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
Vvi4g1262 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1263 . Blo16g00531 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1264 . . Bda04g00335 Bda10g00352 . . . Bma15g00813 . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1296 . . . . . Blo05g00557 . . . . Bpe06g00276 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1265 Blo04g00969 . . . Bpe15g00397 . . . . . Cma03g01081 . Car03g00971 . Sed10g0490 . Cpe10g00348 Bhi03g01379 Tan03g1329 Cmetu08g0165 . Hepe04g1126 . . Cla01g01530 Cam01g1598 Cec04g1243 Cco04g1312 Clacu01g1623 Cmu01g1509 Cre04g1188 . . . . Lsi01g01135 . . Cme08g01069 . . . Bda14g01059 . . Bma03g01034 . . Cmo03g01070 . . . . . . . . . . . . . . . . . . . . . . Csa06g02797 Chy02g01038 .
Vvi4g1266 . . Bda04g00334 . . . . . Cmo02g00625 . Cma03g01083 Cma07g00789 Car03g00973 Car07g00775 Sed10g0492 Cpe19g00539 Cpe10g00346 Bhi03g01378 Tan03g1327 Cmetu08g0065 . Hepe04g1125 . . Cla01g01528 Cam01g1597 Cec04g1242 Cco04g1311 Clacu01g1622 Cmu01g1508 Cre04g1187 . . Cone6ag1295 . Lsi01g01136 . . Cme08g01071 . . . . . Bpe06g00274 . . . . Cmo07g00812 . . . . Cpe05g01067 . Bhi10g02332 Tan07g0873 Cmetu11g1820 . Hepe08g1253 . . Cla02g00066 Cam02g0068 Cec02g0070 Cco02g0063 Clacu02g0067 Cmu02g0066 Cre02g0405 Lsi10g00713 Csa06g02795 Chy02g01040 Cme11g00070
Vvi4g1267 Blo04g00968 . . Bda10g00359 Bpe15g00398 . . . . . Cma03g01085 Cma07g00791 Car03g00975 Car07g00777 . . . Bhi03g01375 . . . Hepe04g1122 . . Cla01g01526 Cam01g1596 Cec04g1240 Cco04g1310 Clacu01g1620 Cmu01g1506 Cre04g1185 . . Cone6ag1293 . Lsi01g01138 . . Cme08g01072 . . . Bda14g01058 . Bpe06g00273 Bma03g01033 Bma06g00513 . Cmo03g01072 Cmo07g00814 . . . . . . . . . . . . . . . . . . . . . Csa06g02793 Chy02g01042 .
Vvi4g1268 . . . . . Bpe13g00023 . . . . . Cma07g00792 Car03g00976 Car07g00778 Sed10g0495 Cpe19g00537 Cpe10g00345 Bhi03g01373 Tan03g1322 Cmetu08g1743 . Hepe04g1121 . . Cla01g01525 Cam01g1595 Cec04g1239 Cco04g1309 Clacu01g1619 Cmu01g1505 Cre04g1184 . . Cone6ag1292 . Lsi01g01139 . . Cme08g01074 . . Bda11g01366 . . . . Bma06g00506 . . Cmo07g00815 . . . . . . . . . . . . . . . . . . . . . Csa06g02792 Chy02g01043 .
Vvi4g1269 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1270 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1271 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 48223308 48224571 - Bda019231.1 Bda04g00334 334
4 48341510 48344510 - Bda019232.1 Bda04g00335 335
10 34257425 34259249 + Bda007154.1 Bda10g00352 352
10 34511239 34514310 + Bda007163.1 Bda10g00359 359
11 16318360 16322503 - Bda007911.3 Bda11g01366 1366
14 9062107 9064244 - Bda027872.1 Bda14g01058 1058
14 9101274 9118168 - Bda027874.1 Bda14g01059 1059
3 28386901 28390555 - XM_039024938.1 Bhi03g01373 1373
3 28391690 28397724 - XM_039026118.1 Bhi03g01375 1375
3 28503564 28505117 - XM_039027814.1 Bhi03g01378 1378
3 28535136 28555132 - XM_039026530.1 Bhi03g01379 1379
10 60735420 60737157 + XM_039045810.1 Bhi10g02332 2332
4 11990343 11993115 - BLOR13880 Blo04g00968 968
4 12051244 12073933 - BLOR13881 Blo04g00969 969
5 11962746 11965708 + BLOR15519 Blo05g00557 557
16 21874332 21876677 + BLOR07779 Blo16g00531 531
3 11964516 11967271 - Bma017388.2 Bma03g01033 1033
