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
Vvi4g1292 . . . . . . . Bma15g00790 . . Cma03g01092 . Car03g00985 . . . Cpe10g00338 Bhi03g01352 . . . . . . Cla01g01517 Cam01g1587 . Cco04g1301 Clacu01g1612 Cmu01g1498 Cre04g1176 . . Cone6ag1286 . Lsi01g01148 . . Cme08g01082 . Blo06g00196 . . Bpe10g00259 . . . . Cmo03g01078 . . . . . . . . . . . . . . . . . . . . . . Csa06g02783 Chy02g01052 .
Vvi4g1293 . . . Bda10g00396 . . . Bma15g00788 . . . . . Car07g00787 . Cpe19g00529 . Bhi03g01351 . . . . . . Cla01g01516 Cam01g1586 Cec04g1229 Cco04g1300 Clacu01g1611 Cmu01g1497 Cre04g1175 . . Cone6ag1285 . Lsi01g01149 . . Cme08g01083 . Blo06g00195 . . Bpe10g00260 . . . . . Cmo07g00824 . . . . . . . . . . . . . . . . . . . . . Csa06g02782 Chy02g01053 .
Vvi4g1294 Blo04g00964 . . . Bpe15g00405 . . . . . Cma03g01093 Cma07g00801 Car03g00986 Car07g00788 Sed10g0504 Cpe19g00528 Cpe10g00337 Bhi03g01350 Tan03g1309 Cmetu08g0010 . Hepe04g1112 . . Cla01g01515 Cam01g1584 Cec04g1227 Cco04g1298 Clacu01g1609 Cmu01g1496 Cre04g1174 . . Cone6ag1283 . Lsi01g01150 . . Cme08g01084 . . . Bda14g01051 . . Bma03g01028 . . Cmo03g01079 Cmo07g00825 . . . . . . . . . . . . . . . . . . . . . Csa06g02780 Chy02g01054 .
Vvi4g1295 . . Bda04g00371 Bda10g00398 . . . Bma15g00786 . . Cma03g01095 Cma07g00803 . Car07g00789 Sed14g1175 Cpe19g00527 Cpe10g00336 Bhi03g01349 Tan03g1307 Cmetu01g1160 . . . . Cla01g01514 Cam01g1583 Cec04g1226 Cco04g1296 Clacu01g1608 Cmu01g1495 . . . . . Lsi01g01151 . . Cme08g01086 . Blo06g00192 . . . Bpe06g00294 . . . Cmo03g01080 Cmo07g00827 . . . . . . . . . . . . . . . . . . . . . Csa06g02778 Chy02g01056 .
Vvi4g1296 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1297 Blo04g00957 Blo16g00538 . . Bpe15g00410 . . . . . Cma03g01096 Cma07g00804 Car03g00987 Car07g00790 Sed14g0231 Cpe19g00526 . Bhi03g01346 Tan03g1304 Cmetu08g2020 . Hepe04g1110 . . Cla01g01513 Cam01g1582 Cec04g1225 Cco04g1295 Clacu01g1607 Cmu01g1494 Cre04g1173 . . . . Lsi01g01153 . . Cme08g01087 . . Bda11g01378 Bda14g01048 . . Bma03g01023 Bma06g00499 . Cmo03g01081 Cmo07g00828 . . . . . . . . . . . . . . . . . . . . . Csa06g02777 Chy02g01058 .
