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
Vvi2g42 . . . . . . . . . . Cma02g01426 Cma15g01253 . Car15g01130 . . Cpe05g00360 . . . . . . . . . . . . . . Cone8ag0277 Cone12ag0284 . . . Csa05g00241 Chy09g01261 . . . . . . Bpe11g00670 . . . Cmo02g01460 Cmo15g01318 . . . . . Cpe13g00132 Bhi12g00316 . . . . . . Cla01g00228 Cam01g0235 Cec01g0226 Cco01g0238 Clacu01g0230 Cmu01g0223 Cre09g2286 Lsi09g00218 . . Cme09g01799
Vvi2g43 . . . . . . . Bma14g00598 . . Cma02g01425 . Car02g01194 . . . Cpe05g00361 . . . . . . . . . . . . . . . . Cone6ag0811 Cone9ag0810 . . Chy09g01262 . . . . . . Bpe11g00671 . . . Cmo02g01459 . . . . . . . . . . . . . . Cla01g00227 Cam01g0234 Cec01g0225 Cco01g0237 Clacu01g0229 Cmu01g0222 Cre09g2287 Lsi09g00217 . . .
Vvi2g44 . . . . . . . Bma14g00597 . . Cma02g01424 . Car02g01193 . . . Cpe05g00362 . . . . . . . . . . . . . . Cone8ag0276 . . . . Csa05g00240 . . . . . . . Bpe11g00672 . . . Cmo02g01458 . . . . . . . Bhi12g00322 . . . . . Lcy12g1610 . . . . . . . . . . Cme09g01800
Vvi2g45 . . . . Bpe05g00659 . . . . Cmo16g00630 . . Car02g00702 . . Cpe14g00491 Cpe05g00637 . . . . . . . Cla07g00748 Cam07g0800 Cec07g0865 Cco07g0839 Clacu07g0780 Cmu07g0788 Cre07g1142 . . Cone6ag0812 Cone9ag0811 . . . Cme07g01614 . . Bda07g01906 . . . Bma05g00832 . . Cmo02g01102 Cmo15g01124 . Cma16g00580 . . . . . . . . . . . . . . . . . . . Csa04g00611 Chy07g01200 .
Vvi2g46 . . . . . . . Bma14g00596 . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0283 . . . Csa05g00238 Chy09g01263 . . . . . . . . . . Cmo02g01457 . . . . . . . Bhi12g00324 . . Lac11g2044 Hepe06g1510 . Lcy12g1609 Cla01g00226 Cam01g0233 Cec01g0224 Cco01g0236 Clacu01g0228 Cmu01g0221 Cre09g2288 Lsi09g00216 . . Cme09g01802
Vvi2g47 . Blo03g00223 Bda06g00120 . . Bpe07g00097 . . . . . . . . . . . . . . . . . . Cla07g00745 Cam07g0798 Cec07g0863 Cco07g0835 Clacu07g0778 Cmu07g0786 Cre07g1139 . . Cone6ag0814 Cone9ag0813 . . . Cme07g01612 . . . . . . . Bma12g00068 . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00613 Chy07g01198 .
Vvi2g48 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0275 . . . . . . . . . Bda07g01908 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g49 . Blo03g00224 . . . Bpe07g00096 . . . . Cma02g01422 . Car02g01191 Car15g01131 . . Cpe05g00363 . . . . . . . . . . . . . . Cone8ag0274 Cone12ag0281 . Cone9ag0814 . Csa05g00237 Chy09g01264 . . . . . . . . Bma12g00067 . Cmo02g01456 Cmo15g01319 . . . . . Cpe13g00131 Bhi12g00325 . . Lac11g2043 Hepe06g1509 . Lcy12g1608 . . . . . . . Lsi09g00214 . . Cme09g01803
Vvi2g50 Blo02g01122 Blo03g00225 Bda06g00121 Bda08g00504 Bpe05g00660 Bpe07g00095 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0815 Cone9ag0815 . . . . . . . . . . Bma05g00834 Bma12g00065 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g51 Blo02g01124 Blo03g00229 Bda06g00123 Bda08g00501 Bpe05g00663 Bpe07g00092 . . . Cmo16g00629 . . . . . Cpe14g00490 . . . . . . . . Cla07g00744 Cam07g0796 Cec07g0862 Cco07g0831 Clacu07g0777 Cmu07g0784 Cre07g1136 Cone8ag0273 Cone12ag0280 . . . . . Cme07g01611 . . . . . . Bma05g00837 Bma12g00062 . . . . Cma16g00579 . . . . . . . . . . . . . . . . . . . Csa04g00614 Chy07g01197 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 1883378 1886627 - Bda023315.1 Bda06g00120 120
