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
Vvi4g32 . . . . . . . . Cmo05g00488 . . Cma05g00431 . . Sed03g1452 . . Bhi04g00878 Tan02g2535 Cmetu03g1217 . Hepe10g0386 . Lcy13g1440 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe11g00405 . . . . . . . . Cla08g01202 . Cec08g1240 . Clacu08g1360 . . . Csa02g02246 . .
Vvi4g33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00165 . . . . . . . . . . Cmo01g01497 . . . . . . . Bhi09g02560 . . . . . . . . . . . . . . . . .
Vvi4g34 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g02319 . . . . . . . . . . . . . . . . . . . . Bhi09g02559 Tan01g3908 . . . . . . . . . . . . . . . .
Vvi4g35 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g36 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda01g00943 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g37 . Blo12g01056 . . . . . . . . Cma01g01444 . Car09g00552 . . . Cpe06g00481 . . . . . . . . . . . . . . . . . Cone20ag0325 Lsi04g02318 Csa03g04537 Chy04g00166 . . . . Bda13g01320 . . . Bma02g00077 . Cmo01g01498 . Cma09g00623 . . . . Cpe02g00504 Bhi09g02557 . . . . Mch11g0757 . . . . . . . . . . . Cme04g00191
Vvi4g38 . . . . . . . . . . . . Car09g00551 . . . Cpe06g00480 . . . . . . . . . . . . . . . . . . . Csa03g04536 Chy04g00167 . . . . Bda13g01319 . . . Bma02g00075 . . . Cma09g00622 . . . . . . . . . . . . . . . . . . . . . . Cme04g00192
Vvi4g39 . . . . . . . . . . Cma01g01445 . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g02317 Csa03g04535 Chy04g00168 . . . . . . . . . Sed05g1516 Cmo01g01499 . . . . . . Cpe02g00503 Bhi09g02556 Tan01g3903 Cmetu04g0903 . Hepe01g2205 Mch11g0755 . . . . . . . . . . . Cme04g00193
Vvi4g40 . . . . . . . . . . Cma01g01446 . Car09g00550 . . . . . . . . . . . . . . . . . . . . . . . Csa03g04534 Chy04g00169 . . . . . . . . . Sed05g1519 Cmo01g01500 . Cma09g00621 . . . . Cpe02g00502 Bhi09g02555 Tan01g3902 Cmetu04g3181 . . . . . . . . . . . . . . Cme04g00195
Vvi4g41 . . . . . . . . . . . . . Car12g00216 . Cpe07g00200 . Bhi04g00880 . . . Hepe10g0388 . Lcy13g1442 . . . . . . . . . . . . . . . . . . Bda13g01318 . . . Bma02g00074 . . . . . . . . . . . . . . . . Cla08g01199 Cam08g1661 Cec08g1238 Cco08g1357 Clacu08g1358 . Cre08g1145 . Csa02g02244 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 42875120 42878596 + Bda003095.1 Bda01g00943 943
13 35414222 35432247 + Bda000127.1 Bda13g01318 1318
13 35433964 35435442 + Bda000128.1 Bda13g01319 1319
13 35437249 35439343 + Bda000129.1 Bda13g01320 1320
4 22037066 22039518 - XM_039030871.1 Bhi04g00878 878
4 22097845 22102396 - XM_039028099.1 Bhi04g00880 880
9 69403221 69406881 - XM_039041354.1 Bhi09g02555 2555
9 69407326 69419298 - XM_039044319.1 Bhi09g02556 2556
9 69455952 69458891 + XM_039043111.1 Bhi09g02557 2557
9 69459760 69462452 + XM_039043142.1 Bhi09g02559 2559
9 69470118 69472205 - XM_039044322.1 Bhi09g02560 2560
12 28344522 28345847 - BLOR05075 Blo12g01056 1056
2 645056 659247 + Bma014530.1 Bma02g00074 74
2 660652 661927 + Bma014531.1 Bma02g00075 75
2 665029 666873 + Bma014533.1 Bma02g00077 77
8 22867309 22886599 + CaPI482276_08g016610.1 Cam08g1661 1661
9 3115988 3119440 - Carg03032-RA Car09g00550 550
9 3118792 3121913 + Carg03033-RA Car09g00551 551
9 3122101 3125027 + Carg03034-RA Car09g00552 552
12 1368693 1378382 + Carg22478-RA Car12g00216 216
8 25504478 25523557 + CcPI632755_08g013570.1 Cco08g1357 1357
8 24347531 24366659 + CePI673135_08g012380.1 Cec08g1238 1238
8 24369192 24371089 + CePI673135_08g012400.1 Cec08g1240 1240
4 1459868 1461751 + Chy4G068830.1 Chy04g00165 165
4 1462430 1464921 - Chy4G068840.1 Chy04g00166 166
