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
Vvi2g492 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g493 . . . . . . . Bma14g00032 . . . . . Car15g01045 . . . . . . . . . . . . . . . . . . . . . . . . . Blo03g00405 . Bda07g00011 . . . . . . . . . . . . . Cpe13g00216 Bhi12g00403 . . Lac11g2248 Hepe06g1650 . Lcy12g1795 . . . . . . . Lsi09g00394 . . Cme09g01649
Vvi2g494 . . . . . . . . . . . Cma15g01150 . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00394 Chy09g01119 . . . . . . Bpe11g00258 . . . . Cmo15g01210 . . . . . Cpe13g00218 Bhi12g00404 . . . . . . Cla01g00366 Cam01g0387 Cec01g0380 Cco01g0398 Clacu01g0386 Cmu01g0367 Cre09g2143 Lsi09g00396 . . .
Vvi2g495 Blo02g01054 . Bda06g00039 Bda08g00564 Bpe05g00592 Bpe07g00159 . Bma14g00033 Cmo06g00784 . . Cma15g01149 . Car15g01044 . . . . . . . . . . Cla10g00285 Cam10g0296 Cec10g0303 Cco10g0299 Clacu10g0295 Cmu10g1134 Cre10g0542 . . Cone6ag0698 Cone9ag0698 Lsi07g01331 Csa05g00395 Chy09g01118 Cme06g02614 Blo03g00407 . Bda07g00010 . . Bpe11g00259 . . . . Cmo15g01209 Cma06g00763 . Car06g00681 . Cpe08g00754 Cpe13g00219 Bhi12g00406 . . . . . Lcy12g1797 Cla01g00368 Cam01g0388 Cec01g0381 Cco01g0399 Clacu01g0387 Cmu01g0368 Cre09g2142 Lsi09g00397 Csa03g00304 Chy06g02018 Cme09g01648
Vvi2g496 . . . . . . Bma07g01605 . . . . Cma15g01148 . Car15g01043 . . . . . . . . . . . . . . . . . . . . . . Csa05g00396 Chy09g01117 . . Blo19g00222 . Bda09g00089 Bpe08g01440 . . . . . Cmo15g01208 . . . . . Cpe13g00220 . . . . . . . Cla01g00369 Cam01g0389 Cec01g0382 Cco01g0400 Clacu01g0388 Cmu01g0369 Cre09g2141 Lsi09g00399 . . Cme09g01647
Vvi2g497 . . . . . . Bma07g01603 Bma14g00034 . . . Cma15g01147 . Car15g01042 . . . . . . . . . . . . . . . . . . . Cone6ag0697 Cone9ag0697 . Csa05g00397 Chy09g01116 . Blo03g00409 . Bda07g00008 Bda09g00090 Bpe08g01439 Bpe11g00261 . . . . Cmo15g01207 . . . . . Cpe13g00221 Bhi12g00407 . . . . . Lcy12g1799 Cla01g00371 Cam01g0390 . Cco01g0401 Clacu01g0390 Cmu01g0371 Cre09g2140 Lsi09g00400 . . Cme09g01646
Vvi2g498 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00398 Chy09g01115 . . Blo19g00230 . Bda09g00091 Bpe08g01438 . . . . . . . . . . . . Bhi12g00411 . . . . . Lcy12g1800 Cla01g00372 Cam01g0391 Cec01g0383 Cco01g0403 Clacu01g0391 Cmu01g0372 Cre09g2139 Lsi09g00401 . . Cme09g01645
Vvi2g499 . Blo03g00173 Bda06g01308 . . Bpe07g00160 . . Cmo06g00785 Cmo16g01108 . . . . . Cpe14g00877 . . . . . . . . Cla10g00284 Cam10g0295 Cec10g0302 Cco10g0298 Clacu10g0294 Cmu10g1133 Cre10g0541 . . . . Lsi07g01330 . . Cme06g02612 . . . . . . Bma05g00775 . . . . Cma06g00764 Cma16g01058 Car06g00683 Car16g01007 Cpe08g00753 . . . . . . . . . . . . . . . . Csa03g00303 Chy06g02019 .