6 1898298 1901121 - Bda023316.1 Bda06g00121 121
6 1924543 1927523 + Bda023318.1 Bda06g00123 123
7 36505363 36506614 + Bda028880.1 Bda07g01906 1906
7 36512771 36516465 + Bda028882.1 Bda07g01908 1908
8 5092682 5096567 - Bda024952.1 Bda08g00501 501
8 5116078 5118838 + Bda024955.1 Bda08g00504 504
12 9014361 9017111 - XM_039050890.1 Bhi12g00316 316
12 9059334 9062871 - XM_039050549.1 Bhi12g00322 322
12 9097455 9103645 - XM_039018950.1 Bhi12g00324 324
12 9112515 9170206 - XM_039018951.1 Bhi12g00325 325
2 42440427 42450793 - BLOR10852 Blo02g01122 1122
2 42519464 42527642 + BLOR10854 Blo02g01124 1124
3 5045764 5053240 - BLOR11404 Blo03g00223 223
3 5053920 5061198 - BLOR11405 Blo03g00224 224
3 5076071 5079242 - BLOR11406 Blo03g00225 225
3 5099696 5103726 + BLOR11410 Blo03g00229 229
5 45698139 45699197 + Bma021942.1 Bma05g00832 832
5 45708243 45710772 - Bma021944.1 Bma05g00834 834
5 45742693 45747483 + Bma021947.1 Bma05g00837 837
12 1187161 1189543 - Bma006933.1 Bma12g00062 62
12 1224784 1227226 + Bma006936.1 Bma12g00065 65
12 1238624 1241963 + Bma006938.1 Bma12g00067 67
12 1243747 1249958 + Bma006939.2 Bma12g00068 68
14 6466512 6468904 + Bma011032.1 Bma14g00596 596
14 6469908 6471990 + Bma011033.1 Bma14g00597 597
14 6472340 6475529 - Bma011034.1 Bma14g00598 598
5 20336426 20337379 + Bpe018072.1 Bpe05g00659 659
5 20340854 20343370 - Bpe018073.1 Bpe05g00660 660
5 20358579 20362476 + Bpe018076.1 Bpe05g00663 663
7 666676 669059 - Bpe020905.1 Bpe07g00092 92
7 686350 689062 + Bpe020909.2 Bpe07g00095 95
7 702091 705211 + Bpe020910.1 Bpe07g00096 96
7 705956 713992 + Bpe020911.1 Bpe07g00097 97
11 5145450 5146957 - Bpe004027.1 Bpe11g00670 670
11 5153224 5158881 + Bpe024776 Bpe11g00671 671
11 5156704 5165989 - Bpe004028.3 Bpe11g00672 672
1 2612790 2632044 + CaPI482276_01g002330.1 Cam01g0233 233
1 2632920 2640510 - CaPI482276_01g002340.1 Cam01g0234 234
1 2641057 2648263 + CaPI482276_01g002350.1 Cam01g0235 235
7 19960090 19967167 - CaPI482276_07g007960.1 Cam07g0796 796
7 20040778 20042695 + CaPI482276_07g007980.1 Cam07g0798 798
7 20106383 20107816 - CaPI482276_07g008000.1 Cam07g0800 800
2 5198233 5199498 + Carg08521-RA Car02g00702 702
2 8109946 8123238 + Carg02557-RA Car02g01191 1191
2 8127450 8129790 + Carg02555-RA Car02g01193 1193
2 8129011 8134669 - Carg02554-RA Car02g01194 1194
15 8898847 8901618 - Carg16612-RA Car15g01130 1130
15 8903736 8918980 - Carg16611-RA Car15g01131 1131
1 2243913 2250284 + CcPI632755_01g002360.1 Cco01g0236 236
1 2251117 2255685 - CcPI632755_01g002370.1 Cco01g0237 237
1 2259281 2266537 + CcPI632755_01g002380.1 Cco01g0238 238
7 19219090 19226020 - CcPI632755_07g008310.1 Cco07g0831 831
7 19280538 19285808 + CcPI632755_07g008350.1 Cco07g0835 835
7 19409511 19410962 - CcPI632755_07g008390.1 Cco07g0839 839
1 2207832 2227830 + CePI673135_01g002240.1 Cec01g0224 224
1 2228705 2233264 - CePI673135_01g002250.1 Cec01g0225 225
1 2234905 2244137 + CePI673135_01g002260.1 Cec01g0226 226
