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
Vvi1g671 . . . . . Bpe10g00844 Bma14g01802 Bma15g00179 . . . . . . Sed07g2568 . . Bhi07g01744 Tan04g0166 Cmetu10g0943 Lac13g0190 Hepe10g0024 . . Cla05g02552 Cam05g2740 Cec05g2772 Cco05g2812 Clacu05g2741 . . . . . . Lsi04g00560 Csa05g02326 Chy10g00893 Cme10g00536 Blo06g00883 . Bda07g01611 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g672 . . Bda01g02217 Bda11g01274 Bpe13g00499 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01274 . . . Bma06g00614 . . . . Cma05g00020 . . . . . . . . . . . . . . . . . . . . . .
Vvi1g673 . . . Bda11g01273 Bpe13g01470 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01273 . . . Bma06g00615 . . . . Cma05g00019 . Car05g00017 . . . . . . . . . . . . . . . . . . . .
Vvi1g674 . . . Bda11g01272 Bpe13g01469 Bpe10g00842 . Bma15g00181 . Cmo18g00794 . Cma18g00792 . . . Cpe09g00510 Cpe01g01540 . . . . . . . Cla05g02551 Cam05g2739 . Cco05g2811 . Cmu05g2593 Cre05g2708 Cone13ag1049 Cone19ag1039 . . Lsi04g00559 Csa05g02327 . Cme10g00533 Blo06g00881 . . Bda11g01272 . . . Bma06g00616 . . . . . Car04g01774 . . . . . . . . . . . . . . . . . . . . .
Vvi1g675 . . . Bda11g01271 Bpe13g01468 . . . . . . . . Car18g00722 . Cpe09g00509 Cpe01g01538 Bhi07g01742 . . Lac13g0191 Hepe10g1630 . . Cla05g02550 . . Cco05g2810 . . . . . Cone8ag0673 . . Csa05g02328 Chy10g00895 Cme10g00532 . . . Bda11g01271 . . Bma01g00045 . . . . Cma04g01740 Cma05g00017 Car04g01773 Car05g00015 . . . . . . . . . . . . . . . . . . . .
Vvi1g676 Blo01g00393 Blo16g01161 Bda01g02218 Bda11g01270 Bpe13g00498 . . . . Cmo18g00796 . Cma18g00793 . Car18g00723 . Cpe09g00508 Cpe01g01537 Bhi07g01741 . . Lac13g0192 Hepe10g1631 . . Cla05g02549 Cam05g2738 Cec05g2770 . Clacu05g2739 Cmu05g2592 Cre05g2707 Cone13ag1048 . Cone8ag0672 . Lsi04g00558 Csa05g02330 Chy10g00897 Cme10g00531 Blo06g00888 . . Bda11g01270 . . . Bma06g00617 . . . Cma04g01739 Cma05g00015 . Car05g00014 . . . . . . . . . . . . . . . . . . . .
Vvi1g677 . . . . . . Bma14g01799 Bma15g00177 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo11g00919 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g678 . . . . . Bpe10g00841 . Bma15g00182 . . . . . . Sed06g1644 . Cpe01g01536 Bhi07g01738 Tan04g1245 Cmetu10g1513 Lac13g0194 Hepe10g1633 . . Cla05g02548 Cam05g2737 Cec05g2768 Cco05g2809 Clacu05g2738 Cmu05g2591 Cre05g2706 . . Cone8ag0671 . Lsi04g00557 Csa05g02331 Chy10g00899 Cme10g00530 Blo06g00880 . . . . . . . . . . Cma04g01737 . Car04g01771 . . . . . . . . . . . . . . . . . . . . .
Vvi1g679 . . Bda01g02219 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0670 . . . . . . . . . . . Bma01g00046 . . . . . Cma05g00014 . Car05g00013 . . . . . . . . . . . . . . . . . . . .