Vvi4g1298 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1299 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1300 Blo04g00956 Blo16g00539 . . Bpe15g00411 Bpe13g00033 . . Cmo02g00631 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01380 Bda14g01047 . . Bma03g01022 Bma06g00497 Sed05g3867 . . . . . . Cpe05g01061 . Bhi10g01671 Tan07g0863 Cmetu11g1206 . Hepe08g1242 . . Cla02g00054 Cam02g0055 Cec02g0058 Cco02g0050 Clacu02g0055 Cmu02g0054 Cre02g0392 Lsi10g00726 . . Cme11g00057
Vvi4g1301 Blo04g00955 . Bda04g00372 Bda10g00399 . . . Bma15g00785 . . Cma03g01097 Cma07g00805 Car03g00988 Car07g00791 . Cpe19g00525 Cpe10g00335 Bhi03g01344 . . . . . . Cla01g01512 Cam01g1580 Cec04g1224 Cco04g1293 Clacu01g1606 Cmu01g1493 Cre04g1172 . . Cone6ag1281 . Lsi01g01155 . . Cme08g01088 Blo05g00537 Blo06g00191 . Bda14g01046 . Bpe06g00295 Bma03g01021 . . Cmo03g01082 Cmo07g00829 . . . . . . . . . . . . . . . . . . . . . Csa06g02776 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 50116392 50118505 + Bda019300.1 Bda04g00371 371
4 50125331 50129548 + Bda019301.1 Bda04g00372 372
10 36013053 36040170 - Bda007223.1 Bda10g00396 396
10 36052059 36053890 + Bda007225.1 Bda10g00398 398
10 36060174 36064301 + Bda007226.1 Bda10g00399 399
11 17061162 17061917 + Bda007931.1 Bda11g01378 1378
11 17064141 17078912 - Bda007933.1 Bda11g01380 1380
14 8802804 8806908 - Bda027856.1 Bda14g01046 1046
14 8814188 8829320 + Bda027857.1 Bda14g01047 1047
14 8831521 8834229 - Bda027858.1 Bda14g01048 1048
14 8965159 8976903 - Bda027865.1 Bda14g01051 1051
3 28028192 28033215 - XM_039025265.1 Bhi03g01344 1344
3 28050244 28059696 - XM_039026313.1 Bhi03g01346 1346
3 28063225 28068212 - XM_039026570.1 Bhi03g01349 1349
3 28069906 28082686 - XM_039025094.1 Bhi03g01350 1350
3 28085103 28090767 - XM_039027023.1 Bhi03g01351 1351
3 28118394 28133392 + XM_039025941.1 Bhi03g01352 1352
10 42283663 42298413 - XM_039045687.1 Bhi10g01671 1671
4 11630212 11641917 - BLOR13867 Blo04g00955 955
4 11670779 11684831 + BLOR13868 Blo04g00956 956
4 11686656 11689535 - BLOR13869 Blo04g00957 957
4 11825815 11839204 - BLOR13876 Blo04g00964 964
5 10594709 10599090 - BLOR15499 Blo05g00537 537
6 8052247 8056920 - BLOR16774 Blo06g00191 191
6 8080810 8083746 - BLOR16775 Blo06g00192 192
6 8128734 8130719 + BLOR16778 Blo06g00195 195
6 8158617 8170650 + BLOR16779 Blo06g00196 196
16 22209267 22211577 + BLOR07786 Blo16g00538 538
16 22212086 22236953 - BLOR07787 Blo16g00539 539
3 11339613 11347429 - Bma017369.3 Bma03g01021 1021
3 11365389 11379401 + Bma017370.1 Bma03g01022 1022
3 11381710 11384568 - Bma017371.1 Bma03g01023 1023
3 11521185 11524470 - Bma017379.1 Bma03g01028 1028
6 24097284 24103431 + Bma023346.1 Bma06g00497 497
6 24106201 24106950 - Bma023348.1 Bma06g00499 499
