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
Vvi2g692 . Blo03g00058 . . . . Bma07g00920 Bma14g00162 . Cmo16g01222 . . . . Sed02g0062 Cpe14g00971 . Bhi11g00019 Tan01g2207 Cmetu01g2686 . . Mch10g1676 . Cla10g00145 Cam10g0140 Cec10g0150 Cco10g0150 Clacu10g0144 Cmu10g0991 Cre10g0402 . Cone5ag0619 . . Lsi07g01180 . Chy04g00110 Cme06g02458 Blo03g00871 Blo19g00200 Bda07g00088 . Bpe08g00823 Bpe11g00325 . . . . Cmo19g00239 . Cma16g01172 . Car16g01105 . Cpe15g00200 Bhi05g00470 . . Lac11g2433 . . . Cla09g01107 Cam09g1161 Cec09g1169 Cco09g1184 . . Cre09g1122 . Csa03g04592 Chy06g02155 Cme04g00134
Vvi2g693 . . . Bda08g00634 Bpe05g00524 . . . . . Cma02g01624 . Car02g01383 . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00112 . . . . . . . Bma05g00709 . . Cmo02g01669 Cmo19g00238 . . . . . . Bhi05g00468 . . . . . Lcy12g1962 Cla09g01106 . . . . . . . Csa03g04590 . Cme04g00135
Vvi2g694 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0595 Cone12ag0582 . . . . . . . . . . . . . . . . . . . . . . . Bhi05g00466 . . Lac11g2437 . . . . . . . . . . . . . .
Vvi2g695 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g696 . . . . . . . . . . . . . . . Cpe14g00973 . Bhi11g00017 Tan01g2209 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car16g01107 . . . . . . . . . . . . . . . . . . . .
Vvi2g697 Blo02g00987 Blo03g00107 Bda06g01263 Bda08g00635 Bpe05g00523 Bpe07g00231 . . . Cmo16g01224 . . . . Sed04g0857 . . Bhi11g00016 Tan01g2210 Cmetu06g2024 . . Mch10g1678 . Cla10g00141 . . . . . . . . . . Lsi07g01179 . . Cme06g02456 . . . . . . Bma05g00708 Bma12g00232 . . . . Cma16g01174 . . . . . . . . . . . . . . . . . . . Csa03g00151 Chy06g02157 .
Vvi2g698 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g699 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00114 . Blo03g00874 . Bda07g00086 . . Bpe11g00323 . . Sed01g4129 . Cmo19g00236 . . . . . Cpe15g00198 Bhi05g00464 Tan07g2001 Cmetu04g1279 Lac11g2439 Hepe06g1792 . Lcy12g1964 Cla09g01103 Cam09g1156 Cec09g1165 Cco09g1180 . . Cre09g1118 . Csa03g04588 . Cme04g00137
Vvi2g700 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda07g00085 . . Bpe11g00322 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g701 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0481 Cone12ag0476 . . . . . . Blo03g00875 . Bda07g00084 . . Bpe11g00321 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 43148054 43151388 + Bda023105.1 Bda06g01263 1263
7 1079572 1082528 + Bda025142.1 Bda07g00084 84
7 1084328 1085815 - Bda025143.1 Bda07g00085 85
7 1098479 1104368 - Bda025144.4 Bda07g00086 86
7 1116837 1117850 - Bda025146.1 Bda07g00088 88
8 6527925 6529059 - Bda029096.1 Bda08g00634 634
8 6534025 6537000 - Bda029097.1 Bda08g00635 635
5 9830089 9835142 - XM_039033077.1 Bhi05g00464 464
5 9878382 9885773 - XM_039033116.1 Bhi05g00466 466
5 9967487 9968800 + XM_039032729.1 Bhi05g00468 468