Vvi1g680 . Blo16g01160 . Bda11g01269 Bpe13g01466 . . . . Cmo18g00798 . Cma18g00794 . . Sed06g1643 . . Bhi07g01737 Tan04g1244 Cmetu03g0260 . . . . Cla05g02547 . . Cco05g2808 . . Cre05g2705 . . . . Lsi04g00556 Csa05g02332 Chy10g00900 . . . . Bda11g01269 . . . Bma06g00618 . Cmo04g02828 . Cma04g01736 . . . . . . . . . . . . . . . . . . . . . Chy09g00345 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 58015152 58016812 + Bda004557.1 Bda01g02217 2217
1 58022147 58025517 + Bda004558.1 Bda01g02218 2218
1 58026725 58033248 + Bda004559.1 Bda01g02219 2219
7 29818837 29820234 + Bda028483.1 Bda07g01611 1611
11 13321646 13323182 - Bda007787.1 Bda11g01269 1269
11 13327600 13330876 - Bda007788.1 Bda11g01270 1270
11 13337943 13340700 - Bda007789.1 Bda11g01271 1271
11 13342287 13343576 - Bda007790.1 Bda11g01272 1272
11 13345715 13348337 + Bda007791.1 Bda11g01273 1273
11 13349207 13351511 - Bda007792.1 Bda11g01274 1274
7 47892849 47896105 - XM_039037333.1 Bhi07g01737 1737
7 47897360 47904157 - XM_039037434.1 Bhi07g01738 1738
7 47942508 47946196 - XM_039037459.1 Bhi07g01741 1741
7 47952281 47958654 - XM_039036685.1 Bhi07g01742 1742
7 47975166 47976288 + XM_039037223.1 Bhi07g01744 1744
1 4454504 4465187 + BLOR00393 Blo01g00393 393
6 32072854 32075767 - BLOR17463 Blo06g00880 880
6 32076289 32077986 - BLOR17464 Blo06g00881 881
6 32083572 32084913 + BLOR17466 Blo06g00883 883
6 32109788 32112407 + BLOR17471 Blo06g00888 888
11 19314395 19317972 - BLOR03795 Blo11g00919 919
16 40129744 40136792 - BLOR21947 Blo16g01160 1160
16 40145134 40157704 - BLOR21948 Blo16g01161 1161
1 503141 504309 + Bma000213.1 Bma01g00045 45
1 518171 518444 + Bma000214.1 Bma01g00046 46
6 32710582 32712253 + Bma023553.1 Bma06g00614 614
6 32714404 32715393 - Bma023554.1 Bma06g00615 615
6 32715897 32718302 + Bma023555.1 Bma06g00616 616
6 32761220 32764356 + Bma023556.1 Bma06g00617 617
6 32793714 32795326 + Bma023558.1 Bma06g00618 618
14 38592848 38597626 - Bma012571.1 Bma14g01799 1799
14 38614325 38615869 - Bma012575.1 Bma14g01802 1802
15 1878430 1880876 - Bma013159.1 Bma15g00177 177
15 1883417 1884847 - Bma013161.1 Bma15g00179 179
15 1901919 1903586 + Bma013163.1 Bma15g00181 181
15 1904127 1906780 + Bma013164.1 Bma15g00182 182
10 14371715 14374335 - Bpe003147.1 Bpe10g00841 841
10 14374892 14376485 - Bpe003148.1 Bpe10g00842 842
10 14382909 14384417 + Bpe003150.1 Bpe10g00844 844
13 12392227 12395809 - Bpe010209.1 Bpe13g00498 498
13 12401092 12402753 - Bpe010210.1 Bpe13g00499 499
13 19938333 19940664 - Bpe011131.1 Bpe13g01466 1466
13 19963898 19966594 - Bpe011132.1 Bpe13g01468 1468
13 19968159 19970609 - Bpe011133.1 Bpe13g01469 1469
13 19971105 19972113 + Bpe011134.1 Bpe13g01470 1470
5 34651534 34661528 - CaPI482276_05g027370.1 Cam05g2737 2737
5 34667396 34670468 - CaPI482276_05g027380.1 Cam05g2738 2738
5 34676569 34682500 - CaPI482276_05g027390.1 Cam05g2739 2739
5 34684017 34684473 + CaPI482276_05g027400.1 Cam05g2740 2740
4 10126593 10129040 - Carg14334-RA Car04g01771 1771