Vvi2g500 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g501 . Blo03g00172 Bda06g00038 . . Bpe07g00161 . . Cmo06g00786 . . . . . . . . . . . . . . . Cla10g00283 Cam10g0294 Cec10g0301 Cco10g0297 Clacu10g0293 Cmu10g1132 Cre10g0540 . . . . Lsi07g01328 . . Cme06g02611 . . . . . . Bma05g00774 Bma12g00152 . . . Cma06g00766 . Car06g00684 . Cpe08g00752 . . . . . . . . . . . . . . . . Csa03g00302 Chy06g02020 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 378972 380302 - Bda023207.1 Bda06g00038 38
6 403357 404932 - Bda023208.1 Bda06g00039 39
6 43745786 43748697 + Bda023162.1 Bda06g01308 1308
7 127083 130095 - Bda025054.1 Bda07g00008 8
7 155652 157942 - Bda025057.1 Bda07g00010 10
7 169022 173788 + Bda025058.1 Bda07g00011 11
8 5726069 5727995 + Bda029023.1 Bda08g00564 564
9 1759852 1763028 - Bda034073 Bda09g00089 89
9 1780176 1781544 - Bda030625.1 Bda09g00090 90
9 1784456 1788339 - Bda030626.1 Bda09g00091 91
12 13595782 13599449 - XM_039020057.1 Bhi12g00403 403
12 13595782 13599294 - XM_039020060.1 Bhi12g00404 404
12 13603558 13606650 - XM_039051060.1 Bhi12g00406 406
12 13679127 13682608 - XM_039050841.1 Bhi12g00407 407
12 13733133 13736945 - XM_039050964.1 Bhi12g00411 411
2 40693906 40695801 - BLOR10784 Blo02g01054 1054
3 4334843 4336171 - BLOR11353 Blo03g00172 172
3 4345450 4350005 + BLOR11354 Blo03g00173 173
3 11070346 11087757 - BLOR11586 Blo03g00405 405
3 11414194 11416202 + BLOR11588 Blo03g00407 407
3 11590687 11594919 - BLOR11590 Blo03g00409 409
19 11149334 11157486 - BLOR09565 Blo19g00222 222
19 11442973 11451967 - BLOR09573 Blo19g00230 230
5 44614731 44616077 - Bma021874.1 Bma05g00774 774
5 44677916 44687413 + Bma021875.1 Bma05g00775 775
7 51356653 51461570 + Bma031413 Bma07g01603 1603
7 51465522 51468708 + Bma026901.1 Bma07g01605 1605
12 2174848 2176176 + Bma007032.1 Bma12g00152 152
14 410642 412271 - Bma030631 Bma14g00032 32
14 456429 458644 + Bma010441.1 Bma14g00033 33
14 474945 478065 + Bma010442.1 Bma14g00034 34
5 19976884 19978803 - Bpe018009.1 Bpe05g00592 592
7 1098565 1100249 + Bpe020969.1 Bpe07g00159 159
7 1102763 1105001 - Bpe020970.1 Bpe07g00160 160
7 1110353 1111681 + Bpe020971.1 Bpe07g00161 161
8 15131502 15135229 + Bpe023552.1 Bpe08g01438 1438
8 15139227 15141969 + Bpe023553.1 Bpe08g01439 1439
8 15146426 15149737 + Bpe023554.1 Bpe08g01440 1440
11 1864623 1871382 - Bpe003634.1 Bpe11g00258 258
11 1881777 1883932 + Bpe003635.1 Bpe11g00259 259
11 1894621 1897820 + Bpe003637.1 Bpe11g00261 261
1 4266257 4270084 - CaPI482276_01g003870.1 Cam01g0387 387
1 4275557 4278084 - CaPI482276_01g003880.1 Cam01g0388 388