15 16763102 16767056 - Bma013864.1 Bma15g00785 785
15 16771719 16773592 - Bma013865.1 Bma15g00786 786
15 16800296 16805524 + Bma013868.2 Bma15g00788 788
15 16842626 16864449 + Bma013871.1 Bma15g00790 790
6 14068545 14070493 + Bpe019790.1 Bpe06g00294 294
6 14077626 14081840 + Bpe019791.1 Bpe06g00295 295
10 9724814 9738130 - Bpe002594.1 Bpe10g00259 259
10 9746805 9752411 - Bpe002595.1 Bpe10g00260 260
13 932030 950499 - Bpe006120.3 Bpe13g00033 33
15 15543600 15555747 + Bpe001343.1 Bpe15g00405 405
15 15603350 15604168 + Bpe001348.1 Bpe15g00410 410
15 15607964 15621770 - Bpe001349.1 Bpe15g00411 411
1 29279225 29283287 - CaPI482276_01g015800.1 Cam01g1580 1580
1 29303152 29303898 - CaPI482276_01g015820.1 Cam01g1582 1582
1 29307172 29310202 - CaPI482276_01g015830.1 Cam01g1583 1583
1 29313979 29331364 - CaPI482276_01g015840.1 Cam01g1584 1584
1 29334914 29340506 - CaPI482276_01g015860.1 Cam01g1586 1586
1 29343829 29355037 + CaPI482276_01g015870.1 Cam01g1587 1587
2 1664829 1679705 + CaPI482276_02g000550.1 Cam02g0055 55
3 7585848 7592546 - Carg10536-RA Car03g00985 985
3 7593770 7603873 + Carg10535-RA Car03g00986 986
3 7604528 7613277 + Carg10533-RA Car03g00987 987
3 7617163 7620817 + Carg10532-RA Car03g00988 988
7 4118261 4124763 + Carg05311-RA Car07g00787 787
7 4125611 4138506 + Carg05312-RA Car07g00788 788
7 4140490 4147577 + Carg05313-RA Car07g00789 789
7 4149757 4155593 + Carg05314-RA Car07g00790 790
7 4161278 4165512 + Carg05315-RA Car07g00791 791
2 532331 546957 + CcPI632755_02g000500.1 Cco02g0050 50
4 28210022 28214098 - CcPI632755_04g012930.1 Cco04g1293 1293
4 28234318 28235076 - CcPI632755_04g012950.1 Cco04g1295 1295
4 28238209 28241206 - CcPI632755_04g012960.1 Cco04g1296 1296
4 28244818 28261561 - CcPI632755_04g012980.1 Cco04g1298 1298
4 28265140 28270431 - CcPI632755_04g013000.1 Cco04g1300 1300
4 28273936 28286172 + CcPI632755_04g013010.1 Cco04g1301 1301
2 542328 554065 + CePI673135_02g000580.1 Cec02g0058 58
4 31766434 31770505 - CePI673135_04g012240.1 Cec04g1224 1224
4 31783248 31790879 - CePI673135_04g012250.1 Cec04g1225 1225
4 31794189 31797207 - CePI673135_04g012260.1 Cec04g1226 1226
4 31797455 31818517 - CePI673135_04g012270.1 Cec04g1227 1227
4 31822535 31827820 - CePI673135_04g012290.1 Cec04g1229 1229
2 7216656 7232194 - Chy2G033190.1 Chy02g01052 1052
2 7235019 7239418 + Chy2G033200.1 Chy02g01053 1053
2 7241939 7256155 + Chy2G033210.1 Chy02g01054 1054
2 7259060 7262678 + Chy2G033230.1 Chy02g01056 1056
2 7270531 7291968 + Chy2G033250.1 Chy02g01058 1058
1 28072097 28076167 - ClG42_01g0160600.10 Clacu01g1606 1606
1 28088740 28096535 - ClG42_01g0160700.10 Clacu01g1607 1607
1 28099798 28102767 - ClG42_01g0160800.10 Clacu01g1608 1608
1 28103012 28123905 - ClG42_01g0160900.10 Clacu01g1609 1609
1 28127465 28132765 - ClG42_01g0161100.10 Clacu01g1611 1611
