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
Vvi17g496 . . . . . . . Bma12g01007 . . . . Car10g00168 . . . . . . . . . . . . . . . . . . . . Cone13ag0088 Cone19ag0091 . . . . . Blo15g00305 . . . . . . Sed08g2640 Cmo10g00197 . . . . . . . Bhi08g01181 Tan05g2690 Cmetu03g1526 . Hepe07g1730 . . . . . . . . . . . . .
Vvi17g497 . . Bda06g00555 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo15g00306 . . Bpe07g00796 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g498 Blo04g00757 . . . . . . . Cmo13g01186 Cmo18g00099 . . . . . Cpe20g00204 . . . . . . . . . . . . . . . . Cone16ag0146 . . Lsi02g00317 Csa01g00794 Chy12g01322 Cme12g01747 . . . . . . Bma03g00812 . Sed08g2571 . . Cma13g01131 Cma18g00129 Car13g00964 Car18g00120 Cpe09g01064 . Bhi08g01419 Tan05g2078 Cmetu12g1270 Lac10g0376 Hepe07g2280 . . Cla01g01421 Cam01g1488 Cec01g1527 Cco01g1574 Clacu01g1512 Cmu01g1404 . . . . .
Vvi17g499 Blo04g00758 Blo16g00197 . . . Bpe13g00275 . . Cmo13g00956 Cmo18g00098 . . . . . Cpe20g00203 . . . . . . . . . . . . . . . . Cone16ag0147 . Cone19ag0090 Lsi02g00316 Csa01g00793 Chy12g01323 Cme12g01748 . . . Bda14g00838 . Bpe15g00614 Bma03g00813 . . . . Cma13g00928 Cma18g00128 Car13g00767 Car18g00118 Cpe09g01065 . Bhi08g01418 Tan05g2080 . Lac10g0375 . . . Cla01g01422 Cam01g1489 Cec04g1119 Cco01g1575 Clacu01g1513 Cmu01g1405 Cre01g1323 . . . .
Vvi17g500 . . . . . . . . . . . Cma11g00164 . Car11g00136 Sed14g1540 . Cpe04g01516 Bhi02g00348 Tan09g2161 Cmetu04g2777 . Hepe09g0138 . . . . . . . . . . . Cone13ag0087 Cone19ag0089 . . . . . . . . . . . . . . Cmo11g00146 . . . . . . . . . . . . . . . . . . . . Lsi06g01486 Csa01g00214 Chy02g02518 Cme02g01905
Vvi17g501 . Blo16g00196 . . . Bpe13g00276 Bma06g00185 . Cmo13g00957 . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00315 Csa01g00792 Chy12g01324 Cme12g01749 . . Bda11g01687 . . . . . Sed01g1833 . . Cma13g00929 . Car13g00768 . . . Bhi08g01416 Tan05g2082 Cmetu12g1516 Lac10g0373 Hepe07g2282 . . Cla01g01423 Cam01g1490 Cec01g1531 Cco01g1576 Clacu01g1514 Cmu01g1406 Cre01g1324 . . . .