3 12032447 12052477 - Bma017391.1 Bma03g01034 1034
6 25505441 25509573 + Bma023366.1 Bma06g00506 506
6 26694669 26696649 - Bma023386.1 Bma06g00513 513
15 19480611 19482988 + Bma013924.1 Bma15g00813 813
6 13662358 13665370 - Bpe019768.1 Bpe06g00273 273
6 13678948 13680141 - Bpe019769.2 Bpe06g00274 274
6 13710977 13713938 - Bpe019771.1 Bpe06g00276 276
13 538922 542978 - Bpe006109.1 Bpe13g00023 23
15 15474664 15491541 + Bpe001334.1 Bpe15g00397 397
15 15503646 15506225 + Bpe001335.1 Bpe15g00398 398
1 29436880 29440119 - CaPI482276_01g015950.1 Cam01g1595 1595
1 29445401 29448367 - CaPI482276_01g015960.1 Cam01g1596 1596
1 29485252 29486478 - CaPI482276_01g015970.1 Cam01g1597 1597
1 29515683 29528862 - CaPI482276_01g015980.1 Cam01g1598 1598
2 1772781 1774016 + CaPI482276_02g000680.1 Cam02g0068 68
3 7506016 7520105 + Carg10550-RA Car03g00971 971
3 7531698 7532936 + Carg10548-RA Car03g00973 973
3 7543895 7547031 + Carg10546-RA Car03g00975 975
3 7547128 7550182 + Carg10545-RA Car03g00976 976
7 4053735 4054973 + Carg05297-RA Car07g00775 775
7 4068641 4072502 + Carg05299-RA Car07g00777 777
7 4072649 4076746 + Carg05300-RA Car07g00778 778
2 644858 646093 + CcPI632755_02g000630.1 Cco02g0063 63
4 28366669 28369903 - CcPI632755_04g013090.1 Cco04g1309 1309
4 28376148 28379102 - CcPI632755_04g013100.1 Cco04g1310 1310
4 28423546 28424772 - CcPI632755_04g013110.1 Cco04g1311 1311
4 28454414 28467137 - CcPI632755_04g013120.1 Cco04g1312 1312
2 644687 645922 + CePI673135_02g000700.1 Cec02g0070 70
4 31928151 31931402 - CePI673135_04g012390.1 Cec04g1239 1239
4 31937578 31940544 - CePI673135_04g012400.1 Cec04g1240 1240
4 31977467 31978693 - CePI673135_04g012420.1 Cec04g1242 1242
4 32007678 32020723 - CePI673135_04g012430.1 Cec04g1243 1243
2 7079790 7092923 + Chy2G033050.1 Chy02g01038 1038
2 7116973 7118199 + Chy2G033070.1 Chy02g01040 1040
2 7144278 7147266 + Chy2G033090.1 Chy02g01042 1042
2 7148999 7152243 + Chy2G033100.1 Chy02g01043 1043
1 28221376 28232235 - ClG42_01g0161900.10 Clacu01g1619 1619
1 28238419 28241384 - ClG42_01g0162000.10 Clacu01g1620 1620
1 28278215 28279441 - ClG42_01g0162200.10 Clacu01g1622 1622
1 28308517 28323477 - ClG42_01g0162300.10 Clacu01g1623 1623
2 664261 665496 + ClG42_02g0006700.10 Clacu02g0067 67
1 29764028 29767278 - ClCG01G015540.2 Cla01g01525 1525
1 29773160 29778851 - ClCG01G015550.1 Cla01g01526 1526
1 29819686 29820912 - ClCG01G015580.1 Cla01g01528 1528
1 29853147 29866446 - ClCG01G015590.1 Cla01g01530 1530
2 659105 660809 + ClCG02G000630.2 Cla02g00066 66
3 7399675 7414393 + CmaCh03G010810.1 Cma03g01081 1081
3 7425706 7426944 + CmaCh03G010830.1 Cma03g01083 1083
3 7437804 7440454 + CmaCh03G010850.1 Cma03g01085 1085
7 3573014 3574252 + CmaCh07G007890.1 Cma07g00789 789
7 3588454 3591990 + CmaCh07G007910.1 Cma07g00791 791
7 3592281 3597153 + CmaCh07G007920.1 Cma07g00792 792
8 6981826 6996862 + MELO3C008038.2.1 Cme08g01069 1069
8 7018231 7019690 + MELO3C008040.2.1 Cme08g01071 1071
8 7044027 7051026 + MELO3C008041.2.1 Cme08g01072 1072
8 7052972 7056722 + MELO3C008043.2.1 Cme08g01074 1074
11 576543 578232 + MELO3C023258.2.1 Cme11g00070 70
8 18497385 18499233 - PI0016064.1 Cmetu08g0065 65
8 18524408 18538327 - PI0015494.1 Cmetu08g0165 165
