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
Vvi18g310 . . . . . . . . Cmo04g02452 Cmo15g00713 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo17g00186 . . Bda13g01491 Bpe02g01628 Bpe14g00373 . Bma02g00227 . . . . . Car04g02271 Car15g00645 Cpe01g02032 . . . . . . . . . . . . . . . . . . .
Vvi18g311 . . . . . . . . Cmo04g02451 Cmo15g00714 . . . . . . . . . . . . . . . . . . . . . Cone4ag1381 Cone7ag1550 . . . . . . . Blo18g00192 . Bda01g01414 Bpe02g01627 . . . . . . . . Car04g02270 Car15g00646 . . . . . . . . . . . . . . . . . . . .
Vvi18g312 . Blo12g00682 . Bda03g00524 . Bpe04g00478 . . . . Cma01g01403 Cma09g00811 . . . Cpe06g00645 Cpe07g00146 . . . . . . . Cla08g01128 Cam08g1584 Cec08g1154 Cco08g1280 Clacu08g1284 . Cre08g1066 Cone4ag1380 Cone7ag1551 Cone17ag1267 . Lsi04g02374 Csa04g01819 . . . . . . . . . . . Cmo01g01453 Cmo09g00804 . . . Car09g00726 . Cpe02g00539 Bhi09g02645 . . . Hepe01g2262 Mch11g0812 . Cla11g01520 Cam11g1580 Cec11g1609 Cco11g1608 Clacu11g1736 Cmu11g1554 Cre11g1972 Lsi08g00985 . Chy07g00668 Cme07g00876
Vvi18g313 . . . . . . . . Cmo04g02450 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo18g00193 . Bda01g01413 Bpe02g01626 . . . . . . . . Car04g02262 . Cpe01g02030 . . . . . . . . . . . . . . . . . . .
Vvi18g314 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g315 . Blo12g00683 . Bda03g00523 Bpe02g00078 Bpe04g00477 . Bma01g02640 Cmo04g02449 Cmo15g00715 . . . . . . . . . . . . . . . . . . . . . Cone4ag1379 Cone7ag1552 Cone17ag1266 . . . . . Blo17g00187 . . Bda01g01412 Bpe02g01625 . Bma01g00833 Bma02g00231 . . . . . Car04g02261 Car15g00647 . . . . . . . . . . . . . . . . . . . .
Vvi18g316 . . . Bda03g00522 . Bpe04g00476 . . Cmo04g02447 Cmo15g00716 . . . . . . . . . . . . . . . . . . . . . Cone4ag1378 Cone7ag1553 . Cone20ag0460 . . . . Blo17g00188 . . Bda13g01492 . Bpe14g00372 . Bma02g00233 . . . . . Car04g02260 Car15g00648 Cpe01g02029 . . . . . . . . . . . . . . . . . . .
Vvi18g317 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g318 . . . . . . . . . Cmo15g00718 . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0461 . . . . Blo17g00189 . . Bda13g01493 . Bpe14g00371 . Bma02g00234 . . . . . . Car15g00650 . . . . . . . . . . . . . . . . . . . .
