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
Vvi5g639 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme06g00522 . . . . . . . . . . . . . . . . . Bhi12g01650 . . . . . . . . . . . . . . Csa03g01243 Chy06g00496 .
Vvi5g640 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g641 . . . . . . . . . . . Cma14g01789 . Car14g01610 . . Cpe03g01498 . . . . . . . Cla06g00643 Cam06g0688 Cec06g0690 Cco06g0697 Clacu06g0674 Cmu06g0665 Cre06g1433 . . . Cone4ag0304 Lsi05g01693 . Chy05g00345 Cme06g00521 . . . . . . . . . . Cmo14g01826 . . . Car17g00157 . . . . . . . . . Cla05g00470 Cam05g0511 Cec05g0525 Cco05g0526 Clacu05g0512 Cmu05g0488 Cre05g0552 Lsi09g01255 Csa03g01242 Chy06g00495 Cme05g00538
Vvi5g642 . . . . . Bpe14g01236 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme06g00520 Blo02g00620 . . Bda13g00081 . . . . . . . . . . . . . . . . . . . . Cla05g00469 Cam05g0510 Cec05g0524 Cco05g0525 Clacu05g0511 Cmu05g0487 Cre05g0551 . Csa03g01241 Chy06g00494 .
Vvi5g643 . . . . . . . . . . . . . Car14g01611 . . Cpe03g01499 . . . . . . . . . . . . . . . . . . Lsi05g01694 . . . . . . . . . . . . . Cmo14g01827 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g644 . . . . . Bpe14g01237 . . . . . Cma14g01794 Car06g01151 Car14g01613 . Cpe08g00319 Cpe03g01501 . . . . . . . . . . . . . . Cone14ag0140 Cone15ag0148 Cone7ag0305 Cone4ag0306 Lsi05g01696 . . Cme06g00518 Blo02g00624 Blo07g00250 Bda11g00618 Bda13g00079 . Bpe13g00568 . Bma06g01589 . Cmo06g01346 Cmo14g01832 . . . . . . . . . . . . . Cla05g00467 Cam05g0508 Cec05g0522 Cco05g0523 Clacu05g0509 Cmu05g0485 Cre05g0549 . Csa03g01239 Chy06g00492 .
Vvi5g645 . . . . . Bpe14g01239 . . Cmo08g01071 Cmo17g00172 . . . . . . . . . . . . . . Cla06g00647 Cam06g0691 Cec06g0694 Cco06g0700 Clacu06g0678 Cmu06g0669 Cre06g1438 . Cone15ag0149 Cone7ag0308 Cone4ag0309 . Csa02g01080 Chy05g00340 . Blo02g00625 Blo07g00251 Bda11g00620 Bda13g00078 . Bpe13g00567 Bma02g00798 Bma06g01591 Sed04g1971 . . Cma08g01095 Cma17g00175 Car08g00970 Car17g00155 Cpe12g00150 Cpe17g00184 Bhi12g01642 Tan06g2433 Cmetu05g0804 Lac12g2197 Hepe03g0264 . Lcy13g0353 . . . . . . . Lsi09g01250 . . Cme05g00544
Vvi5g646 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g647 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag0310 Cone4ag0312 Lsi05g01699 . . Cme06g00516 . . . . . . . . . . . . . . . . . . . . . . . . Cla05g00464 Cam05g0505 Cec05g0518 Cco05g0519 Clacu05g0506 Cmu05g0482 Cre05g0546 . Csa03g01237 Chy06g00490 .