5 9988429 9993151 - XM_039032798.1 Bhi05g00470 470
11 300470 304835 + XM_039047976.1 Bhi11g00016 16
11 300470 304835 + XM_039047977.1 Bhi11g00017 17
11 317118 319108 - XM_039048843.1 Bhi11g00019 19
2 38195620 38200339 + BLOR10717 Blo02g00987 987
3 2174773 2178474 - BLOR11239 Blo03g00058 58
3 3359748 3376359 + BLOR11288 Blo03g00107 107
3 34539452 34540465 + BLOR12052 Blo03g00871 871
3 34559841 34593183 + BLOR12055 Blo03g00874 874
3 34594901 34597808 - BLOR12056 Blo03g00875 875
19 8951809 8952915 + BLOR09543 Blo19g00200 200
5 41135268 41138423 + Bma021783.1 Bma05g00708 708
5 41173612 41174745 + Bma021784.1 Bma05g00709 709
7 33309702 33310811 - Bma026021.1 Bma07g00920 920
12 3024284 3028061 - Bma007122.1 Bma12g00232 232
14 2183112 2184149 + Bma010569.1 Bma14g00162 162
5 19422098 19425519 + Bpe017940.1 Bpe05g00523 523
5 19431322 19432456 + Bpe017941.1 Bpe05g00524 524
7 1639176 1643117 - Bpe021042.1 Bpe07g00231 231
8 10325183 10326289 - Bpe022945.1 Bpe08g00823 823
11 2362536 2365482 + Bpe003695.1 Bpe11g00321 321
11 2367523 2369463 - Bpe003696.1 Bpe11g00322 322
11 2372097 2376184 - Bpe003697.1 Bpe11g00323 323
11 2387897 2388904 - Bpe003699.1 Bpe11g00325 325
9 12267895 12272445 - CaPI482276_09g011560.1 Cam09g1156 1156
9 12351044 12352129 - CaPI482276_09g011610.1 Cam09g1161 1161
10 3029534 3030613 - CaPI482276_10g001400.1 Cam10g0140 140
2 9103845 9104732 - Carg08850-RA Car02g01383 1383
16 9510332 9511435 + Carg26205-RA Car16g01105 1105
16 9519005 9524902 - Carg26207-RA Car16g01107 1107
9 11639237 11644164 - CcPI632755_09g011800.1 Cco09g1180 1180
9 11722803 11726867 - CcPI632755_09g011840.1 Cco09g1184 1184
10 1446590 1447669 - CcPI632755_10g001500.1 Cco10g0150 150
9 11677654 11684383 - CePI673135_09g011650.1 Cec09g1165 1165
9 11783014 11785637 - CePI673135_09g011690.1 Cec09g1169 1169
10 1459863 1460942 - CePI673135_10g001500.1 Cec10g0150 150
4 1007994 1009082 + Chy4G068280.1 Chy04g00110 110
4 1016376 1017538 - Chy4G068300.1 Chy04g00112 112
4 1035320 1037361 + Chy4G068320.1 Chy04g00114 114
6 25859901 25860983 + Chy6G126830.1 Chy06g02155 2155
6 25872096 25875409 - Chy6G126850.1 Chy06g02157 2157
10 1757180 1758259 - ClG42_10g0014400.10 Clacu10g0144 144
9 11909649 11914187 - ClCG09G011740.2 Cla09g01103 1103
9 11960603 11964030 + ClCG09G011757.1 Cla09g01106 1106
9 11990514 11997183 - ClCG09G011760.1 Cla09g01107 1107
10 1490923 1495240 + ClCG10G001420.1 Cla10g00141 141
10 1503712 1505098 - ClCG10G001460.2 Cla10g00145 145
2 9205161 9206317 - CmaCh02G016240.1 Cma02g01624 1624
16 8977736 8978839 + CmaCh16G011720.1 Cma16g01172 1172
16 8986427 8992310 - CmaCh16G011740.1 Cma16g01174 1174
4 1004171 1005705 + MELO3C003426.2.1 Cme04g00134 134
4 1011130 1012468 - MELO3C003427.2.1 Cme04g00135 135
4 1029807 1034063 + MELO3C003429.2.1 Cme04g00137 137
6 31591146 31595636 + MELO3C013838.2.1 Cme06g02456 2456