8 18458996 18462809 - PI0000471.1 Cmetu08g1743 1743
11 30430052 30431489 - PI0014389.1 Cmetu11g1820 1820
2 3880872 3882101 - CmoCh02G006250.1 Cmo02g00625 625
3 7977554 7993195 + CmoCh03G010700.1 Cmo03g01070 1070
3 8019754 8022749 + CmoCh03G010720.1 Cmo03g01072 1072
7 3753755 3754993 + CmoCh07G008120.1 Cmo07g00812 812
7 3770048 3773581 + CmoCh07G008140.1 Cmo07g00814 814
7 3774038 3778293 + CmoCh07G008150.1 Cmo07g00815 815
1 28569783 28580640 - CmPI595203_01g015050.1 Cmu01g1505 1505
1 28586829 28589794 - CmPI595203_01g015060.1 Cmu01g1506 1506
1 28626593 28627819 - CmPI595203_01g015080.1 Cmu01g1508 1508
1 28656889 28670069 - CmPI595203_01g015090.1 Cmu01g1509 1509
2 663475 664710 + CmPI595203_02g000660.1 Cmu02g0066 66
6 10353034 10356220 - Conep06aG0134000.1 Cone6ag1292 1292
6 10360292 10364641 - Conep06aG0134100.1 Cone6ag1293 1293
6 10383394 10384953 - Conep06aG0134300.1 Cone6ag1295 1295
6 10408117 10412073 - Conep06aG0134400.1 Cone6ag1296 1296
5 7063600 7064829 + Cp4.1LG05g10560.1 Cpe05g01067 1067
10 2018858 2027538 - Cp4.1LG10g03440.1 Cpe10g00345 345
10 2037028 2038200 - Cp4.1LG10g03430.1 Cpe10g00346 346
10 2049807 2064296 - Cp4.1LG10g03470.1 Cpe10g00348 348
19 4552220 4556698 - Cp4.1LG19g12120.1 Cpe19g00537 537
19 4573975 4575213 - Cp4.1LG19g11940.1 Cpe19g00539 539
2 1199953 1201326 + CrPI670011_02g004050.1 Cre02g0405 405
4 30441441 30444677 - CrPI670011_04g011840.1 Cre04g1184 1184
4 30453864 30456830 - CrPI670011_04g011850.1 Cre04g1185 1185
4 30496225 30497451 - CrPI670011_04g011870.1 Cre04g1187 1187
4 30525411 30541654 - CrPI670011_04g011880.1 Cre04g1188 1188
6 24339325 24343170 - CsaV3_6G041780.1 Csa06g02792 2792
6 24344313 24351470 - CsaV3_6G041790.1 Csa06g02793 2793
6 24372700 24375096 - CsaV3_6G041810.1 Csa06g02795 2795
6 24398015 24411869 - CsaV3_6G041830.1 Csa06g02797 2797
4 66127871 66134503 - Hsped.04g11210.1 Hepe04g1121 1121
4 66138952 66144327 - Hsped.04g11220.1 Hepe04g1122 1122
4 66242902 66244454 - Hsped.04g11250.1 Hepe04g1125 1125
4 66285206 66298054 - Hsped.04g11260.1 Hepe04g1126 1126
8 13367380 13368866 + Hsped.08g12530.1 Hepe08g1253 1253
1 9487940 9502162 + Lsi01G011350.1 Lsi01g01135 1135
1 9537778 9539004 + Lsi01G011360.1 Lsi01g01136 1136
1 9572277 9575564 + Lsi01G011380.1 Lsi01g01138 1138
1 9578210 9581970 + Lsi01G011390.1 Lsi01g01139 1139
10 9983755 9984972 - Lsi10G007130.1 Lsi10g00713 713
10 3139161 3150608 + Sed0011527.1 Sed10g0490 490
10 3191672 3193228 + Sed0008178.1 Sed10g0492 492
10 3253301 3258287 + Sed0001106.1 Sed10g0495 495
3 69701490 69705742 - Tan0013642.1 Tan03g1322 1322
3 69777159 69778837 - Tan0019741.1 Tan03g1327 1327
3 69807918 69823090 - Tan0010356.2 Tan03g1329 1329
7 15125864 15127295 + Tan0010187.1 Tan07g0873 873
4 21972741 21972843 + Vvi4g1262 Vvi4g1262 1262
4 21979115 21981077 - Vvi4g1263 Vvi4g1263 1263
4 21993961 21997860 + Vvi4g1264 Vvi4g1264 1264
4 22005530 22034340 + Vvi4g1265 Vvi4g1265 1265
4 22059054 22060769 + Vvi4g1266 Vvi4g1266 1266
4 22096877 22101390 + Vvi4g1267 Vvi4g1267 1267
4 22115187 22125583 + Vvi4g1268 Vvi4g1268 1268
4 22138850 22138988 - Vvi4g1269 Vvi4g1269 1269
4 22169177 22170552 + Vvi4g1270 Vvi4g1270 1270
4 22176306 22182016 + Vvi4g1271 Vvi4g1271 1271
       

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