Vvi5g648 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 6246838 6249212 + Bda005362.1 Bda11g00618 618
11 6256678 6258285 - Bda005364.1 Bda11g00620 620
13 999355 1005413 + Bda000924.2 Bda13g00078 78
13 1011258 1013159 - Bda000925.1 Bda13g00079 79
13 1050392 1050994 - Bda000929.1 Bda13g00081 81
12 53144757 53148123 + XM_039019892.1 Bhi12g01642 1642
12 53316653 53322568 - XM_039020254.1 Bhi12g01650 1650
2 12678647 12679249 + BLOR10350 Blo02g00620 620
2 12934424 12956915 + BLOR10354 Blo02g00624 624
2 13076332 13078092 - BLOR10355 Blo02g00625 625
7 3078235 3080916 + BLOR18182 Blo07g00250 250
7 3091540 3099030 - BLOR18183 Blo07g00251 251
2 42836585 42838366 + Bma015531.1 Bma02g00798 798
6 52135437 52137779 + Bma024705.1 Bma06g01589 1589
6 52147668 52149275 - Bma024707.1 Bma06g01591 1591
13 12842623 12847812 + Bpe010270.1 Bpe13g00567 567
13 12849867 12852223 - Bpe010271.1 Bpe13g00568 568
14 9277464 9278066 + Bpe014597.1 Bpe14g01236 1236
14 9313251 9315634 + Bpe014599.1 Bpe14g01237 1237
14 9332880 9338401 - Bpe014601.1 Bpe14g01239 1239
5 4490091 4495859 + CaPI482276_05g005050.1 Cam05g0505 505
5 4523039 4526494 - CaPI482276_05g005080.1 Cam05g0508 508
5 4559089 4559667 - CaPI482276_05g005100.1 Cam05g0510 510
5 4563062 4564723 - CaPI482276_05g005110.1 Cam05g0511 511
6 9214412 9215944 + CaPI482276_06g006880.1 Cam06g0688 688
6 9259495 9273527 - CaPI482276_06g006910.1 Cam06g0691 691
6 8522615 8525407 - Carg06206-RA Car06g01151 1151
8 6462208 6465179 + Carg10952-RA Car08g00970 970
14 13000472 13002088 + Carg16577-RA Car14g01610 1610
14 13002826 13003386 + Carg16576-RA Car14g01611 1611
14 13010317 13013988 + Carg16574-RA Car14g01613 1613
17 961143 962747 + Carg10076-RA Car17g00155 155
17 967875 969491 - Carg10074-RA Car17g00157 157
5 4148166 4153935 + CcPI632755_05g005190.1 Cco05g0519 519
5 4181220 4184118 - CcPI632755_05g005230.1 Cco05g0523 523
5 4218901 4219476 - CcPI632755_05g005250.1 Cco05g0525 525
5 4222715 4224319 - CcPI632755_05g005260.1 Cco05g0526 526
6 7793893 7795434 + CcPI632755_06g006970.1 Cco06g0697 697
6 7843527 7857722 - CcPI632755_06g007000.1 Cco06g0700 700
5 4142392 4148124 + CePI673135_05g005180.1 Cec05g0518 518
5 4174353 4178958 - CePI673135_05g005220.1 Cec05g0522 522
5 4213512 4214090 - CePI673135_05g005240.1 Cec05g0524 524
5 4217294 4218943 - CePI673135_05g005250.1 Cec05g0525 525
6 7806779 7808314 + CePI673135_06g006900.1 Cec06g0690 690
6 7873327 7881480 - CePI673135_06g006940.1 Cec06g0694 694
5 3528123 3529868 + Chy5G093860.1 Chy05g00340 340
5 3557828 3559357 - Chy5G093910.1 Chy05g00345 345
6 3299227 3304905 + Chy6G110180.1 Chy06g00490 490
6 3325491 3328365 - Chy6G110200.1 Chy06g00492 492
6 3354543 3356605 - Chy6G110220.1 Chy06g00494 494
6 3358171 3359763 - Chy6G110230.1 Chy06g00495 495
6 3361374 3367117 - Chy6G110240.1 Chy06g00496 496
5 4199249 4205013 + ClG42_05g0050600.10 Clacu05g0506 506
5 4232071 4234974 - ClG42_05g0050900.10 Clacu05g0509 509
5 4268417 4268995 - ClG42_05g0051100.10 Clacu05g0511 511
5 4272361 4274001 - ClG42_05g0051200.10 Clacu05g0512 512
6 7766196 7767731 + ClG42_06g0067400.10 Clacu06g0674 674
6 7826847 7828592 - ClG42_06g0067800.10 Clacu06g0678 678
5 4194947 4200711 + ClCG05G004470.1 Cla05g00464 464
5 4227158 4230859 - ClCG05G004500.1 Cla05g00467 467
5 4279261 4279839 - ClCG05G004504.1 Cla05g00469 469
5 4284570 4286216 - ClCG05G004506.1 Cla05g00470 470
6 7924745 7926280 + ClCG06G006775.1 Cla06g00643 643
6 7991313 8005381 - ClCG06G006820.2 Cla06g00647 647
8 6821815 6823488 + CmaCh08G010950.1 Cma08g01095 1095
14 12922071 12926435 + CmaCh14G017890.1 Cma14g01789 1789
14 12936332 12939948 + CmaCh14G017940.1 Cma14g01794 1794
17 904430 908313 + CmaCh17G001750.1 Cma17g00175 175