1 4291605 4295449 - CaPI482276_01g003890.1 Cam01g0389 389
1 4308899 4311729 - CaPI482276_01g003900.1 Cam01g0390 390
1 4316997 4328251 - CaPI482276_01g003910.1 Cam01g0391 391
10 5065662 5067032 - CaPI482276_10g002940.1 Cam10g0294 294
10 5092624 5095985 + CaPI482276_10g002950.1 Cam10g0295 295
10 5098968 5103204 - CaPI482276_10g002960.1 Cam10g0296 296
6 4056093 4057992 + Carg21601-RA Car06g00681 681
6 4059968 4062210 - Carg21599-RA Car06g00683 683
6 4069037 4070404 + Carg21598-RA Car06g00684 684
15 8205135 8208273 + Carg27387-RA Car15g01042 1042
15 8213450 8218445 + Carg27386-RA Car15g01043 1043
15 8220769 8222486 - Carg27385-RA Car15g01044 1044
15 8227359 8230599 + Carg27383-RA Car15g01045 1045
16 8560264 8563147 - Carg23211-RA Car16g01007 1007
1 3942885 3948683 - CcPI632755_01g003980.1 Cco01g0398 398
1 3954180 3956647 - CcPI632755_01g003990.1 Cco01g0399 399
1 3970037 3973884 - CcPI632755_01g004000.1 Cco01g0400 400
1 3986057 3988888 - CcPI632755_01g004010.1 Cco01g0401 401
1 3998928 4005932 - CcPI632755_01g004030.1 Cco01g0403 403
10 3527576 3529114 - CcPI632755_10g002970.1 Cco10g0297 297
10 3546176 3548945 + CcPI632755_10g002980.1 Cco10g0298 298
10 3552306 3556504 - CcPI632755_10g002990.1 Cco10g0299 299
1 3953340 3956751 - CePI673135_01g003800.1 Cec01g0380 380
1 3962653 3965296 - CePI673135_01g003810.1 Cec01g0381 381
1 3978358 3982259 - CePI673135_01g003820.1 Cec01g0382 382
1 3993337 4013173 - CePI673135_01g003830.1 Cec01g0383 383
10 3696432 3697802 - CePI673135_10g003010.1 Cec10g0301 301
10 3714334 3717692 + CePI673135_10g003020.1 Cec10g0302 302
10 3720703 3724948 - CePI673135_10g003030.1 Cec10g0303 303
6 24129827 24134466 + Chy6G125460.1 Chy06g02018 2018
6 24136292 24138656 - Chy6G125470.1 Chy06g02019 2019
6 24151191 24152549 + Chy6G125480.1 Chy06g02020 2020
9 13406320 13410127 + Chy9G168310.1 Chy09g01115 1115
9 13412783 13415561 + Chy9G168320.1 Chy09g01116 1116
9 13423932 13427743 + Chy9G168330.1 Chy09g01117 1117
9 13448472 13450106 + Chy9G168340.1 Chy09g01118 1118
9 13454895 13459518 + Chy9G168350.1 Chy09g01119 1119
1 3906341 3910124 - ClG42_01g0038600.10 Clacu01g0386 386
1 3915633 3918177 - ClG42_01g0038700.10 Clacu01g0387 387
1 3931609 3935457 - ClG42_01g0038800.10 Clacu01g0388 388
1 3948821 3951659 - ClG42_01g0039000.10 Clacu01g0390 390
1 3956970 3968230 - ClG42_01g0039100.10 Clacu01g0391 391
10 3826217 3827587 - ClG42_10g0029300.10 Clacu10g0293 293
10 3843260 3846639 + ClG42_10g0029400.10 Clacu10g0294 294
10 3849611 3853716 - ClG42_10g0029500.10 Clacu10g0295 295
