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
Vvi17g286 . . . . . . . . . . . Cma11g00287 Car10g00293 Car11g00261 . . Cpe04g01392 . . . . . . . Cla06g01451 Cam06g1605 Cec06g1666 Cco06g1660 Clacu06g1570 Cmu06g1522 Cre06g2334 . . . . . . . . . . . . . . . . . Cmo10g00330 Cmo11g00290 . . . . . . . . . . . . . . . . . . . . Lsi06g01316 Csa01g00399 Chy02g02349 Cme02g01726
Vvi17g287 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g288 . Blo16g00132 . . . . . . Cmo13g01053 . . . . . . . . . . . . . . . . . . . . . . . Cone16ag0561 . . Lsi02g00197 Csa01g00685 Chy12g01425 Cme12g01863 . . . . . . . . . . . Cma13g01012 . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g289 . . . Bda15g00513 . Bpe13g00359 Bma06g00049 . Cmo13g01055 . Cma10g00308 Cma11g00286 Car10g00292 Car11g00260 . . . . . . . . . . Cla06g01453 . . . . . . Cone11ag0305 Cone18ag1190 Cone2ag0439 Cone16ag0560 Lsi02g00194 Csa01g00680 . Cme12g01864 . . . . . Bpe15g00530 Bma03g00899 Bma08g00058 . Cmo10g00329 Cmo11g00288 Cma13g01013 . Car13g00846 . . . Bhi08g01255 . . . . . . Cla04g01079 . . . . . . Lsi06g01317 Csa01g00398 Chy02g02350 Cme02g01727
Vvi17g290 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi08g01245 . . . . . . . . . . . . . . . . .
Vvi17g291 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g292 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0732 . . Cone19ag0282 . . . . . . . . . . . . . . . Cma13g01015 . . . . . . . . . . . . . . . . . . . . Csa01g00177 . .
Vvi17g293 Blo04g00832 . . . . . . . Cmo13g01056 Cmo18g00039 . . . . . . . . . . . . . . . . . . . . . . . . . . Csa01g00676 . . . . . . . . . . Sed08g2191 . . . Cma18g00048 . Car18g00042 . . Bhi08g01244 Tan05g2251 Cmetu12g0949 Lac10g0248 Hepe07g2379 . . Cla04g01080 Cam04g1127 Cec01g1640 Cco01g1686 Clacu04g1157 Cmu04g1138 Cre01g1436 . . . .
Vvi17g294 . . . . . . . . . . . . . . . Cpe20g00130 . . . . . . . . . . . . . . . Cone2ag0623 . . . Lsi02g00191 . Chy12g01428 Cme12g01866 . . . . . Bpe15g00529 . . . . . . . Car13g00849 . . Cpe18g00828 . . . . . . . . . . . . . . . . . .
Vvi17g295 . . . . . . . . Cmo13g01057 . . . . . . . . . . . . . . . Cla06g01454 Cam06g1608 Cec06g1669 Cco06g1664 Clacu06g1573 Cmu06g1525 Cre06g2336 . . . . . Csa01g00673 . . . . . . . . . . Sed12g2090 . . Cma13g01017 . . . . . Bhi08g01243 Tan05g2257 Cmetu02g1431 Lac10g0247 Hepe07g2380 . . Cla04g01081 Cam04g1133 Cec01g1643 Cco01g1692 Clacu04g1161 Cmu04g1142 Cre01g1438 Lsi06g01318 . Chy02g02352 Cme02g01728
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
15 8203506 8204730 + Bda012343.1 Bda15g00513 513
8 38400253 38403554 + XM_039038153.1 Bhi08g01243 1243
8 38444614 38447104 + XM_039040096.1 Bhi08g01244 1244
8 38484467 38487413 - XM_039038439.1 Bhi08g01245 1245
8 38656870 38661628 - XM_039038112.1 Bhi08g01255 1255
4 8833973 8843761 + BLOR13744 Blo04g00832 832
16 2986830 2994023 + BLOR07380 Blo16g00132 132
3 8936250 8940300 - Bma017224.1 Bma03g00899 899
6 825598 826860 - Bma022659.1 Bma06g00049 49
8 741666 744042 + Bma027054.1 Bma08g00058 58
13 11362735 11365698 - Bpe006486.1 Bpe13g00359 359