5 5213001 5214578 + MELO3C026784.2.1 Cme05g00538 538
5 5292846 5294922 - MELO3C031219.2.1 Cme05g00544 544
6 3238245 3245240 + MELO3C006446.2.1 Cme06g00516 516
6 3263120 3267518 - MELO3C006451.2.1 Cme06g00518 518
6 3292146 3292720 - MELO3C006453.2.1 Cme06g00520 520
6 3294460 3296070 - MELO3C006454.2.1 Cme06g00521 521
6 3297183 3302001 - MELO3C006455.2.1 Cme06g00522 522
5 18577541 18580684 + PI0011060.1 Cmetu05g0804 804
6 9978895 9982724 - CmoCh06G013460.1 Cmo06g01346 1346
8 6906698 6908368 + CmoCh08G010710.1 Cmo08g01071 1071
14 13910049 13911656 + CmoCh14G018260.1 Cmo14g01826 1826
14 13912429 13913346 + CmoCh14G018270.1 Cmo14g01827 1827
14 13921131 13923737 + CmoCh14G018320.1 Cmo14g01832 1832
17 1007279 1011428 + CmoCh17G001720.1 Cmo17g00172 172
5 4035428 4041192 + CmPI595203_05g004820.1 Cmu05g0482 482
5 4068216 4071119 - CmPI595203_05g004850.1 Cmu05g0485 485
5 4104544 4105122 - CmPI595203_05g004870.1 Cmu05g0487 487
5 4108463 4110097 - CmPI595203_05g004880.1 Cmu05g0488 488
6 7571930 7573468 + CmPI595203_06g006650.1 Cmu06g0665 665
6 7638408 7640153 - CmPI595203_06g006690.1 Cmu06g0669 669
4 1392541 1394295 + Conep04aG0031600.1 Cone4ag0304 304
4 1400003 1402390 + Conep04aG0031800.1 Cone4ag0306 306
4 1413537 1416162 - Conep04aG0032100.1 Cone4ag0309 309
4 1421931 1422426 - Conep04aG0032400.1 Cone4ag0312 312
7 1324020 1326409 + Conep07aG0031300.1 Cone7ag0305 305
7 1338378 1340205 - Conep07aG0031600.1 Cone7ag0308 308
7 1343583 1345602 - Conep07aG0031800.1 Cone7ag0310 310
14 677298 679677 + Conep14aG0014400.1 Cone14ag0140 140
15 711034 714392 + Conep15aG0015100.1 Cone15ag0148 148
15 720428 723830 - Conep15aG0015300.1 Cone15ag0149 149
3 11812109 11813716 + Cp4.1LG03g10100.1 Cpe03g01498 1498
3 11814415 11814963 + Cp4.1LG03g10150.1 Cpe03g01499 1499
3 11822114 11826068 + Cp4.1LG03g10030.1 Cpe03g01501 1501
8 2014220 2019012 + Cp4.1LG08g03550.1 Cpe08g00319 319
12 964195 965799 + Cp4.1LG12g01440.1 Cpe12g00150 150
17 1184271 1185938 - Cp4.1LG17g01860.1 Cpe17g00184 184
5 4829267 4835033 + CrPI670011_05g005460.1 Cre05g0546 546
5 4863032 4866421 - CrPI670011_05g005490.1 Cre05g0549 549
5 4900842 4901420 - CrPI670011_05g005510.1 Cre05g0551 551
5 4904613 4906265 - CrPI670011_05g005520.1 Cre05g0552 552
6 8671485 8673017 + CrPI670011_06g014330.1 Cre06g1433 1433
6 8717930 8727443 - CrPI670011_06g014380.1 Cre06g1438 1438
2 10537977 10539722 + CsaV3_2G012960.1 Csa02g01080 1080
3 9475809 9481494 + CsaV3_3G012370.1 Csa03g01237 1237
3 9500060 9505354 - CsaV3_3G012390.1 Csa03g01239 1239
3 9528332 9529772 - CsaV3_3G012410.1 Csa03g01241 1241
3 9531131 9533457 - CsaV3_3G012420.1 Csa03g01242 1242
3 9534685 9540217 - CsaV3_3G012430.1 Csa03g01243 1243
3 3455355 3458283 - Hsped.03g02640.1 Hepe03g0264 264
12 39086047 39087792 + Lag0016569.1 Lac12g2197 2197
13 3945977 3947722 - Maker00023969 Lcy13g0353 353
5 24479118 24480722 + Lsi05G016930.1 Lsi05g01693 1693
5 24483621 24484187 + Lsi05G016940.1 Lsi05g01694 1694
5 24521450 24525357 + Lsi05G016960.1 Lsi05g01696 1696
5 24548561 24554684 - Lsi05G016990.1 Lsi05g01699 1699
9 20178244 20179989 + Lsi09G012500.1 Lsi09g01250 1250
9 20212599 20214155 - Lsi09G012550.1 Lsi09g01255 1255
4 34313934 34316555 - Sed0013172.2 Sed04g1971 1971
6 76811411 76814654 + Tan0003228.2 Tan06g2433 2433
5 7032951 7035431 + Vvi5g639 Vvi5g639 639
5 7052204 7076037 + Vvi5g640 Vvi5g640 640
5 7076728 7078360 + Vvi5g641 Vvi5g641 641
5 7082503 7083190 + Vvi5g642 Vvi5g642 642
5 7094696 7095305 + Vvi5g643 Vvi5g643 643
5 7139728 7144533 + Vvi5g644 Vvi5g644 644
5 7174675 7177875 - Vvi5g645 Vvi5g645 645
5 7189686 7189941 + Vvi5g646 Vvi5g646 646
5 7206104 7216168 - Vvi5g647 Vvi5g647 647
5 7221873 7236640 - Vvi5g648 Vvi5g648 648
       

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