Vvi17g502 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g503 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0088 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g504 . . Bda06g00554 Bda15g00593 Bpe12g00557 . . Bma12g01006 . . . Cma11g00163 . Car11g00137 Sed08g1721 . Cpe04g01515 Bhi02g00346 Tan09g2160 Cmetu03g0832 . Hepe09g0137 . . Cla06g01607 Cam06g1781 Cec06g1832 Cco06g1841 Clacu06g1743 Cmu06g1688 Cre06g2504 . . . . . . . . Blo13g00022 . . . Bpe07g00795 . . Bma08g00211 . . Cmo11g00147 . . . . . . . . . . . . . . . . . . . . Lsi06g01485 . Chy02g02517 Cme02g01904
Vvi17g505 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7816288 7817850 - Bda023814.1 Bda06g00554 554
6 7821760 7822530 - Bda023815.1 Bda06g00555 555
11 51020324 51020671 - Bda008584.1 Bda11g01687 1687
14 6445781 6452386 - Bda027612.1 Bda14g00838 838
15 9129924 9131225 + Bda012436.1 Bda15g00593 593
2 6738137 6740990 - XM_039023715.1 Bhi02g00346 346
2 6780534 6786551 - XM_039022462.1 Bhi02g00348 348
8 37024081 37025589 + XM_039039469.1 Bhi08g01181 1181
8 41895707 41897213 - XM_039039737.1 Bhi08g01416 1416
8 41915467 41917714 + XM_039038970.1 Bhi08g01418 1418
8 41954273 41957922 - XM_039038710.1 Bhi08g01419 1419
4 7165929 7168534 + BLOR13669 Blo04g00757 757
4 7188204 7194757 - BLOR13670 Blo04g00758 758
13 335697 345413 - BLOR05303 Blo13g00022 22
15 3434098 3434868 - BLOR06699 Blo15g00305 305
15 3441734 3442504 - BLOR06700 Blo15g00306 306
16 4375135 4375941 + BLOR07444 Blo16g00196 196
16 4403153 4404452 + BLOR07445 Blo16g00197 197
3 7543634 7545755 + Bma017126.1 Bma03g00812 812
3 7546782 7547192 - Bma017127.1 Bma03g00813 813
6 2293622 2294083 + Bma022800.1 Bma06g00185 185
8 2610009 2614626 - Bma027220.1 Bma08g00211 211
12 42144177 42145739 - Bma008354.1 Bma12g01006 1006
12 42163574 42163993 - Bma008355.1 Bma12g01007 1007
7 14341969 14343510 - Bpe021640.1 Bpe07g00795 795
7 14346974 14347744 - Bpe021641.1 Bpe07g00796 796
12 11412724 11414027 - Bpe005821.1 Bpe12g00557 557
13 10675184 10676402 - Bpe006400.1 Bpe13g00275 275
13 10679250 10680052 - Bpe006401.1 Bpe13g00276 276
15 17020322 17021506 + Bpe001547.1 Bpe15g00614 614
1 28432848 28435130 + CaPI482276_01g014880.1 Cam01g1488 1488
1 28446946 28448523 - CaPI482276_01g014890.1 Cam01g1489 1489
1 28456470 28458159 + CaPI482276_01g014900.1 Cam01g1490 1490
6 28972161 28974115 - CaPI482276_06g017810.1 Cam06g1781 1781
10 813967 814758 + Carg10400-RA Car10g00168 168
11 770168 773302 + Carg18173-RA Car11g00136 136
11 776604 777984 + Carg18174-RA Car11g00137 137
13 8605745 8607879 - Carg07717-RA Car13g00767 767
13 8609947 8611297 + Carg07718-RA Car13g00768 768
13 9692782 9694000 + Carg04707-RA Car13g00964 964
18 635442 637417 + Carg06683-RA Car18g00118 118
18 640184 641092 - Carg06685-RA Car18g00120 120
1 28448949 28451285 + CcPI632755_01g015740.1 Cco01g1574 1574