15 16449076 16456879 + Bpe001464.1 Bpe15g00529 529
15 16458801 16463571 - Bpe001465.1 Bpe15g00530 530
4 25347818 25349671 - CaPI482276_04g011270.1 Cam04g1127 1127
4 25429795 25432974 - CaPI482276_04g011330.1 Cam04g1133 1133
6 27515439 27516099 + CaPI482276_06g016050.1 Cam06g1605 1605
6 27535122 27538621 - CaPI482276_06g016080.1 Cam06g1608 1608
10 1407109 1410759 - Carg15159-RA Car10g00292 292
10 1413762 1417286 + Carg15160-RA Car10g00293 293
11 1441603 1443801 - Carg09129-RA Car11g00260 260
11 1446460 1448931 + Carg09128-RA Car11g00261 261
13 9077538 9080755 + Carg04826-RA Car13g00846 846
13 9091912 9093807 - Carg04823-RA Car13g00849 849
18 185924 188450 + Carg22744-RA Car18g00042 42
1 29580226 29582169 - CcPI632755_01g016860.1 Cco01g1686 1686
1 29657101 29669694 - CcPI632755_01g016920.1 Cco01g1692 1692
6 27185724 27186382 + CcPI632755_06g016600.1 Cco06g1660 1660
6 27206304 27209759 - CcPI632755_06g016640.1 Cco06g1664 1664
1 31003234 31008508 - CePI673135_01g016400.1 Cec01g1640 1640
1 31095420 31108738 - CePI673135_01g016430.1 Cec01g1643 1643
6 30258426 30259086 + CePI673135_06g016660.1 Cec06g1666 1666
6 30278591 30281952 - CePI673135_06g016690.1 Cec06g1669 1669
2 27380356 27382920 - Chy2G046160.1 Chy02g02349 2349
2 27390919 27392253 + Chy2G046170.1 Chy02g02350 2350
2 27393509 27396602 - Chy2G046190.1 Chy02g02352 2352
12 18286926 18290574 + Chy12G220250.1 Chy12g01425 1425
12 18307264 18309095 - Chy12G220280.1 Chy12g01428 1428
4 25733561 25735457 - ClG42_04g0115700.10 Clacu04g1157 1157
4 25818197 25821349 - ClG42_04g0116100.10 Clacu04g1161 1161
6 26571970 26573124 + ClG42_06g0157000.10 Clacu06g1570 1570
6 26592065 26595482 - ClG42_06g0157300.10 Clacu06g1573 1573
4 25947478 25948797 + ClCG04G010968.1 Cla04g01079 1079
4 25964672 25966836 - ClCG04G010970.1 Cla04g01080 1080
4 26008303 26017080 - ClCG04G010980.1 Cla04g01081 1081
6 28077547 28079053 + ClCG06G014617.1 Cla06g01451 1451
6 28092258 28101658 + ClCG06G014640.2 Cla06g01453 1453
6 28096199 28101636 - ClCG06G014650.2 Cla06g01454 1454
10 1393265 1396280 - CmaCh10G003080.1 Cma10g00308 308
11 1425816 1429058 - CmaCh11G002860.1 Cma11g00286 286
11 1429877 1433655 + CmaCh11G002870.1 Cma11g00287 287
13 7790968 7794826 + CmaCh13G010120.1 Cma13g01012 1012
13 7795485 7797810 + CmaCh13G010130.1 Cma13g01013 1013
13 7800931 7803356 - CmaCh13G010150.1 Cma13g01015 1015
13 7809539 7814790 - CmaCh13G010170.1 Cma13g01017 1017
18 196723 199315 + CmaCh18G000480.1 Cma18g00048 48
2 24266819 24270641 - MELO3C017323.2.1 Cme02g01726 1726
2 24275353 24280275 + MELO3C017322.2.1 Cme02g01727 1727
2 24280322 24283674 - MELO3C017321.2.1 Cme02g01728 1728
12 24876373 24879034 + MELO3C002101.2.1 Cme12g01863 1863
12 24879168 24880552 + MELO3C035551.2.1 Cme12g01864 1864
12 24886995 24889492 - MELO3C002099.2.1 Cme12g01866 1866
2 22651032 22654573 - PI0027898.1 Cmetu02g1431 1431
12 1338218 1343281 + PI0025802.2 Cmetu12g0949 949
10 1483079 1486094 - CmoCh10G003290.1 Cmo10g00329 329
10 1489137 1492985 + CmoCh10G003300.1 Cmo10g00330 330
11 1407876 1410242 - CmoCh11G002880.1 Cmo11g00288 288