4 1466748 1468422 - Chy4G068850.1 Chy04g00167 167
4 1470027 1481029 + Chy4G068860.1 Chy04g00168 168
4 1481375 1486366 + Chy4G068870.1 Chy04g00169 169
8 23640968 23660045 + ClG42_08g0135800.10 Clacu08g1358 1358
8 23662541 23664438 + ClG42_08g0136000.10 Clacu08g1360 1360
8 24920298 24941010 + ClCG08G012030.1 Cla08g01199 1199
8 24942315 24944709 + ClCG08G012060.1 Cla08g01202 1202
1 10169837 10172496 - CmaCh01G014440.1 Cma01g01444 1444
1 10174465 10185936 + CmaCh01G014450.1 Cma01g01445 1445
1 10186637 10190463 + CmaCh01G014460.1 Cma01g01446 1446
5 1956044 1962423 + CmaCh05G004310.1 Cma05g00431 431
9 2924217 2927144 - CmaCh09G006210.1 Cma09g00621 621
9 2927647 2930125 + CmaCh09G006220.1 Cma09g00622 622
9 2930397 2934506 + CmaCh09G006230.1 Cma09g00623 623
4 1429442 1432300 - MELO3C003476.2.1 Cme04g00191 191
4 1433743 1436220 - MELO3C003477.2.1 Cme04g00192 192
4 1437242 1448693 + MELO3C003478.2.1 Cme04g00193 193
4 1450088 1453353 + MELO3C003479.2.1 Cme04g00195 195
3 3290150 3292562 + PI0000416.1 Cmetu03g1217 1217
4 31957235 31968776 - PI0001445.1 Cmetu04g0903 903
4 31950752 31955709 - PI0008327.1 Cmetu04g3181 3181
1 11574731 11582050 + CmoCh01G014970.1 Cmo01g01497 1497
1 11583006 11585802 - CmoCh01G014980.1 Cmo01g01498 1498
1 11587942 11599692 + CmoCh01G014990.1 Cmo01g01499 1499
1 11600159 11603438 + CmoCh01G015000.1 Cmo01g01500 1500
5 2294562 2307726 + CmoCh05G004880.1 Cmo05g00488 488
20 1450077 1451868 + Conep20aG0033900.1 Cone20ag0325 325
2 2935881 2939217 - Cp4.1LG02g03710.1 Cpe02g00502 502
2 2939790 2951303 - Cp4.1LG02g03590.1 Cpe02g00503 503
2 2953293 2956188 + Cp4.1LG02g03670.1 Cpe02g00504 504
6 2830029 2833391 + Cp4.1LG06g03850.1 Cpe06g00480 480
6 2833608 2836553 + Cp4.1LG06g03870.1 Cpe06g00481 481
7 1268921 1284706 + Cp4.1LG07g02470.1 Cpe07g00200 200
11 2241463 2246350 + Cp4.1LG11g03990.1 Cpe11g00405 405
8 24673945 24693164 + CrPI670011_08g011450.1 Cre08g1145 1145
2 20153673 20167663 + CsaV3_2G030630.1 Csa02g02244 2244
2 20169404 20171244 + CsaV3_2G030650.1 Csa02g02246 2246
3 39527893 39531872 - CsaV3_3G048400.1 Csa03g04534 4534
3 39531560 39544545 - CsaV3_3G048410.1 Csa03g04535 4535
3 39545607 39548196 + CsaV3_3G048420.1 Csa03g04536 4536
3 39549126 39552044 + CsaV3_3G048430.1 Csa03g04537 4537
1 86761665 86773653 - Hsped.01g22050.1 Hepe01g2205 2205
10 4228549 4230250 - Hsped.10g03860.1 Hepe10g0386 386
10 4233715 4251409 - Hsped.10g03880.1 Hepe10g0388 388
13 32869378 32872088 - Maker00034262 Lcy13g1440 1440
13 32876564 32894339 - Maker00034038 Lcy13g1442 1442
4 30364106 30382133 - Lsi04G023170.1 Lsi04g02317 2317
4 30387878 30390920 + Lsi04G023180.1 Lsi04g02318 2318
4 30391453 30393225 + Lsi04G023190.1 Lsi04g02319 2319
11 5080524 5091958 - MC11g0634 Mch11g0755 755
11 5096907 5102607 + MC11g0636 Mch11g0757 757
3 9324367 9326971 + Sed0020740.1 Sed03g1452 1452
5 28815990 28827255 + Sed0028022.1 Sed05g1516 1516
5 28828703 28833921 + Sed0009640.3 Sed05g1519 1519
1 104003646 104012192 - Tan0009617.2 Tan01g3902 3902
1 104012904 104028033 - Tan0006107.1 Tan01g3903 3903
1 104045473 104048214 + Tan0008101.1 Tan01g3908 3908
2 93925100 93928517 + Tan0005504.1 Tan02g2535 2535
4 409521 413243 - Vvi4g32 Vvi4g32 32
4 415711 418685 + Vvi4g33 Vvi4g33 33
4 418733 421550 - Vvi4g34 Vvi4g34 34
4 450930 456000 - Vvi4g35 Vvi4g35 35
4 458258 466276 + Vvi4g36 Vvi4g36 36
4 466491 470163 - Vvi4g37 Vvi4g37 37
4 475334 480636 - Vvi4g38 Vvi4g38 38
4 480826 497305 + Vvi4g39 Vvi4g39 39
4 498014 503312 + Vvi4g40 Vvi4g40 40
4 503962 528680 - Vvi4g41 Vvi4g41 41
       

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