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
Vvi4g1312 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1313 . . . . . . . . . Cmo20g01059 . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1271 . . . . . . . . . . . . . . . . . Cma20g01053 . . . Cpe16g00093 . . . . . . . . . . . . . . . . . .
Vvi4g1314 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1315 . . . Bda10g00403 . . . Bma15g00782 . . Cma03g01102 . Car03g00991 . Sed10g1074 . Cpe10g00329 Bhi03g01336 Tan03g1298 Cmetu08g0340 . Hepe04g1105 . . Cla01g01508 Cam01g1576 Cec04g1220 Cco04g1288 Clacu01g1601 Cmu01g1489 Cre04g1168 . . Cone6ag1270 . Lsi01g01160 . . Cme08g01092 . . . . Bpe10g00263 . . . . Cmo03g01085 . . . . . . . . . . . . . . . . . . . . . . Csa06g02772 Chy02g01062 .
Vvi4g1316 . . Bda04g00380 . . . Bma09g00428 . . . Cma03g01103 . Car03g00992 . Sed14g0236 . Cpe10g00328 Bhi03g01334 Tan03g1297 Cmetu08g0533 . Hepe04g1104 . . Cla01g01507 Cam01g1575 Cec04g1219 Cco04g1287 Clacu01g1600 Cmu01g1488 Cre04g1167 . . Cone6ag1269 . Lsi01g01161 . . Cme08g01093 Blo05g00536 . . . . Bpe06g00297 . . . Cmo03g01086 . . . . . . . . . . . . . . . . . . . . . . Csa06g02771 Chy02g01063 .
Vvi4g1317 . . . . . . . . Cmo02g00643 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01390 . . . . Bma06g00491 Sed05g3849 . . . . . . . . Bhi10g01692 Tan07g0845 Cmetu11g1623 . Hepe08g1230 . . Cla02g00044 Cam02g0047 . Cco02g0040 Clacu02g0046 Cmu02g0046 Cre02g0385 Lsi10g00744 . . Cme11g00046
Vvi4g1318 . . . Bda10g00405 . . . Bma15g00779 . . Cma03g01104 . Car03g00993 . Sed11g1186 . Cpe10g00327 Bhi03g01333 Tan03g1296 Cmetu08g1459 . Hepe04g1102 . . Cla01g01506 Cam01g1574 Cec04g1218 Cco04g1286 Clacu01g1599 Cmu01g1487 . . . . . Lsi01g01162 . . Cme08g01094 . Blo06g00188 . . Bpe10g00264 . . . . Cmo03g01087 . . . . . . . . . . . . . . . . . . . . . . Csa06g02770 Chy02g01064 .
Vvi4g1319 . . . . . . Bma09g00430 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo05g00535 . . . . Bpe06g00298 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1320 Blo04g00928 . . . Bpe15g00439 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1321 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe06g00303 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 50611795 50616731 - Bda019321.1 Bda04g00380 380
10 36153990 36156918 + Bda007232.1 Bda10g00403 403
10 36169169 36175720 - Bda007236.1 Bda10g00405 405
11 17419539 17421383 - Bda007950.1 Bda11g01390 1390
3 27865077 27873805 - XM_039026621.1 Bhi03g01333 1333
3 27877096 27881110 + XM_039028019.1 Bhi03g01334 1334
3 27893935 27897190 - XM_039025045.1 Bhi03g01336 1336
10 42681279 42684934 - XM_039044970.1 Bhi10g01692 1692
4 10987893 10989380 - BLOR13840 Blo04g00928 928