1 4033588 4037191 - ClCG01G003790.1 Cla01g00366 366
1 4042952 4045698 - ClCG01G003810.2 Cla01g00368 368
1 4059241 4063590 - ClCG01G003820.1 Cla01g00369 369
1 4078625 4081463 - ClCG01G003840.2 Cla01g00371 371
1 4091728 4107757 - ClCG01G003850.2 Cla01g00372 372
10 3732264 3735721 - ClCG10G002980.2 Cla10g00283 283
10 3750012 3752993 + ClCG10G002990.1 Cla10g00284 284
10 3758007 3762131 - ClCG10G003000.2 Cla10g00285 285
6 3875334 3877797 + CmaCh06G007630.1 Cma06g00763 763
6 3878314 3881576 - CmaCh06G007640.1 Cma06g00764 764
6 3888515 3890086 + CmaCh06G007660.1 Cma06g00766 766
15 7291104 7294401 + CmaCh15G011470.1 Cma15g01147 1147
15 7299986 7305294 + CmaCh15G011480.1 Cma15g01148 1148
15 7308199 7310013 - CmaCh15G011490.1 Cma15g01149 1149
15 7315280 7318502 + CmaCh15G011500.1 Cma15g01150 1150
16 8103258 8105523 - CmaCh16G010580.1 Cma16g01058 1058
6 33353853 33355454 - MELO3C013968.2.1 Cme06g02611 2611
6 33362898 33369525 + MELO3C013969.2.1 Cme06g02612 2612
6 33374327 33375436 - MELO3C032275.2.1 Cme06g02614 2614
9 21176913 21182298 + MELO3C005559.2.1 Cme09g01645 1645
9 21185515 21188314 + MELO3C005560.2.1 Cme09g01646 1646
9 21194490 21199222 + MELO3C005561.2.1 Cme09g01647 1647
9 21213884 21215442 + MELO3C000087.2.1 Cme09g01648 1648
9 21220559 21225495 + MELO3C005562.2.1 Cme09g01649 1649
6 4096291 4098688 + CmoCh06G007840.1 Cmo06g00784 784
6 4099984 4106590 - CmoCh06G007850.1 Cmo06g00785 785
6 4109778 4111145 + CmoCh06G007860.1 Cmo06g00786 786
15 8366832 8370085 + CmoCh15G012070.1 Cmo15g01207 1207
15 8374274 8381082 + CmoCh15G012080.1 Cmo15g01208 1208
15 8382484 8384352 - CmoCh15G012090.1 Cmo15g01209 1209
15 8389329 8392631 + CmoCh15G012100.1 Cmo15g01210 1210
16 7823738 7829820 - CmoCh16G011080.1 Cmo16g01108 1108
1 3853181 3856959 - CmPI595203_01g003670.1 Cmu01g0367 367
1 3862439 3865524 - CmPI595203_01g003680.1 Cmu01g0368 368
1 3878390 3882236 - CmPI595203_01g003690.1 Cmu01g0369 369
1 3895583 3898421 - CmPI595203_01g003710.1 Cmu01g0371 371
1 3903738 3915007 - CmPI595203_01g003720.1 Cmu01g0372 372
10 3943220 3944590 - CmPI595203_10g011320.1 Cmu10g1132 1132
10 3960277 3963655 + CmPI595203_10g011330.1 Cmu10g1133 1133
10 3966563 3970761 - CmPI595203_10g011340.1 Cmu10g1134 1134
6 3525340 3528611 + Conep06aG0071900.1 Cone6ag0697 697
6 3531312 3533667 - Conep06aG0072000.1 Cone6ag0698 698
9 3350702 3354024 + Conep09aG0071400.1 Cone9ag0697 697
9 3356189 3358563 - Conep09aG0071500.1 Cone9ag0698 698
8 6056643 6058010 - Cp4.1LG08g07590.1 Cpe08g00752 752
8 6061781 6068844 + Cp4.1LG08g07510.1 Cpe08g00753 753