1 28135031 28147464 + ClG42_01g0161200.10 Clacu01g1612 1612
2 557477 572344 + ClG42_02g0005500.10 Clacu02g0055 55
1 29593529 29597583 - ClCG01G015400.2 Cla01g01512 1512
1 29609962 29618081 - ClCG01G015410.1 Cla01g01513 1513
1 29622332 29626922 - ClCG01G015420.1 Cla01g01514 1514
1 29622399 29647899 - ClCG01G015430.2 Cla01g01515 1515
1 29650496 29656379 - ClCG01G015440.2 Cla01g01516 1516
1 29658376 29669587 + ClCG01G015450.2 Cla01g01517 1517
2 550464 589465 + ClCG02G000530.1 Cla02g00054 54
3 7478412 7490888 - CmaCh03G010920.1 Cma03g01092 1092
3 7492419 7502387 + CmaCh03G010930.1 Cma03g01093 1093
3 7504442 7507854 + CmaCh03G010950.1 Cma03g01095 1095
3 7508936 7515895 + CmaCh03G010960.1 Cma03g01096 1096
3 7515915 7520023 + CmaCh03G010970.1 Cma03g01097 1097
7 3652372 3665091 + CmaCh07G008010.1 Cma07g00801 801
7 3668287 3674167 + CmaCh07G008030.1 Cma07g00803 803
7 3676256 3681593 + CmaCh07G008040.1 Cma07g00804 804
7 3686636 3691680 + CmaCh07G008050.1 Cma07g00805 805
8 7117244 7140986 - MELO3C008051.2.1 Cme08g01082 1082
8 7141494 7146816 + MELO3C008053.2.1 Cme08g01083 1083
8 7149604 7165187 + MELO3C008054.2.1 Cme08g01084 1084
8 7167958 7173557 + MELO3C008056.2.1 Cme08g01086 1086
8 7175562 7185187 + MELO3C008057.2.1 Cme08g01087 1087
8 7195247 7200103 + MELO3C008058.2.1 Cme08g01088 1088
11 484415 497007 + MELO3C023241.2.1 Cme11g00057 57
1 21764558 21770051 + PI0028706.1 Cmetu01g1160 1160
8 18357537 18371468 - PI0016000.1 Cmetu08g0010 10
8 18339683 18347403 - PI0027847.1 Cmetu08g2020 2020
11 30514962 30528321 - PI0024794.1 Cmetu11g1206 1206
2 3918920 3934130 - CmoCh02G006310.1 Cmo02g00631 631
3 8060495 8071475 - CmoCh03G010780.1 Cmo03g01078 1078
3 8072740 8082677 + CmoCh03G010790.1 Cmo03g01079 1079
3 8083490 8088853 + CmoCh03G010800.1 Cmo03g01080 1080
3 8088858 8092307 + CmoCh03G010810.1 Cmo03g01081 1081
3 8095928 8100823 + CmoCh03G010820.1 Cmo03g01082 1082
7 3839303 3845564 + CmoCh07G008240.1 Cmo07g00824 824
7 3846609 3859563 + CmoCh07G008250.1 Cmo07g00825 825
7 3862655 3869248 + CmoCh07G008270.1 Cmo07g00827 827
7 3870628 3877261 + CmoCh07G008280.1 Cmo07g00828 828
7 3882446 3886877 + CmoCh07G008290.1 Cmo07g00829 829
1 28420481 28424551 - CmPI595203_01g014930.1 Cmu01g1493 1493
1 28437141 28444937 - CmPI595203_01g014940.1 Cmu01g1494 1494
1 28448187 28451156 - CmPI595203_01g014950.1 Cmu01g1495 1495
1 28451404 28472308 - CmPI595203_01g014960.1 Cmu01g1496 1496
1 28475860 28481160 - CmPI595203_01g014970.1 Cmu01g1497 1497
1 28483449 28495911 + CmPI595203_01g014980.1 Cmu01g1498 1498
2 556757 571624 + CmPI595203_02g000540.1 Cmu02g0054 54
6 10240385 10252386 - Conep06aG0132900.1 Cone6ag1281 1281
6 10262712 10273563 - Conep06aG0133100.1 Cone6ag1283 1283
6 10277224 10282049 - Conep06aG0133300.1 Cone6ag1285 1285