5 10173384 10175507 - BLOR15497 Blo05g00535 535
5 10398637 10400939 + BLOR15498 Blo05g00536 536
6 7961420 7978954 + BLOR16771 Blo06g00188 188
6 23109431 23111290 + Bma023337.1 Bma06g00491 491
9 37031744 37038210 - Bma029419.1 Bma09g00428 428
9 37593101 37595111 + Bma029425.1 Bma09g00430 430
15 16506394 16512571 + Bma013856.1 Bma15g00779 779
15 16609773 16613749 - Bma013859.1 Bma15g00782 782
6 14171362 14179503 - Bpe019797.1 Bpe06g00297 297
6 14253376 14255485 + Bpe019798.1 Bpe06g00298 298
6 14355437 14356993 + Bpe019803.1 Bpe06g00303 303
10 9901029 9913875 + Bpe002600.1 Bpe10g00263 263
10 9932076 9936460 - Bpe002601.1 Bpe10g00264 264
15 15870430 15871887 - Bpe001375.1 Bpe15g00439 439
1 29239826 29247973 - CaPI482276_01g015740.1 Cam01g1574 1574
1 29250079 29253818 + CaPI482276_01g015750.1 Cam01g1575 1575
1 29255213 29258570 - CaPI482276_01g015760.1 Cam01g1576 1576
2 1597741 1598746 + CaPI482276_02g000470.1 Cam02g0047 47
3 7630481 7633665 + Carg10529-RA Car03g00991 991
3 7633933 7637825 - Carg10528-RA Car03g00992 992
3 7638459 7643578 + Carg10527-RA Car03g00993 993
2 464717 467492 + CcPI632755_02g000400.1 Cco02g0040 40
4 28173770 28178840 - CcPI632755_04g012860.1 Cco04g1286 1286
4 28181001 28184714 + CcPI632755_04g012870.1 Cco04g1287 1287
4 28186109 28189463 - CcPI632755_04g012880.1 Cco04g1288 1288
4 31726236 31731748 - CePI673135_04g012180.1 Cec04g1218 1218
4 31733727 31737519 + CePI673135_04g012190.1 Cec04g1219 1219
4 31738929 31742284 - CePI673135_04g012200.1 Cec04g1220 1220
2 7304866 7307605 + Chy2G033290.1 Chy02g01062 1062
2 7308817 7312097 - Chy2G033300.1 Chy02g01063 1063
2 7314039 7318695 + Chy2G033310.1 Chy02g01064 1064
1 28035842 28040897 - ClG42_01g0159900.10 Clacu01g1599 1599
1 28043010 28046754 + ClG42_01g0160000.10 Clacu01g1600 1600
1 28048138 28051490 - ClG42_01g0160100.10 Clacu01g1601 1601
2 492960 495156 + ClG42_02g0004600.10 Clacu02g0046 46
1 29556298 29562423 - ClCG01G015340.2 Cla01g01506 1506
1 29564196 29568363 + ClCG01G015350.1 Cla01g01507 1507
1 29569539 29572891 - ClCG01G015360.2 Cla01g01508 1508
2 485076 487461 + ClCG02G000420.2 Cla02g00044 44
3 7529964 7533137 + CmaCh03G011020.1 Cma03g01102 1102
3 7532983 7536996 - CmaCh03G011030.1 Cma03g01103 1103
3 7537313 7542950 + CmaCh03G011040.1 Cma03g01104 1104
20 7858032 7868023 + CmaCh20G010530.1 Cma20g01053 1053
8 7214236 7217169 + MELO3C008062.2.1 Cme08g01092 1092
8 7217886 7222020 - MELO3C008063.2.1 Cme08g01093 1093
8 7223224 7232583 + MELO3C008064.2.1 Cme08g01094 1094
11 399325 401488 + MELO3C023230.2.1 Cme11g00046 46
8 18305816 18309250 - PI0028797.1 Cmetu08g0340 340
8 18301283 18304924 + PI0023101.1 Cmetu08g0533 533
8 18275258 18275785 - PI0026855.1 Cmetu08g1459 1459
