CaPI482276_06g017340.1 Cam06g1734 1734
6 28639645 28660242 + CaPI482276_06g017350.1 Cam06g1735 1735
6 28704381 28705859 - CaPI482276_06g017430.1 Cam06g1743 1743
10 937448 952286 - Carg17947-RA Car10g00196 196
11 909897 912834 + Carg18203-RA Car11g00166 166
11 915046 916428 + Carg18205-RA Car11g00168 168
11 921605 937261 + Carg18206-RA Car11g00169 169
11 942519 957111 - Carg18208-RA Car11g00171 171
13 9535938 9545722 + Carg04742-RA Car13g00929 929
1 30651277 30660776 + CcPI632755_01g017940.1 Cco01g1794 1794
6 28333184 28335465 + CcPI632755_06g017940.1 Cco06g1794 1794
6 28351065 28366477 + CcPI632755_06g017950.1 Cco06g1795 1795
6 28407408 28411026 - CcPI632755_06g018030.1 Cco06g1803 1803
1 32075253 32084903 + CePI673135_01g017480.1 Cec01g1748 1748
6 31407091 31409445 + CePI673135_06g017940.1 Cec06g1794 1794
6 31425987 31446449 + CePI673135_06g017960.1 Cec06g1796 1796
6 31488168 31491743 - CePI673135_06g018020.1 Cec06g1802 1802
2 28307502 28309588 + Chy2G047410.1 Chy02g02474 2474
2 28320742 28324393 + Chy2G047420.1 Chy02g02475 2475
2 28347703 28355595 - Chy2G047460.1 Chy02g02479 2479
2 28359372 28360754 - Chy2G047470.1 Chy02g02480 2480
12 18995713 19011992 + Chy12G221230.1 Chy12g01523 1523
12 19020856 19025288 - Chy12G221260.1 Chy12g01526 1526
4 26752246 26761936 + ClG42_04g0126500.10 Clacu04g1265 1265
6 27685016 27687291 + ClG42_06g0170100.10 Clacu06g1701 1701
6 27698462 27718876 + ClG42_06g0170200.10 Clacu06g1702 1702
6 27763147 27764529 - ClG42_06g0170900.10 Clacu06g1709 1709
4 26985318 26991349 + ClCG04G012050.2 Cla04g01180 1180
4 26995366 27006299 + ClCG04G012060.2 Cla04g01181 1181
4 27017923 27025766 - ClCG04G012090.2 Cla04g01184 1184
6 29242457 29246019 + ClCG06G015940.2 Cla06g01568 1568
6 29256796 29279739 + ClCG06G015960.1 Cla06g01570 1570
6 29289936 29306339 - ClCG06G015990.2 Cla06g01573 1573
6 29319586 29324800 - ClCG06G016017.1 Cla06g01576 1576
10 913650 919689 + CmaCh10G002060.1 Cma10g00206 206
10 925548 941379 - CmaCh10G002090.1 Cma10g00209 209
11 651235 653736 + CmaCh11G001220.1 Cma11g00122 122
11 655413 671728 + CmaCh11G001230.1 Cma11g00123 123
11 680972 691978 - CmaCh11G001260.1 Cma11g00126 126
11 694475 696012 - CmaCh11G001280.1 Cma11g00128 128
13 8224255 8230094 + CmaCh13G010920.1 Cma13g01092 1092
13 8230983 8242737 + CmaCh13G010930.1 Cma13g01093 1093
2 25231195 25233679 + MELO3C017197.2.1 Cme02g01860 1860
2 25245447 25260426 + MELO3C017195.2.1 Cme02g01861 1861
2 25266955 25280818 - MELO3C017192.2.1 Cme02g01864 1864
2 25289352 25290108 - MELO3C000841.2.1 Cme02g01866 1866
12 25535067 25540602 + MELO3C002003.2.1 Cme12g01970 1970
12 25543931 25552911 + MELO3C002002.2.1 Cme12g01971 1971
12 25560215 25565043 - MELO3C001999.2.1 Cme12g01975 1975
2 23565422 23579157 + PI0022888.1 Cmetu02g1238 1238
2 23716657 23720102 - PI0026321.3 Cmetu02g1591 1591
5 5653355 5660121 + PI0024786.1 Cmetu05g1231 1231
6 20524810 20527538 + PI0021747.1 Cmetu06g0079 79
12 556771 560405 + PI0027470.1 Cmetu12g2014 2014
10 978024 979406 + CmoCh10G002240.1 Cmo10g00224 224
10 985213 1000189 - CmoCh10G002270.1 Cmo10g00227 227
11 877863 881446 + CmoCh11G001820.1 Cmo11g00182 182
11 883710 888219 + CmoCh11G001840.1 Cmo11g00184 184
11 890779 901883 + CmoCh11G001850.1 Cmo11g00185 185
11 912910 920010 - CmoCh11G001870.1 Cmo11g00187 187
11 931562 933832 - CmoCh11G001900.1 Cmo11g00190 190
13 9242670 9259233 + CmoCh13G011410.1 Cmo13g01141 1141
4 26934156 26944077 + CmPI595203_04g012440.1 Cmu04g1244 1244
6 27593618 27595909 + CmPI595203_06g016470.1 Cmu06g1647 1647
6 27607055 27627435 + CmPI595203_06g016480.1 Cmu06g1648 1648
6 27671694 27673172 - CmPI595203_06g016540.1 Cmu06g1654 1654