Vvi18g319 . . . . . . . . Cmo04g02446 . . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0462 . . . . . Blo18g00194 . Bda01g01411 Bpe02g01624 . Bma01g00836 . . . . . . Car04g02259 Car15g00651 Cpe01g02028 . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 50026875 50030374 - Bda003654.1 Bda01g01411 1411
1 50041254 50041964 + Bda003656.1 Bda01g01412 1412
1 50044079 50046142 - Bda003657.1 Bda01g01413 1413
1 50048553 50050590 - Bda003658.1 Bda01g01414 1414
3 4368655 4373120 - Bda016491.1 Bda03g00522 522
3 4373738 4375085 + Bda016492.1 Bda03g00523 523
3 4376080 4379975 - Bda016493.1 Bda03g00524 524
13 37824650 37825540 + Bda000334.1 Bda13g01491 1491
13 37985016 37986814 + Bda000338.1 Bda13g01492 1492
13 37991004 37995350 - Bda000339.2 Bda13g01493 1493
9 71285296 71290762 - XM_039041195.1 Bhi09g02645 2645
12 25078018 25081974 + BLOR04701 Blo12g00682 682
12 25082669 25084010 - BLOR04702 Blo12g00683 683
17 1904974 1908017 + BLOR16007 Blo17g00186 186
17 1909693 1911163 - BLOR16008 Blo17g00187 187
17 1912747 1917110 + BLOR16009 Blo17g00188 188
17 1917818 1924334 - BLOR16010 Blo17g00189 189
18 1864808 1869145 + BLOR08680 Blo18g00192 192
18 1871117 1873180 + BLOR08681 Blo18g00193 193
18 1876405 1887861 + BLOR08682 Blo18g00194 194
1 7839060 7840250 - Bma001053.1 Bma01g00833 833
1 7894567 7898154 + Bma001057.1 Bma01g00836 836
1 83911540 83912868 + Bma003525.1 Bma01g02640 2640
2 2387002 2387910 + Bma014683.1 Bma02g00227 227
2 2421948 2423334 - Bma014687.1 Bma02g00231 231
2 2438123 2439769 + Bma014689.1 Bma02g00233 233
2 2440212 2446136 - Bma014690.1 Bma02g00234 234
2 591296 592621 - Bpe025057 Bpe02g00078 78
2 19108448 19111918 - Bpe009471.1 Bpe02g01624 1624
2 19116278 19117561 + Bpe009472.1 Bpe02g01625 1625
2 19119721 19121784 - Bpe009473.1 Bpe02g01626 1626
2 19123033 19125075 - Bpe009474.1 Bpe02g01627 1627
2 19125861 19126960 - Bpe009475.1 Bpe02g01628 1628
4 3007360 3011801 - Bpe015162.1 Bpe04g00476 476
4 3012432 3013776 + Bpe025626 Bpe04g00477 477
4 3014810 3018977 - Bpe015163.2 Bpe04g00478 478
14 3521675 3525156 + Bpe007026.1 Bpe14g00371 371
14 3528628 3532965 - Bpe007027.1 Bpe14g00372 372
14 3539637 3540536 - Bpe024975 Bpe14g00373 373
8 21999419 22007032 - CaPI482276_08g015840.1 Cam08g1584 1584
11 28547933 28552610 - CaPI482276_11g015800.1 Cam11g1580 1580
4 18244445 18249970 - Carg18224-RA Car04g02259 2259
4 18250911 18255958 - Carg18223-RA Car04g02260 2260
4 18260093 18261945 + Carg18222-RA Car04g02261 2261
4 18264623 18267066 - Carg18221-RA Car04g02262 2262
4 18293669 18296153 - Carg24459-RA Car04g02270 2270
4 18297072 18298043 - Carg24458-RA Car04g02271 2271
9 4301911 4307272 + Carg17046-RA Car09g00726 726
15 3564862 3565908 + Carg01510-RA Car15g00645 645
15 3566653 3570284 + Carg01509-RA Car15g00646 646
15 3571696 3572972 - Carg01508-RA Car15g00647 647
15 3574832 3579405 + Carg01507-RA Car15g00648 648
15 3580211 3587020 - Carg01505-RA Car15g00650 650
15 3587858 3592267 + Carg01504-RA Car15g00651 651
8 24586015 24593638 - CcPI632755_08g012800.1 Cco08g1280 1280
11 28923074 28928367 - CcPI632755_11g016080.1 Cco11g1608 1608
8 23436457 23436881 - CePI673135_08g011540.1 Cec08g1154 1154
11 30373382 30381269 - CePI673135_11g016090.1 Cec11g1609 1609
7 6413510 6418209 + Chy7G134980.1 Chy07g00668 668