11 30629179 30631965 - PI0028338.2 Cmetu11g1623 1623
2 3992512 3995091 - CmoCh02G006430.1 Cmo02g00643 643
3 8109826 8113244 + CmoCh03G010850.1 Cmo03g01085 1085
3 8113201 8117140 - CmoCh03G010860.1 Cmo03g01086 1086
3 8117733 8122863 + CmoCh03G010870.1 Cmo03g01087 1087
20 9767041 9770956 + CmoCh20G010590.1 Cmo20g01059 1059
1 28384176 28389231 - CmPI595203_01g014870.1 Cmu01g1487 1487
1 28391345 28395089 + CmPI595203_01g014880.1 Cmu01g1488 1488
1 28396487 28399839 - CmPI595203_01g014890.1 Cmu01g1489 1489
2 492250 494442 + CmPI595203_02g000460.1 Cmu02g0046 46
6 10144131 10147513 + Conep06aG0131700.1 Cone6ag1269 1269
6 10147510 10150823 - Conep06aG0131800.1 Cone6ag1270 1270
6 10152369 10155279 + Conep06aG0131900.1 Cone6ag1271 1271
10 1920825 1926660 - Cp4.1LG10g03550.1 Cpe10g00327 327
10 1927179 1931638 + Cp4.1LG10g03630.1 Cpe10g00328 328
10 1930773 1934303 - Cp4.1LG10g03580.1 Cpe10g00329 329
16 1768499 1772868 - Cp4.1LG16g00960.1 Cpe16g00093 93
2 1016539 1018920 + CrPI670011_02g003850.1 Cre02g0385 385
4 30252862 30256635 + CrPI670011_04g011670.1 Cre04g1167 1167
4 30258086 30261427 - CrPI670011_04g011680.1 Cre04g1168 1168
6 24179546 24185907 - CsaV3_6G041560.1 Csa06g02770 2770
6 24186533 24191116 + CsaV3_6G041570.1 Csa06g02771 2771
6 24191401 24194819 - CsaV3_6G041580.1 Csa06g02772 2772
4 65926070 65933009 - Hsped.04g11020.1 Hepe04g1102 1102
4 65943200 65946999 + Hsped.04g11040.1 Hepe04g1104 1104
4 65948776 65952684 - Hsped.04g11050.1 Hepe04g1105 1105
8 13060032 13063290 + Hsped.08g12300.1 Hepe08g1230 1230
1 9748205 9753880 + Lsi01G011600.1 Lsi01g01160 1160
1 9754300 9759972 - Lsi01G011610.1 Lsi01g01161 1161
1 9761848 9769022 + Lsi01G011620.1 Lsi01g01162 1162
10 10272552 10275972 - Lsi10G007440.1 Lsi10g00744 744
5 46112890 46115494 + Sed0023825.2 Sed05g3849 3849
10 9884339 9888927 + Sed0005361.1 Sed10g1074 1074
11 27723512 27727131 + Sed0017478.1 Sed11g1186 1186
14 2601502 2606207 - Sed0025264.1 Sed14g0236 236
3 69433545 69441124 - Tan0019768.1 Tan03g1296 1296
3 69465071 69469015 + Tan0010546.1 Tan03g1297 1297
3 69470511 69474195 - Tan0015041.1 Tan03g1298 1298
7 14120509 14124242 + Tan0017554.1 Tan07g0845 845
4 22980322 22981237 + Vvi4g1312 Vvi4g1312 1312
4 22994814 22997726 - Vvi4g1313 Vvi4g1313 1313
4 23005417 23029795 + Vvi4g1314 Vvi4g1314 1314
4 23029802 23039786 + Vvi4g1315 Vvi4g1315 1315
4 23045581 23049328 - Vvi4g1316 Vvi4g1316 1316
4 23068713 23069602 - Vvi4g1317 Vvi4g1317 1317
4 23072107 23108432 - Vvi4g1318 Vvi4g1318 1318
4 23110637 23112150 - Vvi4g1319 Vvi4g1319 1319
4 23134465 23135818 - Vvi4g1320 Vvi4g1320 1320
4 23141978 23143556 + Vvi4g1321 Vvi4g1321 1321
       

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