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
Vvi1g871 . . . . . . . Bma15g00167 . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0973 . . . . . . . Blo06g00897 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g872 . . . . . Bpe10g00859 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0963 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g873 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0856 Cone16ag0155 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g874 . Blo16g01128 . Bda11g01229 Bpe13g01425 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0606 Cone9ag0611 . . . . . . . Bda11g01229 . . . Bma06g00669 . . . . . . . . Cpe07g00590 . . . . . . . . . . . . . . . . . .
Vvi1g875 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g876 . Blo16g01127 . Bda11g01228 Bpe13g01424 Bpe10g00860 . Bma15g00166 Cmo04g01718 Cmo18g01191 . Cma18g01167 . Car18g01076 Sed06g1547 Cpe09g00162 Cpe01g01451 Bhi07g01593 Tan04g1107 Cmetu10g1539 Lac13g0297 Hepe10g1722 . . Cla05g02462 Cam05g2649 Cec05g2682 Cco05g2718 Clacu05g2652 Cmu05g2505 Cre05g2619 Cone13ag0972 Cone19ag0962 . . Lsi04g00445 Csa05g02429 Chy10g00982 Cme10g00436 Blo06g00898 . . Bda11g01228 . . . Bma06g00674 . . . Cma04g01639 . Car04g01681 . . . . . . . . . . . . . . . . . . . . .
Vvi1g877 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g878 . Blo16g01126 Bda01g02168 . Bpe13g01423 . Bma14g01635 . Cmo04g01719 Cmo18g01189 . Cma18g01165 . Car18g01075 Sed12g2082 Cpe09g00163 Cpe01g01452 Bhi07g01592 Tan04g1106 . . . . . Cla05g02461 Cam05g2648 Cec05g2681 Cco05g2717 Clacu05g2651 Cmu05g2504 Cre05g2618 Cone13ag0971 Cone19ag0961 Cone6ag0605 Cone9ag0610 Lsi04g00444 Csa05g02430 Chy10g00983 Cme10g00435 Blo06g00899 . . . Bpe11g01632 Bpe02g02354 . . . . . Cma04g01641 . Car04g01682 . . Cpe07g00226 . . . . . . . . . . . . . . . . . .
Vvi1g879 Blo01g00421 Blo16g01125 Bda01g02167 Bda11g01227 Bpe13g01422 . Bma14g01636 . Cmo04g01722 Cmo18g01188 . . . Car18g01074 Sed06g1545 Cpe09g00164 Cpe01g01454 Bhi07g01589 Tan04g1101 Cmetu10g1011 Lac13g0301 Hepe10g1725 . . Cla05g02458 Cam05g2646 Cec05g2678 Cco05g2715 Clacu05g2649 Cmu05g2502 Cre05g2616 Cone13ag0969 Cone19ag0959 Cone6ag0604 Cone9ag0609 Lsi04g00442 Csa05g02432 Chy10g00985 Cme10g00433 . Blo11g00762 Bda07g01460 Bda11g01227 Bpe11g01633 Bpe02g02353 Bma01g00088 Bma06g00675 . Cmo04g02884 . Cma04g01643 . Car04g01684 Car15g00277 . . . . . . . . . . . . . . . . . . . .
Vvi1g880 Blo01g00422 . Bda01g02166 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0603 Cone9ag0608 . . . . . . . . . Bpe02g02352 Bma01g00089 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57566065 57572176 + Bda004504.1 Bda01g02166 2166
1 57581698 57582967 + Bda004505.1 Bda01g02167 2167
1 57596029 57599179 + Bda004506.1 Bda01g02168 2168
7 27137122 27145819 - Bda028292.1 Bda07g01460 1460
11 12694178 12695424 + Bda033141 Bda11g01227 1227
11 12792133 12794369 - Bda033142 Bda11g01228 1228
11 12805584 12807712 + Bda007738.1 Bda11g01229 1229
7 45297549 45299471 + XM_039036113.1 Bhi07g01589 1589
7 45373438 45379461 + XM_039037018.1 Bhi07g01592 1592
7 45451281 45454167 - XM_039035364.1 Bhi07g01593 1593
1 4753880 4764740 - BLOR00421 Blo01g00421 421
1 4767036 4773159 - BLOR00422 Blo01g00422 422
6 32205002 32207076 - BLOR17480 Blo06g00897 897
6 32227452 32230184 + BLOR17481 Blo06g00898 898
6 32230758 32237630 - BLOR17482 Blo06g00899 899