11 1412666 1415692 + CmoCh11G002900.1 Cmo11g00290 290
13 8787253 8791319 + CmoCh13G010530.1 Cmo13g01053 1053
13 8793129 8794857 + CmoCh13G010550.1 Cmo13g01055 1055
13 8797595 8799689 - CmoCh13G010560.1 Cmo13g01056 1056
13 8810733 8812147 - CmoCh13G010570.1 Cmo13g01057 1057
18 236785 239895 + CmoCh18G000390.1 Cmo18g00039 39
4 25914070 25916576 - CmPI595203_04g011380.1 Cmu04g1138 1138
4 26000161 26003346 - CmPI595203_04g011420.1 Cmu04g1142 1142
6 26476049 26476709 + CmPI595203_06g015220.1 Cmu06g1522 1522
6 26494993 26498408 - CmPI595203_06g015250.1 Cmu06g1525 1525
2 2358824 2362442 - Conep02aG0045000.1 Cone2ag0439 439
2 3944448 3949841 - Conep02aG0063700.1 Cone2ag0623 623
2 33001012 33004211 + Conep02aG0174500.1 Cone2ag0732 732
11 1489818 1494946 + Conep11aG0031300.1 Cone11ag0305 305
16 7508271 7511614 + Conep16aG0292100.1 Cone16ag0560 560
16 7512546 7525906 + Conep16aG0292200.1 Cone16ag0561 561
18 8501767 8507091 - Conep18aG0122900.1 Cone18ag1190 1190
19 2021172 2024227 + Conep19aG0029200.1 Cone19ag0282 282
4 11258086 11261695 - Cp4.1LG04g13890.1 Cpe04g01392 1392
18 7671185 7681095 + Cp4.1LG18g08230.1 Cpe18g00828 828
20 723081 725709 + Cp4.1LG20g01250.1 Cpe20g00130 130
1 27566720 27569773 - CrPI670011_01g014360.1 Cre01g1436 1436
1 27640401 27653107 - CrPI670011_01g014380.1 Cre01g1438 1438
6 31268503 31271671 - CrPI670011_06g023340.1 Cre06g2334 2334
6 31283839 31287375 - CrPI670011_06g023360.1 Cre06g2336 2336
1 1146544 1153540 - CsaV3_1G001770.1 Csa01g00177 177
1 2483778 2486198 - CsaV3_1G003980.1 Csa01g00398 398
1 2493649 2496928 + CsaV3_1G003990.1 Csa01g00399 399
1 4322051 4324880 + CsaV3_1G006730.1 Csa01g00673 673
1 4339659 4342085 + CsaV3_1G006760.1 Csa01g00676 676
1 4352931 4355752 - CsaV3_1G006800.1 Csa01g00680 680
1 4367399 4370158 - CsaV3_1G006850.1 Csa01g00685 685
7 68151858 68155015 - Hsped.07g23790.1 Hepe07g2379 2379
7 68174359 68178164 - Hsped.07g23800.1 Hepe07g2380 2380
10 1923792 1924409 + Lag0024292.1 Lac10g0247 247
10 1933098 1935269 + Lag0024293.1 Lac10g0248 248
2 1649376 1652203 + Lsi02G001910.1 Lsi02g00191 191
2 1670999 1673189 - Lsi02G001940.1 Lsi02g00194 194
2 1682097 1685584 - Lsi02G001970.1 Lsi02g00197 197
6 23739356 23743867 - Lsi06G013160.1 Lsi06g01316 1316
6 23754335 23759505 + Lsi06G013170.1 Lsi06g01317 1317
6 23759581 23764459 - Lsi06G013180.1 Lsi06g01318 1318
8 35799514 35802454 + Sed0027586.2 Sed08g2191 2191
12 31640263 31644404 + Sed0004266.1 Sed12g2090 2090
5 73456852 73459870 - Tan0007403.2 Tan05g2251 2251
5 73488113 73492920 - Tan0002983.1 Tan05g2257 2257
17 3169136 3179314 - Vvi17g286 Vvi17g286 286
17 3189752 3194345 + Vvi17g287 Vvi17g287 287
17 3215528 3219814 + Vvi17g288 Vvi17g288 288
17 3220545 3228158 - Vvi17g289 Vvi17g289 289
17 3231772 3232558 - Vvi17g290 Vvi17g290 290
17 3235697 3236363 - Vvi17g291 Vvi17g291 291
17 3248574 3251784 - Vvi17g292 Vvi17g292 292
17 3256477 3260269 - Vvi17g293 Vvi17g293 293
17 3261765 3265505 - Vvi17g294 Vvi17g294 294
17 3272924 3279659 - Vvi17g295 Vvi17g295 295
       

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