7 21107436 21116235 - CePI673135_07g008620.1 Cec07g0862 862
7 21157700 21185946 + CePI673135_07g008630.1 Cec07g0863 863
7 21284517 21285904 - CePI673135_07g008650.1 Cec07g0865 865
7 16824875 16830922 - Chy7G140270.1 Chy07g01197 1197
7 16832742 16843703 + Chy7G140280.1 Chy07g01198 1198
7 16850218 16851532 - Chy7G140300.1 Chy07g01200 1200
9 14638110 14644217 - Chy9G169770.1 Chy09g01261 1261
9 14646093 14649993 + Chy9G169780.1 Chy09g01262 1262
9 14650993 14654436 - Chy9G169790.1 Chy09g01263 1263
9 14657723 14673632 - Chy9G169800.1 Chy09g01264 1264
1 2229142 2248983 + ClG42_01g0022800.10 Clacu01g0228 228
1 2249837 2254394 - ClG42_01g0022900.10 Clacu01g0229 229
1 2256022 2265240 + ClG42_01g0023000.10 Clacu01g0230 230
7 19620784 19630393 - ClG42_07g0077700.10 Clacu07g0777 777
7 19668320 19700059 + ClG42_07g0077800.10 Clacu07g0778 778
7 19791952 19793415 - ClG42_07g0078000.10 Clacu07g0780 780
1 2257712 2284667 + ClCG01G002310.1 Cla01g00226 226
1 2282781 2289028 - ClCG01G002320.2 Cla01g00227 227
1 2289237 2298455 + ClCG01G002330.2 Cla01g00228 228
7 20717472 20723917 - ClCG07G007820.2 Cla07g00744 744
7 20764880 20796953 + ClCG07G007830.2 Cla07g00745 745
7 20890213 20893769 - ClCG07G007870.1 Cla07g00748 748
2 8201022 8214635 + CmaCh02G014220.1 Cma02g01422 1422
2 8219948 8222494 + CmaCh02G014240.1 Cma02g01424 1424
2 8222303 8227127 - CmaCh02G014250.1 Cma02g01425 1425
2 8227347 8229755 + CmaCh02G014260.1 Cma02g01426 1426
15 7947326 7966774 - CmaCh15G012530.1 Cma15g01253 1253
16 2991629 2997317 - CmaCh16G005790.1 Cma16g00579 579
16 2998775 2999747 - CmaCh16G005800.1 Cma16g00580 580
7 21901828 21907966 - MELO3C016335.2.1 Cme07g01611 1611
7 21910119 21921719 + MELO3C016336.2.1 Cme07g01612 1612
7 21928416 21930176 - MELO3C016338.2.1 Cme07g01614 1614
9 22370604 22373333 - MELO3C005713.2.1 Cme09g01799 1799
9 22374786 22378061 - MELO3C005714.2.1 Cme09g01800 1800
9 22383320 22387129 - MELO3C005716.2.1 Cme09g01802 1802
9 22389841 22399115 - MELO3C005717.2.1 Cme09g01803 1803
2 6677813 6679130 + CmoCh02G011020.1 Cmo02g01102 1102
2 8563141 8572134 + CmoCh02G014560.1 Cmo02g01456 1456
2 8573431 8577030 + CmoCh02G014570.1 Cmo02g01457 1457
2 8577972 8580738 + CmoCh02G014580.1 Cmo02g01458 1458
2 8580590 8585893 - CmoCh02G014590.1 Cmo02g01459 1459
2 8586242 8588709 + CmoCh02G014600.1 Cmo02g01460 1460
15 7806671 7807927 - CmoCh15G011240.1 Cmo15g01124 1124
15 9044682 9047361 - CmoCh15G013180.1 Cmo15g01318 1318
15 9049528 9070410 - CmoCh15G013190.1 Cmo15g01319 1319
16 3094110 3099357 - CmoCh16G006290.1 Cmo16g00629 629
16 3100583 3101717 - CmoCh16G006300.1 Cmo16g00630 630
1 2182227 2202119 + CmPI595203_01g002210.1 Cmu01g0221 221
1 2202973 2207530 - CmPI595203_01g002220.1 Cmu01g0222 222
1 2209034 2218375 + CmPI595203_01g002230.1 Cmu01g0223 223
7 19835243 19843936 - CmPI595203_07g007840.1 Cmu07g0784 784
7 19912437 19914500 + CmPI595203_07g007860.1 Cmu07g0786 786
7 20006302 20007765 - CmPI595203_07g007880.1 Cmu07g0788 788
6 4120888 4123601 + Conep06aG0083500.1 Cone6ag0811 811
6 4127490 4128756 + Conep06aG0083600.1 Cone6ag0812 812
6 4130196 4137290 - Conep06aG0083800.1 Cone6ag0814 814