8 22774556 22782792 - ClG42_08g0128400.10 Clacu08g1284 1284
11 28572508 28577188 - ClG42_11g0173600.10 Clacu11g1736 1736
8 24015061 24019680 - ClCG08G011300.1 Cla08g01128 1128
11 28847104 28852088 - ClCG11G015570.1 Cla11g01520 1520
1 9923886 9928190 + CmaCh01G014030.1 Cma01g01403 1403
9 3958489 3969009 + CmaCh09G008110.1 Cma09g00811 811
7 8769772 8774932 + MELO3C010457.2.1 Cme07g00876 876
1 11331371 11336142 + CmoCh01G014530.1 Cmo01g01453 1453
4 18125767 18131124 - CmoCh04G024460.1 Cmo04g02446 2446
4 18131170 18137433 - CmoCh04G024470.1 Cmo04g02447 2447
4 18141668 18143566 + CmoCh04G024490.1 Cmo04g02449 2449
4 18145477 18148715 - CmoCh04G024500.1 Cmo04g02450 2450
4 18149268 18151614 - CmoCh04G024510.1 Cmo04g02451 2451
4 18152431 18154979 - CmoCh04G024520.1 Cmo04g02452 2452
9 4114324 4121224 + CmoCh09G008040.1 Cmo09g00804 804
15 3469520 3470599 + CmoCh15G007130.1 Cmo15g00713 713
15 3471566 3474403 + CmoCh15G007140.1 Cmo15g00714 714
15 3476055 3477331 - CmoCh15G007150.1 Cmo15g00715 715
15 3479276 3484062 + CmoCh15G007160.1 Cmo15g00716 716
15 3485778 3491938 - CmoCh15G007180.1 Cmo15g00718 718
11 27824669 27829349 - CmPI595203_11g015540.1 Cmu11g1554 1554
4 11174201 11177230 - Conep04aG0142700.1 Cone4ag1378 1378
4 11178786 11180122 + Conep04aG0142800.1 Cone4ag1379 1379
4 11180786 11185211 - Conep04aG0142900.1 Cone4ag1380 1380
4 11188649 11190489 - Conep04aG0143000.1 Cone4ag1381 1381
7 10675828 10678193 + Conep07aG0159600.1 Cone7ag1550 1550
7 10679741 10684261 + Conep07aG0159700.1 Cone7ag1551 1551
7 10684926 10686247 - Conep07aG0159800.1 Cone7ag1552 1552
7 10688013 10691394 + Conep07aG0159900.1 Cone7ag1553 1553
17 9127782 9129225 + Conep17aG0129700.1 Cone17ag1266 1266
17 9130587 9132798 - Conep17aG0129800.1 Cone17ag1267 1267
20 2387780 2391264 + Conep20aG0047500.1 Cone20ag0460 460
20 2390693 2394768 - Conep20aG0047600.1 Cone20ag0461 461
20 2394803 2397768 + Conep20aG0047700.1 Cone20ag0462 462
1 17263325 17271319 - Cp4.1LG01g20300.1 Cpe01g02028 2028
1 17271978 17277114 - Cp4.1LG01g20250.1 Cpe01g02029 2029
1 17279931 17291308 - Cp4.1LG01g20330.1 Cpe01g02030 2030
1 17292240 17295536 - Cp4.1LG01g20320.1 Cpe01g02032 2032
2 3201216 3206154 - Cp4.1LG02g03310.1 Cpe02g00539 539
6 3990296 3995529 + Cp4.1LG06g06520.1 Cpe06g00645 645
7 811137 816572 - Cp4.1LG07g01490.1 Cpe07g00146 146
8 23778745 23786364 - CrPI670011_08g010660.1 Cre08g1066 1066
11 31473195 31477916 - CrPI670011_11g019720.1 Cre11g1972 1972
4 17843195 17848806 + CsaV3_4G028450.1 Csa04g01819 1819
1 87261690 87267225 - Hsped.01g22620.1 Hepe01g2262 2262
4 30862758 30868274 - Lsi04G023740.1 Lsi04g02374 2374
8 18296828 18305444 - Lsi08G009850.1 Lsi08g00985 985
11 5485749 5491263 - MC11g0684 Mch11g0812 812
18 3387827 3389344 + Vvi18g310 Vvi18g310 310
18 3389496 3394322 + Vvi18g311 Vvi18g311 311
18 3401892 3411202 + Vvi18g312 Vvi18g312 312
18 3412344 3414417 + Vvi18g313 Vvi18g313 313
18 3417192 3418012 - Vvi18g314 Vvi18g314 314
18 3422178 3424178 - Vvi18g315 Vvi18g315 315
18 3432982 3445082 + Vvi18g316 Vvi18g316 316
18 3445759 3445939 + Vvi18g317 Vvi18g317 317
18 3446049 3490947 - Vvi18g318 Vvi18g318 318
18 3491629 3505392 + Vvi18g319 Vvi18g319 319
       

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