11 10558154 10568824 - BLOR03638 Blo11g00762 762
16 39769985 39771209 + BLOR21912 Blo16g01125 1125
16 39792572 39797248 + BLOR21913 Blo16g01126 1126
16 39798129 39800761 - BLOR21914 Blo16g01127 1127
16 39810742 39812785 + BLOR21915 Blo16g01128 1128
1 994635 995884 - Bma030170 Bma01g00088 88
1 1005691 1010530 - Bma000254.1 Bma01g00089 89
6 35919201 35922956 + Bma023637.1 Bma06g00669 669
6 36152636 36155279 + Bma023644.1 Bma06g00674 674
6 36232778 36233992 - Bma023646.1 Bma06g00675 675
14 34554758 34556433 - Bma012346.1 Bma14g01635 1635
14 34559003 34574664 - Bma012347.1 Bma14g01636 1636
15 1756860 1765274 - Bma013147.1 Bma15g00166 166
15 1774526 1776669 + Bma013148.1 Bma15g00167 167
2 23995825 24001869 + Bpe010170.1 Bpe02g02352 2352
2 24009360 24010628 + Bpe010171.1 Bpe02g02353 2353
2 24021620 24024761 + Bpe010172.2 Bpe02g02354 2354
10 14473091 14473716 - Bpe003163.1 Bpe10g00859 859
10 14479181 14481913 + Bpe003164.1 Bpe10g00860 860
11 12443056 12445538 - Bpe004945.1 Bpe11g01632 1632
11 12447351 12452875 - Bpe004946.1 Bpe11g01633 1633
13 19482171 19483424 + Bpe011085.1 Bpe13g01422 1422
13 19533319 19536432 + Bpe011086.1 Bpe13g01423 1423
13 19538677 19541272 - Bpe011087.1 Bpe13g01424 1424
13 19544187 19546255 + Bpe011088.1 Bpe13g01425 1425
5 33938861 33941648 + CaPI482276_05g026460.1 Cam05g2646 2646
5 33970197 33974870 + CaPI482276_05g026480.1 Cam05g2648 2648
5 33976885 33981279 - CaPI482276_05g026490.1 Cam05g2649 2649
4 9660366 9663174 + Carg01718-RA Car04g01681 1681
4 9664669 9669830 - Carg01717-RA Car04g01682 1682
4 9680977 9682330 - Carg01715-RA Car04g01684 1684
15 1511662 1512822 + Carg02258-RA Car15g00277 277
18 10902709 10904427 + Carg17256-RA Car18g01074 1074
18 10916625 10920506 + Carg17255-RA Car18g01075 1075
18 10921252 10924114 - Carg17254-RA Car18g01076 1076
5 35056980 35059803 + CcPI632755_05g027150.1 Cco05g2715 2715
5 35088539 35093177 + CcPI632755_05g027170.1 Cco05g2717 2717
5 35093881 35097887 - CcPI632755_05g027180.1 Cco05g2718 2718
5 37381137 37382412 + CePI673135_05g026780.1 Cec05g2678 2678
5 37411215 37415913 + CePI673135_05g026810.1 Cec05g2681 2681
5 37416624 37422330 - CePI673135_05g026820.1 Cec05g2682 2682
10 15295581 15298591 + Chy10G181760.1 Chy10g00982 982
10 15301183 15304743 - Chy10G181770.1 Chy10g00983 983
10 15331665 15333135 - Chy10G181790.1 Chy10g00985 985
5 34142026 34144754 + ClG42_05g0264900.10 Clacu05g2649 2649
5 34171928 34176617 + ClG42_05g0265100.10 Clacu05g2651 2651
5 34178631 34183040 - ClG42_05g0265200.10 Clacu05g2652 2652
5 36029033 36044353 + ClCG05G024440.2 Cla05g02458 2458
5 36070004 36075837 + ClCG05G024470.1 Cla05g02461 2461
5 36076833 36082081 - ClCG05G024480.2 Cla05g02462 2462
4 8263661 8271192 + CmaCh04G016390.1 Cma04g01639 1639
4 8271971 8277942 - CmaCh04G016410.1 Cma04g01641 1641
4 8287930 8290868 - CmaCh04G016430.1 Cma04g01643 1643
18 9349100 9353720 + CmaCh18G011650.1 Cma18g01165 1165
18 9354049 9362762 - CmaCh18G011670.1 Cma18g01167 1167
10 2749165 2751595 + MELO3C012079.2.1 Cme10g00433 433
10 2773855 2779353 + MELO3C012077.2.1 Cme10g00435 435
10 2780724 2784175 - MELO3C012076.2.1 Cme10g00436 436
10 19252961 19255321 - PI0006035.1 Cmetu10g1011 1011
10 19217089 19220383 + PI0014593.1 Cmetu10g1539 1539
4 8701145 8705845 + CmoCh04G017180.1 Cmo04g01718 1718
4 8705865 8713018 - CmoCh04G017190.1 Cmo04g01719 1719
4 8724214 8726346 - CmoCh04G017220.1 Cmo04g01722 1722