4 10131470 10139681 - Carg14332-RA Car04g01773 1773
4 10140294 10142568 - Carg14331-RA Car04g01774 1774
5 65088 75150 - Carg21813-RA Car05g00013 13
5 75855 79483 - Carg21814-RA Car05g00014 14
5 82239 87673 - Carg21815-RA Car05g00015 15
5 90640 95898 + Carg21817-RA Car05g00017 17
18 8395486 8398709 + Carg14476-RA Car18g00722 722
18 8402845 8404777 + Carg14475-RA Car18g00723 723
5 35793778 35796575 - CcPI632755_05g028080.1 Cco05g2808 2808
5 35799234 35803500 - CcPI632755_05g028090.1 Cco05g2809 2809
5 35809537 35812604 - CcPI632755_05g028100.1 Cco05g2810 2810
5 35818538 35824399 - CcPI632755_05g028110.1 Cco05g2811 2811
5 35825962 35826414 + CcPI632755_05g028120.1 Cco05g2812 2812
5 38108832 38118827 - CePI673135_05g027680.1 Cec05g2768 2768
5 38124874 38128368 - CePI673135_05g027700.1 Cec05g2770 2770
5 38141990 38142440 + CePI673135_05g027720.1 Cec05g2772 2772
9 3013921 3018630 - Chy9G160610.1 Chy09g00345 345
10 14691012 14691991 - Chy10G180870.1 Chy10g00893 893
10 14693925 14698708 + Chy10G180890.1 Chy10g00895 895
10 14704662 14707693 + Chy10G180910.1 Chy10g00897 897
10 14711402 14715973 + Chy10G180930.1 Chy10g00899 899
10 14717824 14719430 + Chy10G180940.1 Chy10g00900 900
5 34859300 34869295 - ClG42_05g0273800.10 Clacu05g2738 2738
5 34875254 34879122 - ClG42_05g0273900.10 Clacu05g2739 2739
5 34891874 34892330 + ClG42_05g0274100.10 Clacu05g2741 2741
5 36795739 36797828 - ClCG05G025400.1 Cla05g02547 2547
5 36801238 36805751 - ClCG05G025410.2 Cla05g02548 2548
5 36811459 36814780 - ClCG05G025420.2 Cla05g02549 2549
5 36820642 36823502 - ClCG05G025430.2 Cla05g02550 2550
5 36823832 36826708 - ClCG05G025440.2 Cla05g02551 2551
5 36828330 36828786 + ClCG05G025450.1 Cla05g02552 2552
4 8727945 8730921 - CmaCh04G017360.1 Cma04g01736 1736
4 8732065 8734802 - CmaCh04G017370.1 Cma04g01737 1737
4 8737754 8740340 - CmaCh04G017390.1 Cma04g01739 1739
4 8743573 8746682 - CmaCh04G017400.1 Cma04g01740 1740
5 60526 76786 - CmaCh05G000140.1 Cma05g00014 14
5 77098 80992 - CmaCh05G000150.1 Cma05g00015 15
5 86362 89423 - CmaCh05G000170.1 Cma05g00017 17
5 91837 96347 + CmaCh05G000190.1 Cma05g00019 19
5 96312 99604 - CmaCh05G000200.1 Cma05g00020 20
18 6983258 6989544 + CmaCh18G007920.1 Cma18g00792 792
18 6994072 6997515 + CmaCh18G007930.1 Cma18g00793 793
18 7001250 7005661 + CmaCh18G007940.1 Cma18g00794 794
10 3397363 3401888 - MELO3C011988.2.1 Cme10g00530 530
10 3405615 3408698 - MELO3C011987.2.1 Cme10g00531 531
10 3414250 3416814 - MELO3C011986.2.1 Cme10g00532 532
10 3417591 3420477 - MELO3C011984.2.1 Cme10g00533 533
10 3421588 3422456 + MELO3C034128.2.1 Cme10g00536 536
3 63000 65893 - PI0026543.1 Cmetu03g0260 260
10 14701972 14705599 + PI0009832.1 Cmetu10g0943 943
10 18607272 18613129 + PI0017480.1 Cmetu10g1513 1513
4 20244906 20249432 + CmoCh04G028280.1 Cmo04g02828 2828
18 9446007 9452197 + CmoCh18G007940.1 Cmo18g00794 794
18 9456747 9460197 + CmoCh18G007960.1 Cmo18g00796 796
18 9462991 9467770 + CmoCh18G007980.1 Cmo18g00798 798