1 28463235 28464811 - CcPI632755_01g015750.1 Cco01g1575 1575
1 28473475 28475201 + CcPI632755_01g015760.1 Cco01g1576 1576
6 28680880 28682841 - CcPI632755_06g018410.1 Cco06g1841 1841
1 29868718 29871471 + CePI673135_01g015270.1 Cec01g1527 1527
1 29901746 29902450 + CePI673135_01g015310.1 Cec01g1531 1531
4 30730177 30732501 - CePI673135_04g011190.1 Cec04g1119 1119
6 31742503 31744398 - CePI673135_06g018320.1 Cec06g1832 1832
2 28555292 28557109 - Chy2G047840.1 Chy02g02517 2517
2 28560519 28564352 - Chy2G047850.1 Chy02g02518 2518
12 17579908 17581092 + Chy12G219220.1 Chy12g01322 1322
12 17588638 17590255 - Chy12G219230.1 Chy12g01323 1323
12 17598272 17598980 + Chy12G219240.1 Chy12g01324 1324
1 27214623 27216809 + ClG42_01g0151200.10 Clacu01g1512 1512
1 27228531 27230108 - ClG42_01g0151300.10 Clacu01g1513 1513
1 27238230 27239982 + ClG42_01g0151400.10 Clacu01g1514 1514
6 28026721 28028675 - ClG42_06g0174300.10 Clacu06g1743 1743
1 28705428 28708171 + ClCG01G014370.1 Cla01g01421 1421
1 28719454 28721638 - ClCG01G014380.1 Cla01g01422 1422
1 28729330 28731017 + ClCG01G014390.2 Cla01g01423 1423
6 29591022 29594154 - ClCG06G016370.1 Cla06g01607 1607
11 841315 843301 - CmaCh11G001630.1 Cma11g00163 163
11 846414 850949 - CmaCh11G001640.1 Cma11g00164 164
13 7361934 7364250 - CmaCh13G009280.1 Cma13g00928 928
13 7366535 7368551 + CmaCh13G009290.1 Cma13g00929 929
13 8382898 8384826 + CmaCh13G011310.1 Cma13g01131 1131
18 627359 629878 + CmaCh18G001280.1 Cma18g00128 128
18 630766 634226 - CmaCh18G001290.1 Cma18g00129 129
2 25491639 25494714 - MELO3C017155.2.1 Cme02g01904 1904
2 25497088 25500973 - MELO3C017154.2.1 Cme02g01905 1905
12 24180988 24184177 + MELO3C002210.2.1 Cme12g01747 1747
12 24189271 24191582 - MELO3C002209.2.1 Cme12g01748 1748
12 24197636 24198805 + MELO3C002208.2.1 Cme12g01749 1749
3 6835114 6836906 - PI0026314.1 Cmetu03g0832 832
3 250974 252957 + PI0014364.1 Cmetu03g1526 1526
4 1485257 1487480 - PI0025778.1 Cmetu04g2777 2777
12 2111334 2114729 - PI0024977.1 Cmetu12g1270 1270
12 2093629 2095371 - PI0013086.1 Cmetu12g1516 1516
10 882948 885068 + CmoCh10G001970.1 Cmo10g00197 197
11 735771 740157 + CmoCh11G001460.1 Cmo11g00146 146
11 743051 744849 + CmoCh11G001470.1 Cmo11g00147 147
13 8306478 8308785 - CmoCh13G009560.1 Cmo13g00956 956
13 8310841 8312900 + CmoCh13G009570.1 Cmo13g00957 957
13 9410118 9416297 + CmoCh13G011860.1 Cmo13g01186 1186
18 676252 678940 + CmoCh18G000980.1 Cmo18g00098 98
18 679234 681845 - CmoCh18G000990.1 Cmo18g00099 99
1 27557440 27560571 + CmPI595203_01g014040.1 Cmu01g1404 1404
1 27572278 27573855 - CmPI595203_01g014050.1 Cmu01g1405 1405
1 27581976 27583728 + CmPI595203_01g014060.1 Cmu01g1406 1406
6 27935088 27937043 - CmPI595203_06g016880.1 Cmu06g1688 1688
13 547390 549977 - Conep13aG0009200.1 Cone13ag0087 87
13 554080 555404 - Conep13aG0009300.1 Cone13ag0088 88