4 20528681 20529969 - CmoCh04G028840.1 Cmo04g02884 2884
18 11928384 11930570 + CmoCh18G011880.1 Cmo18g01188 1188
18 11943318 11947227 + CmoCh18G011890.1 Cmo18g01189 1189
18 11948725 11951420 - CmoCh18G011910.1 Cmo18g01191 1191
5 33870270 33882612 + CmPI595203_05g025020.1 Cmu05g2502 2502
5 33909748 33916092 + CmPI595203_05g025040.1 Cmu05g2504 2504
5 33916446 33920815 - CmPI595203_05g025050.1 Cmu05g2505 2505
2 34552522 34554293 + Conep02aG0188600.1 Cone2ag0856 856
6 2956879 2963354 + Conep06aG0061600.1 Cone6ag0603 603
6 2966504 2968962 + Conep06aG0061700.1 Cone6ag0604 604
6 2975294 2977932 + Conep06aG0061800.1 Cone6ag0605 605
6 2979059 2981410 + Conep06aG0061900.1 Cone6ag0606 606
9 2869636 2875715 + Conep09aG0061800.1 Cone9ag0608 608
9 2879326 2881845 + Conep09aG0061900.1 Cone9ag0609 609
9 2888054 2890520 + Conep09aG0062000.1 Cone9ag0610 610
9 2891069 2893306 + Conep09aG0062100.1 Cone9ag0611 611
13 8272664 8274171 + Conep13aG0099700.1 Cone13ag0969 969
13 8282866 8286591 + Conep13aG0099900.1 Cone13ag0971 971
13 8287595 8289586 - Conep13aG0100000.1 Cone13ag0972 972
13 8293963 8295281 + Conep13aG0100300.1 Cone13ag0973 973
16 901913 904210 - Conep16aG0015900.1 Cone16ag0155 155
19 7311391 7312528 + Conep19aG0098700.1 Cone19ag0959 959
19 7320273 7324025 + Conep19aG0098900.1 Cone19ag0961 961
19 7324944 7327159 - Conep19aG0099000.1 Cone19ag0962 962
19 7333410 7335252 + Conep19aG0099500.1 Cone19ag0963 963
1 8687005 8691752 + Cp4.1LG01g12670.1 Cpe01g01451 1451
1 8688898 8697035 - Cp4.1LG01g12580.1 Cpe01g01452 1452
1 8707125 8717830 - Cp4.1LG01g12610.1 Cpe01g01454 1454
7 1461089 1468905 - Cp4.1LG07g02300.1 Cpe07g00226 226
7 3954274 3956313 - Cp4.1LG07g05800.1 Cpe07g00590 590
9 935453 943563 + Cp4.1LG09g01520.1 Cpe09g00162 162
9 937870 943563 - Cp4.1LG09g01650.1 Cpe09g00163 163
9 956347 958677 - Cp4.1LG09g01620.1 Cpe09g00164 164
5 37241809 37244525 + CrPI670011_05g026160.1 Cre05g2616 2616
5 37273388 37278090 + CrPI670011_05g026180.1 Cre05g2618 2618
5 37280164 37282864 - CrPI670011_05g026190.1 Cre05g2619 2619
5 26263263 26266892 + CsaV3_5G032480.1 Csa05g02429 2429
5 26268005 26273655 - CsaV3_5G032490.1 Csa05g02430 2430
5 26297535 26299545 - CsaV3_5G032510.1 Csa05g02432 2432
10 54000082 54004440 + Hsped.10g17220.1 Hepe10g1722 1722
10 54054519 54056366 - Hsped.10g17250.1 Hepe10g1725 1725
13 2098738 2101373 + Lag0040093.1 Lac13g0297 297
13 2133202 2134758 - Lag0040097.1 Lac13g0301 301
4 4239452 4241129 + Lsi04G004420.1 Lsi04g00442 442
4 4271739 4277795 + Lsi04G004440.1 Lsi04g00444 444
4 4278963 4282221 - Lsi04G004450.1 Lsi04g00445 445
6 40270934 40273198 + Sed0011691.1 Sed06g1545 1545
6 40317672 40320612 - Sed0017884.1 Sed06g1547 1547
12 31573850 31575349 + Sed0008359.1 Sed12g2082 2082
4 10006310 10008578 + Tan0012049.1 Tan04g1101 1101
4 10055155 10062012 + Tan0007476.2 Tan04g1106 1106
4 10063005 10066561 - Tan0014918.1 Tan04g1107 1107
1 11184009 11186116 + Vvi1g871 Vvi1g871 871
1 11205575 11207549 + Vvi1g872 Vvi1g872 872
1 11224675 11229121 - Vvi1g873 Vvi1g873 873
1 11232313 11234303 + Vvi1g874 Vvi1g874 874
1 11234423 11239295 - Vvi1g875 Vvi1g875 875
1 11250994 11256179 + Vvi1g876 Vvi1g876 876
1 11257107 11257345 + Vvi1g877 Vvi1g877 877
1 11257556 11265773 - Vvi1g878 Vvi1g878 878
1 11304893 11307266 - Vvi1g879 Vvi1g879 879
1 11312667 11322931 - Vvi1g880 Vvi1g880 880
       

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