6 10288106 10301364 + Conep06aG0133400.1 Cone6ag1286 1286
5 7017017 7032450 + Cp4.1LG05g10600.1 Cpe05g01061 1061
10 1945120 1950066 - Cp4.1LG10g03520.1 Cpe10g00335 335
10 1953896 1962514 - Cp4.1LG10g03530.1 Cpe10g00336 336
10 1963415 1973391 - Cp4.1LG10g03540.1 Cpe10g00337 337
10 1974620 1987610 + Cp4.1LG10g03500.1 Cpe10g00338 338
19 4459172 4463954 - Cp4.1LG19g12030.1 Cpe19g00525 525
19 4469018 4475508 - Cp4.1LG19g12040.1 Cpe19g00526 526
19 4477400 4484141 - Cp4.1LG19g11950.1 Cpe19g00527 527
19 4486197 4501273 - Cp4.1LG19g12060.1 Cpe19g00528 528
19 4502457 4508808 - Cp4.1LG19g12020.1 Cpe19g00529 529
2 1084419 1099248 + CrPI670011_02g003920.1 Cre02g0392 392
4 30282237 30286259 - CrPI670011_04g011720.1 Cre04g1172 1172
4 30299155 30307128 - CrPI670011_04g011730.1 Cre04g1173 1173
4 30310436 30334751 - CrPI670011_04g011740.1 Cre04g1174 1174
4 30338335 30343635 - CrPI670011_04g011750.1 Cre04g1175 1175
4 30347040 30359522 + CrPI670011_04g011760.1 Cre04g1176 1176
6 24207515 24211470 - CsaV3_6G041620.1 Csa06g02776 2776
6 24219840 24229448 - CsaV3_6G041630.1 Csa06g02777 2777
6 24230536 24236572 - CsaV3_6G041640.1 Csa06g02778 2778
6 24237131 24252769 - CsaV3_6G041660.1 Csa06g02780 2780
6 24254374 24259375 - CsaV3_6G041680.1 Csa06g02782 2782
6 24261623 24280689 + CsaV3_6G041690.1 Csa06g02783 2783
4 65990434 65997190 - Hsped.04g11100.1 Hepe04g1110 1110
4 66008913 66038664 - Hsped.04g11120.1 Hepe04g1112 1112
8 13206498 13221981 + Hsped.08g12420.1 Hepe08g1242 1242
1 9655549 9665416 - Lsi01G011480.1 Lsi01g01148 1148
1 9668377 9674052 + Lsi01G011490.1 Lsi01g01149 1149
1 9676393 9692447 + Lsi01G011500.1 Lsi01g01150 1150
1 9694858 9699356 + Lsi01G011510.1 Lsi01g01151 1151
1 9705785 9706531 + Lsi01G011530.1 Lsi01g01153 1153
1 9726565 9731215 + Lsi01G011550.1 Lsi01g01155 1155
10 10105574 10109247 - Lsi10G007260.1 Lsi10g00726 726
5 46193696 46208136 + Sed0007581.1 Sed05g3867 3867
10 3302307 3315048 + Sed0015970.2 Sed10g0504 504
14 2539929 2555160 + Sed0015585.1 Sed14g0231 231
14 21101316 21103605 - Sed0000895.1 Sed14g1175 1175
3 69520073 69526597 - Tan0015490.1 Tan03g1304 1304
3 69529134 69536661 - Tan0017867.3 Tan03g1307 1307
3 69539414 69569211 - Tan0018046.2 Tan03g1309 1309
7 14676671 14689041 + Tan0017073.1 Tan07g0863 863
4 22563527 22600751 - Vvi4g1292 Vvi4g1292 1292
4 22604956 22630739 - Vvi4g1293 Vvi4g1293 1293
4 22650479 22698343 + Vvi4g1294 Vvi4g1294 1294
4 22706306 22713079 + Vvi4g1295 Vvi4g1295 1295
4 22723682 22725448 - Vvi4g1296 Vvi4g1296 1296
4 22732853 22740064 + Vvi4g1297 Vvi4g1297 1297
4 22756098 22766447 + Vvi4g1298 Vvi4g1298 1298
4 22767812 22772249 - Vvi4g1299 Vvi4g1299 1299
4 22776366 22794921 - Vvi4g1300 Vvi4g1300 1300
4 22814275 22820209 + Vvi4g1301 Vvi4g1301 1301
       

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