16 845751 847955 + Conep16aG0014900.1 Cone16ag0146 146
16 853202 854927 - Conep16aG0015000.1 Cone16ag0147 147
19 509911 512090 - Conep19aG0009400.1 Cone19ag0088 88
19 512410 516312 - Conep19aG0009500.1 Cone19ag0089 89
19 519877 521883 + Conep19aG0009600.1 Cone19ag0090 90
19 524594 525625 - Conep19aG0009700.1 Cone19ag0091 91
4 11939065 11941532 - Cp4.1LG04g15110.1 Cpe04g01515 1515
4 11944255 11949383 - Cp4.1LG04g15130.1 Cpe04g01516 1516
9 9271531 9274207 + Cp4.1LG09g10620.1 Cpe09g01064 1064
9 9274308 9278156 - Cp4.1LG09g10710.1 Cpe09g01065 1065
20 1171178 1173838 + Cp4.1LG20g01890.1 Cpe20g00203 203
20 1176145 1178800 - Cp4.1LG20g01980.1 Cpe20g00204 204
1 26449073 26450652 - CrPI670011_01g013230.1 Cre01g1323 1323
1 26458408 26460181 + CrPI670011_01g013240.1 Cre01g1324 1324
6 32749789 32751746 - CrPI670011_06g025040.1 Cre06g2504 2504
1 1386425 1390336 + CsaV3_1G002140.1 Csa01g00214 214
1 5015476 5016513 - CsaV3_1G007920.1 Csa01g00792 792
1 5021575 5024813 + CsaV3_1G007930.1 Csa01g00793 793
1 5027738 5031315 - CsaV3_1G007940.1 Csa01g00794 794
7 59362089 59363110 - Hsped.07g17300.1 Hepe07g1730 1730
7 67124002 67126135 + Hsped.07g22800.1 Hepe07g2280 2280
7 67147312 67148188 - Hsped.07g22820.1 Hepe07g2282 2282
9 1090050 1093467 - Hsped.09g01370.1 Hepe09g0137 137
9 1096357 1099839 - Hsped.09g01380.1 Hepe09g0138 138
10 2917249 2917934 + Lag0024418.1 Lac10g0373 373
10 2929338 2930986 + Lag0024420.1 Lac10g0375 375
10 2937281 2940504 - Lag0024421.1 Lac10g0376 376
2 2702993 2704604 - Lsi02G003150.1 Lsi02g00315 315
2 2714297 2716383 + Lsi02G003160.1 Lsi02g00316 316
2 2726016 2727396 - Lsi02G003170.1 Lsi02g00317 317
6 25327659 25330615 - Lsi06G014850.1 Lsi06g01485 1485
6 25335335 25339577 - Lsi06G014860.1 Lsi06g01486 1486
1 13482683 13483890 + Sed0016194.1 Sed01g1833 1833
8 32222394 32228124 - Sed0011610.1 Sed08g1721 1721
8 38225404 38228246 + Sed0020047.1 Sed08g2571 2571
8 38574720 38576279 - Sed0012196.1 Sed08g2640 2640
14 23609642 23612488 + Sed0020950.1 Sed14g1540 1540
5 71207974 71210634 + Tan0010954.1 Tan05g2078 2078
5 71222985 71225248 - Tan0020504.2 Tan05g2080 2080
5 71252417 71254034 - Tan0002124.1 Tan05g2082 2082
5 78622391 78623583 + Tan0022524.1 Tan05g2690 2690
9 71701900 71703764 - Tan0013766.1 Tan09g2160 2160
9 71709485 71713524 - Tan0011441.1 Tan09g2161 2161
17 6090060 6125149 + Vvi17g496 Vvi17g496 496
17 6125833 6126856 + Vvi17g497 Vvi17g497 497
17 6127855 6130717 + Vvi17g498 Vvi17g498 498
17 6134095 6136429 - Vvi17g499 Vvi17g499 499
17 6144990 6148040 + Vvi17g500 Vvi17g500 500
17 6148095 6149208 - Vvi17g501 Vvi17g501 501
17 6151294 6153981 + Vvi17g502 Vvi17g502 502
17 6154648 6156718 + Vvi17g503 Vvi17g503 503
17 6161760 6166581 + Vvi17g504 Vvi17g504 504
17 6167655 6170182 - Vvi17g505 Vvi17g505 505
       

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