2 34254365 34256851 + Conep02aG0185300.1 Cone2ag0825 825
2 34261546 34270281 + Conep02aG0185400.1 Cone2ag0826 826
2 34275656 34286330 + Conep02aG0185500.1 Cone2ag0827 827
2 34306656 34311003 - Conep02aG0185700.1 Cone2ag0829 829
13 337662 346269 + Conep13aG0005700.1 Cone13ag0054 54
13 347681 354757 - Conep13aG0005900.1 Cone13ag0056 56
13 412102 415077 + Conep13aG0007100.1 Cone13ag0067 67
16 1189286 1193391 + Conep16aG0018800.1 Cone16ag0184 184
16 1198443 1201964 + Conep16aG0019000.1 Cone16ag0186 186
16 1212438 1223998 - Conep16aG0019300.1 Cone16ag0189 189
16 1233246 1238940 - Conep16aG0019400.1 Cone16ag0190 190
16 1246812 1249203 - Conep16aG0019500.1 Cone16ag0191 191
19 373231 378557 - Conep19aG0006300.1 Cone19ag0059 59
19 422560 424285 + Conep19aG0007300.1 Cone19ag0068 68
4 11743707 11753019 + Cp4.1LG04g14660.1 Cpe04g01478 1478
4 11754724 11771159 + Cp4.1LG04g14720.1 Cpe04g01480 1480
4 11779610 11790688 - Cp4.1LG04g14930.1 Cpe04g01483 1483
4 11793118 11794506 - Cp4.1LG04g15000.1 Cpe04g01484 1484
4 11795729 11803152 - Cp4.1LG04g14980.1 Cpe04g01485 1485
18 7393833 7409228 + Cp4.1LG18g07830.1 Cpe18g00780 780
18 7409455 7421659 - Cp4.1LG18g07960.1 Cpe18g00781 781
20 268773 280092 - Cp4.1LG20g00540.1 Cpe20g00055 55
20 281924 287696 - Cp4.1LG20g00560.1 Cpe20g00057 57
1 28597524 28607232 + CrPI670011_01g015380.1 Cre01g1538 1538
6 32388876 32391174 + CrPI670011_06g024580.1 Cre06g2458 2458
6 32402265 32422779 + CrPI670011_06g024590.1 Cre06g2459 2459
6 32464985 32468545 - CrPI670011_06g024660.1 Cre06g2466 2466
1 1587602 1591443 + CsaV3_1G002550.1 Csa01g00255 255
1 1592610 1601117 + CsaV3_1G002560.1 Csa01g00256 256
1 1613373 1627296 - CsaV3_1G002600.1 Csa01g00260 260
1 1636575 1639068 - CsaV3_1G002610.1 Csa01g00261 261
1 3670613 3679554 - CsaV3_1G005710.1 Csa01g00571 571
1 3682563 3687074 - CsaV3_1G005720.1 Csa01g00572 572
7 69251677 69257015 + Hsped.07g24900.1 Hepe07g2490 2490
7 69301279 69304744 - Hsped.07g24940.1 Hepe07g2494 2494
9 740572 744753 + Hsped.09g00940.1 Hepe09g0094 94
9 754604 772171 + Hsped.09g00950.1 Hepe09g0095 95
9 4317416 4324038 - Hsped.09g04690.1 Hepe09g0469 469
10 742038 745838 + Lag0024141.1 Lac10g0096 96
10 895096 905883 - Lag0024163.1 Lac10g0118 118
2 735922 743882 + Lsi02G000880.1 Lsi02g00088 88
2 754442 765043 - Lsi02G000910.1 Lsi02g00091 91
2 769670 774612 - Lsi02G000920.1 Lsi02g00092 92
6 24963033 24965771 + Lsi06G014430.1 Lsi06g01443 1443
6 25001154 25009490 + Lsi06G014450.1 Lsi06g01445 1445
6 25027813 25036835 - Lsi06G014470.1 Lsi06g01447 1447
6 25054351 25055733 - Lsi06G014490.1 Lsi06g01449 1449
8 1371158 1385374 - Sed0009694.1 Sed08g0241 241
8 1391874 1395498 - Sed0001146.2 Sed08g0243 243
8 3248241 3253081 + Sed0011582.1 Sed08g0498 498
8 29155521 29158102 + Sed0019906.1 Sed08g1458 1458
8 35008628 35013096 + Sed0015977.1 Sed08g2087 2087
5 75369701 75381846 + Tan0019620.1 Tan05g2418 2418
5 75394197 75397804 - Tan0016548.1 Tan05g2421 2421
9 68623716 68631597 + Tan0001269.2 Tan09g1708 1708
9 71227130 71230264 + Tan0014859.1 Tan09g2087 2087
9 71269366 71271517 + Tan0012250.1 Tan09g2089 2089
9 71289897 71301379 - Tan0005677.1 Tan09g2092 2092
17 7096185 7098427 + Vvi17g586 Vvi17g586 586
17 7101162 7108526 + Vvi17g587 Vvi17g587 587
17 7109390 7124378 - Vvi17g588 Vvi17g588 588
17 7124402 7126089 + Vvi17g589 Vvi17g589 589
17 7129218 7130944 - Vvi17g590 Vvi17g590 590
17 7139022 7151201 + Vvi17g591 Vvi17g591 591
17 7163668 7183054 - Vvi17g592 Vvi17g592 592
17 7210717 7218050 - Vvi17g593 Vvi17g593 593
17 7223829 7226865 - Vvi17g594 Vvi17g594 594
17 7227853 7230829 - Vvi17g595 Vvi17g595 595
       

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