5 34597295 34607294 - CmPI595203_05g025910.1 Cmu05g2591 2591
5 34613255 34617123 - CmPI595203_05g025920.1 Cmu05g2592 2592
5 34622255 34628093 - CmPI595203_05g025930.1 Cmu05g2593 2593
8 6691833 6700419 - Conep08aG0069300.1 Cone8ag0670 670
8 6702136 6706348 - Conep08aG0069400.1 Cone8ag0671 671
8 6712802 6717542 - Conep08aG0069500.1 Cone8ag0672 672
8 6723871 6726877 - Conep08aG0069600.1 Cone8ag0673 673
13 8634316 8637397 - Conep13aG0107900.1 Cone13ag1048 1048
13 8639999 8641954 - Conep13aG0108000.1 Cone13ag1049 1049
19 7693231 7695558 - Conep19aG0107100.1 Cone19ag1039 1039
1 9188375 9190599 - Cp4.1LG01g15350.1 Cpe01g01536 1536
1 9193506 9196292 - Cp4.1LG01g15410.1 Cpe01g01537 1537
1 9199188 9201919 - Cp4.1LG01g15400.1 Cpe01g01538 1538
1 9201983 9204732 - Cp4.1LG01g15390.1 Cpe01g01540 1540
9 3379898 3383963 - Cp4.1LG09g05280.1 Cpe09g00508 508
9 3387363 3390525 - Cp4.1LG09g05300.1 Cpe09g00509 509
9 3391624 3395344 - Cp4.1LG09g05240.1 Cpe09g00510 510
5 37958823 37962177 - CrPI670011_05g027050.1 Cre05g2705 2705
5 37964534 37968971 - CrPI670011_05g027060.1 Cre05g2706 2706
5 37973343 37978093 - CrPI670011_05g027070.1 Cre05g2707 2707
5 37984089 37989955 - CrPI670011_05g027080.1 Cre05g2708 2708
5 25683997 25685378 - CsaV3_5G031450.1 Csa05g02326 2326
5 25686869 25688544 + CsaV3_5G031460.1 Csa05g02327 2327
5 25689614 25691799 + CsaV3_5G031470.1 Csa05g02328 2328
5 25697891 25701370 + CsaV3_5G031490.1 Csa05g02330 2330
5 25704456 25709546 + CsaV3_5G031500.1 Csa05g02331 2331
5 25710504 25713701 + CsaV3_5G031510.1 Csa05g02332 2332
10 229206 233716 + Hsped.10g00240.1 Hepe10g0024 24
10 53020132 53023205 + Hsped.10g16300.1 Hepe10g1630 1630
10 53024364 53026588 + Hsped.10g16310.1 Hepe10g1631 1631
10 53043763 53046777 + Hsped.10g16330.1 Hepe10g1633 1633
13 1335332 1336063 - Lag0039986.1 Lac13g0190 190
13 1339768 1341170 + Lag0039987.1 Lac13g0191 191
13 1342217 1344499 + Lag0039988.1 Lac13g0192 192
13 1357457 1360050 + Lag0039990.1 Lac13g0194 194
4 5081799 5083859 - Lsi04G005560.1 Lsi04g00556 556
4 5086662 5090114 - Lsi04G005570.1 Lsi04g00557 557
4 5091579 5095870 - Lsi04G005580.1 Lsi04g00558 558
4 5103476 5109283 - Lsi04G005590.1 Lsi04g00559 559
4 5111007 5111757 + Lsi04G005600.1 Lsi04g00560 560
6 41207502 41211145 - Sed0022848.1 Sed06g1643 1643
6 41215988 41221068 - Sed0013752.1 Sed06g1644 1644
7 41217222 41221059 - Sed0024436.1 Sed07g2568 2568
4 1248595 1251701 + Tan0008038.1 Tan04g0166 166
4 11790807 11796243 - Tan0004394.1 Tan04g1244 1244
4 11797885 11802977 - Tan0010102.1 Tan04g1245 1245
1 7699112 7701565 - Vvi1g671 Vvi1g671 671
1 7707924 7712877 + Vvi1g672 Vvi1g672 672
1 7713303 7718420 - Vvi1g673 Vvi1g673 673
1 7718699 7722677 + Vvi1g674 Vvi1g674 674
1 7724619 7736183 + Vvi1g675 Vvi1g675 675
1 7736721 7740705 + Vvi1g676 Vvi1g676 676
1 7746063 7751765 + Vvi1g677 Vvi1g677 677
1 7756583 7759818 + Vvi1g678 Vvi1g678 678
1 7763407 7789751 + Vvi1g679 Vvi1g679 679
1 7791433 7798899 + Vvi1g680 Vvi1g680 680
       

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