8 6069752 6071866 - Cp4.1LG08g07580.1 Cpe08g00754 754
13 1640165 1649356 - Cp4.1LG13g02210.1 Cpe13g00216 216
13 1649452 1652175 - Cp4.1LG13g02190.1 Cpe13g00218 218
13 1656187 1659056 + Cp4.1LG13g02080.1 Cpe13g00219 219
13 1663321 1668305 - Cp4.1LG13g02170.1 Cpe13g00220 220
13 1673392 1676933 - Cp4.1LG13g02180.1 Cpe13g00221 221
14 7238298 7244231 - Cp4.1LG14g08720.1 Cpe14g00877 877
9 40385743 40397254 + CrPI670011_09g021390.1 Cre09g2139 2139
9 40402492 40405354 + CrPI670011_09g021400.1 Cre09g2140 2140
9 40418853 40422688 + CrPI670011_09g021410.1 Cre09g2141 2141
9 40436043 40438599 + CrPI670011_09g021420.1 Cre09g2142 2142
9 40444545 40447949 + CrPI670011_09g021430.1 Cre09g2143 2143
10 4909765 4911135 - CrPI670011_10g005400.1 Cre10g0540 540
10 4928361 4931153 + CrPI670011_10g005410.1 Cre10g0541 541
10 4934869 4939076 - CrPI670011_10g005420.1 Cre10g0542 542
3 2564419 2565789 - CsaV3_3G003020.1 Csa03g00302 302
3 2571978 2578551 + CsaV3_3G003030.1 Csa03g00303 303
3 2578889 2583619 - CsaV3_3G003040.1 Csa03g00304 304
5 2552283 2557174 - CsaV3_5G003940.1 Csa05g00394 394
5 2561275 2563717 - CsaV3_5G003950.1 Csa05g00395 395
5 2572766 2577427 - CsaV3_5G003960.1 Csa05g00396 396
5 2583915 2587420 - CsaV3_5G003970.1 Csa05g00397 397
5 2589193 2593519 - CsaV3_5G003980.1 Csa05g00398 398
6 67382396 67391190 - Hsped.06g16500.1 Hepe06g1650 1650
11 38520846 38524138 - Lag0032886.1 Lac11g2248 2248
12 39007454 39009332 - Maker00038144 Lcy12g1795 1795
12 39024582 39027061 + Maker00038293 Lcy12g1797 1797
12 39049175 39054022 - Maker00037847 Lcy12g1799 1799
12 39057401 39061935 - Maker00038209 Lcy12g1800 1800
7 19445238 19448277 - Lsi07G013280.1 Lsi07g01328 1328
7 19463459 19466368 + Lsi07G013300.1 Lsi07g01330 1330
7 19473302 19480706 - Lsi07G013310.1 Lsi07g01331 1331
9 4160075 4161433 - Lsi09G003940.1 Lsi09g00394 394
9 4163248 4164486 - Lsi09G003960.1 Lsi09g00396 396
9 4170250 4173265 - Lsi09G003970.1 Lsi09g00397 397
9 4204472 4209101 - Lsi09G003990.1 Lsi09g00399 399
9 4221114 4225034 - Lsi09G004000.1 Lsi09g00400 400
9 4229949 4234394 - Lsi09G004010.1 Lsi09g00401 401
2 4841364 4841723 - Vvi2g492 Vvi2g492 492
2 4846173 4851433 - Vvi2g493 Vvi2g493 493
2 4851662 4855934 - Vvi2g494 Vvi2g494 494
2 4861964 4864774 + Vvi2g495 Vvi2g495 495
2 4870556 4875422 - Vvi2g496 Vvi2g496 496
2 4882098 4884289 - Vvi2g497 Vvi2g497 497
2 4887317 4897426 - Vvi2g498 Vvi2g498 498
2 4898033 4901145 - Vvi2g499 Vvi2g499 499
2 4914167 4914984 + Vvi2g500 Vvi2g500 500
2 4921779 4923609 + Vvi2g501 Vvi2g501 501
       

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