6 31604508 31606222 - MELO3C013840.2.1 Cme06g02458 2458
1 1402360 1410782 + PI0024697.1 Cmetu01g2686 2686
4 32404918 32413954 - PI0004561.1 Cmetu04g1279 1279
6 29814423 29819210 - PI0003493.1 Cmetu06g2024 2024
2 9580722 9581813 - CmoCh02G016690.1 Cmo02g01669 1669
16 8754420 8755523 + CmoCh16G012220.1 Cmo16g01222 1222
16 8764732 8769546 - CmoCh16G012240.1 Cmo16g01224 1224
19 1649353 1659138 - CmoCh19G002360.1 Cmo19g00236 236
19 1681403 1683546 + CmoCh19G002380.1 Cmo19g00238 238
19 1689817 1690902 - CmoCh19G002390.1 Cmo19g00239 239
10 1908345 1909424 - CmPI595203_10g009910.1 Cmu10g0991 991
5 2651875 2653938 - Conep05aG0064100.1 Cone5ag0619 619
8 3306137 3308519 - Conep08aG0050200.1 Cone8ag0481 481
8 5053599 5058927 - Conep08aG0061600.1 Cone8ag0595 595
12 3094828 3097602 - Conep12aG0049500.1 Cone12ag0476 476
12 4535622 4539287 + Conep12aG0060300.1 Cone12ag0582 582
14 8221391 8224575 + Cp4.1LG14g09640.1 Cpe14g00971 971
14 8231859 8236874 - Cp4.1LG14g09680.1 Cpe14g00973 973
15 1638593 1641957 - Cp4.1LG15g01990.1 Cpe15g00198 198
15 1675146 1676189 - Cp4.1LG15g01960.1 Cpe15g00200 200
9 11848036 11858441 - CrPI670011_09g011180.1 Cre09g1118 1118
9 11933676 11934761 - CrPI670011_09g011220.1 Cre09g1122 1122
10 2873782 2874861 - CrPI670011_10g004020.1 Cre10g0402 402
3 1167633 1172345 + CsaV3_3G001510.1 Csa03g00151 151
3 39941662 39945329 - CsaV3_3G048940.1 Csa03g04588 4588
3 39962183 39963483 + CsaV3_3G048960.1 Csa03g04590 4590
3 39970757 39971845 - CsaV3_3G048980.1 Csa03g04592 4592
6 68988985 68992733 + Hsped.06g17920.1 Hepe06g1792 1792
11 40523396 40523803 + Lag0033071.1 Lac11g2433 2433
11 40543018 40550883 - Lag0033075.1 Lac11g2437 2437
11 40559921 40566982 + Lag0033077.1 Lac11g2439 2439
12 40971687 40973404 - Maker00038195 Lcy12g1962 1962
12 41002940 41007683 + Maker00038123 Lcy12g1964 1964
7 17303864 17317497 + Lsi07G011790.1 Lsi07g01179 1179
7 17320336 17321418 - Lsi07G011800.1 Lsi07g01180 1180
10 16823491 16824528 + MC10g1331 Mch10g1676 1676
10 16832707 16837305 - MC10g1333 Mch10g1678 1678
1 70095979 70100465 + Sed0025660.1 Sed01g4129 4129
2 7348713 7351347 + Sed0011567.1 Sed02g0062 62
4 7408572 7413694 - Sed0019094.2 Sed04g0857 857
1 26163945 26165811 + Tan0019251.1 Tan01g2207 2207
1 26198772 26203157 - Tan0005454.1 Tan01g2209 2209
1 26198772 26203157 - Tan0005454.2 Tan01g2210 2210
7 71694042 71698912 + Tan0008867.1 Tan07g2001 2001
2 7918084 7919566 + Vvi2g692 Vvi2g692 692
2 7942403 7943735 - Vvi2g693 Vvi2g693 693
2 7963835 7972650 - Vvi2g694 Vvi2g694 694
2 7997843 7999451 + Vvi2g695 Vvi2g695 695
2 8014612 8020562 - Vvi2g696 Vvi2g696 696
2 8020587 8023605 - Vvi2g697 Vvi2g697 697
2 8071719 8071824 + Vvi2g698 Vvi2g698 698
2 8123286 8139515 + Vvi2g699 Vvi2g699 699
2 8161665 8170322 + Vvi2g700 Vvi2g700 700
2 8170640 8173950 - Vvi2g701 Vvi2g701 701
       

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