6 4142641 4145227 - Conep06aG0083900.1 Cone6ag0815 815
8 1585392 1589809 - Conep08aG0028800.1 Cone8ag0273 273
8 1592278 1597766 + Conep08aG0028900.1 Cone8ag0274 274
8 1597170 1601572 - Conep08aG0029000.1 Cone8ag0275 275
8 1604013 1609097 + Conep08aG0029100.1 Cone8ag0276 276
8 1610063 1611687 + Conep08aG0029200.1 Cone8ag0277 277
9 3895406 3898194 + Conep09aG0082800.1 Cone9ag0810 810
9 3902804 3904063 + Conep09aG0082900.1 Cone9ag0811 811
9 3905592 3913176 - Conep09aG0083100.1 Cone9ag0813 813
9 3913772 3918421 - Conep09aG0083200.1 Cone9ag0814 814
9 3920141 3922621 - Conep09aG0083300.1 Cone9ag0815 815
12 1508306 1517616 - Conep12aG0029200.1 Cone12ag0280 280
12 1519281 1524995 + Conep12aG0029300.1 Cone12ag0281 281
12 1531112 1533672 + Conep12aG0029500.1 Cone12ag0283 283
12 1537482 1539345 + Conep12aG0029600.1 Cone12ag0284 284
5 2004385 2006862 - Cp4.1LG05g03100.1 Cpe05g00360 360
5 2007180 2012558 + Cp4.1LG05g03200.1 Cpe05g00361 361
5 2011727 2014533 - Cp4.1LG05g03150.1 Cpe05g00362 362
5 2021577 2028639 - Cp4.1LG05g03140.1 Cpe05g00363 363
5 3893194 3894413 - Cp4.1LG05g06330.1 Cpe05g00637 637
13 948873 963773 + Cp4.1LG13g01290.1 Cpe13g00131 131
13 966323 969073 + Cp4.1LG13g01270.1 Cpe13g00132 132
14 3110001 3115581 - Cp4.1LG14g02210.1 Cpe14g00490 490
14 3117647 3119283 - Cp4.1LG14g02220.1 Cpe14g00491 491
7 23183908 23190865 - CrPI670011_07g011360.1 Cre07g1136 1136
7 23290880 23292877 + CrPI670011_07g011390.1 Cre07g1139 1139
7 23410872 23412306 - CrPI670011_07g011420.1 Cre07g1142 1142
9 42071109 42077720 - CrPI670011_09g022860.1 Cre09g2286 2286
9 42078190 42085832 + CrPI670011_09g022870.1 Cre09g2287 2287
9 42086714 42107568 - CrPI670011_09g022880.1 Cre09g2288 2288
4 4040395 4042324 + CsaV3_4G006110.1 Csa04g00611 611
4 4047710 4059410 - CsaV3_4G006130.1 Csa04g00613 613
4 4060703 4067100 + CsaV3_4G006140.1 Csa04g00614 614
5 1449849 1461311 + CsaV3_5G002370.1 Csa05g00237 237
5 1463494 1467124 + CsaV3_5G002380.1 Csa05g00238 238
5 1471911 1475640 + CsaV3_5G002400.1 Csa05g00240 240
5 1476642 1479751 + CsaV3_5G002410.1 Csa05g00241 241
6 65721940 65740324 + Hsped.06g15090.1 Hepe06g1509 1509
6 65746714 65753888 + Hsped.06g15100.1 Hepe06g1510 1510
11 36155480 36173971 + Lag0032681.1 Lac11g2043 2043
11 36185462 36189799 + Lag0032682.1 Lac11g2044 2044
12 36301401 36310097 + Maker00029308 Lcy12g1608 1608
12 36326651 36332488 + Maker00029469 Lcy12g1609 1609
12 36333496 36335867 + Maker00029173 Lcy12g1610 1610
9 2237347 2245236 + Lsi09G002140.1 Lsi09g00214 214
9 2257280 2264015 + Lsi09G002160.1 Lsi09g00216 216
9 2259503 2272791 - Lsi09G002170.1 Lsi09g00217 217
9 2274017 2284745 + Lsi09G002180.1 Lsi09g00218 218
2 488929 493430 - Vvi2g42 Vvi2g42 42
2 495265 504962 + Vvi2g43 Vvi2g43 43
2 505012 508954 - Vvi2g44 Vvi2g44 44
2 512162 513533 + Vvi2g45 Vvi2g45 45
2 515902 519370 - Vvi2g46 Vvi2g46 46
2 520830 533824 - Vvi2g47 Vvi2g47 47
2 537379 544068 + Vvi2g48 Vvi2g48 48
2 557002 570448 - Vvi2g49 Vvi2g49 49
2 571899 578921 - Vvi2g50 Vvi2g50 50
2 584920 595743 + Vvi2g51 Vvi2g51 51
       

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