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
Vvi5g729 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0157 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g730 . . . . . Bpe14g01263 . . . . Cma06g01315 . Car06g01130 Car14g01631 . Cpe08g00340 Cpe03g01523 Bhi01g00717 . . . Hepe05g1665 . . Cla06g00677 Cam06g0727 Cec06g0735 Cco06g0744 Clacu06g0719 Cmu06g0703 Cre06g1475 . . Cone7ag0331 Cone4ag0336 Lsi05g01742 Csa02g01049 Chy05g00311 Cme06g00480 . Blo07g00270 Bda11g00638 Bda13g00056 . Bpe13g00551 Bma02g00768 Bma06g01605 Sed02g1415 Cmo06g01323 Cmo14g01859 . . Car08g00948 Car17g00136 Cpe12g00131 Cpe17g00202 Bhi12g01601 Tan06g2396 Cmetu06g1413 . . . Lcy13g0388 Cla05g00436 Cam05g0475 Cec05g0484 Cco05g0484 Clacu05g0472 Cmu05g0450 Cre05g0512 Lsi09g01222 Csa03g01198 Chy06g00462 Cme05g00582
Vvi5g731 Blo01g00274 Blo12g00152 Bda03g01076 . Bpe04g00999 . Bma04g00990 Bma05g01219 . . . Cma14g01820 . Car14g01632 . . Cpe03g01524 Bhi01g00714 . . . Hepe05g1666 . . . . . . . . . Cone14ag0159 Cone15ag0170 . . Lsi05g01743 . . Cme06g00479 . . Bda11g00639 . Bpe05g01074 Bpe13g00550 . Bma06g01606 . . Cmo14g01860 . . . . . . . . . . . . . Cla05g00435 Cam05g0473 Cec05g0482 Cco05g0482 Clacu05g0470 Cmu05g0448 Cre05g0510 . Csa03g01197 Chy06g00461 .
Vvi5g732 . . . . . Bpe14g01264 . . . . Cma06g01314 Cma14g01821 Car06g01128 Car14g01633 . Cpe08g00341 Cpe03g01525 Bhi01g00713 . . . Hepe05g1667 . . . . . . . . . Cone14ag0160 Cone15ag0171 Cone7ag0332 Cone4ag0337 Lsi05g01744 . . Cme06g00478 Blo02g00752 Blo07g00271 . Bda13g00054 . . Bma02g00767 . . . Cmo14g01861 . . . . . . . . . . . . . Cla05g00434 Cam05g0472 Cec05g0481 Cco05g0481 Clacu05g0469 Cmu05g0447 Cre05g0509 . Csa03g01196 Chy06g00460 .
Vvi5g733 . . . . . . . . . . Cma06g01313 Cma14g01822 Car06g01127 Car14g01635 . Cpe08g00342 . Bhi01g00711 . . . Hepe05g1668 . . . . . . . . . . . . . Lsi05g01745 . . . . . . . . . . . . Cmo06g01321 Cmo14g01862 . . . . . . . . . . . . . . . . . . . . . Csa03g01195 Chy06g00459 .
Vvi5g734 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma02g00766 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g735 . . . . . Bpe14g01265 . . Cmo08g01050 Cmo17g00152 . . . . . . . . . . . . . . . . . . . . . Cone14ag0161 Cone15ag0172 . Cone4ag0340 . Csa02g01048 . . Blo02g00696 . . Bda13g00053 . . . . Sed09g0662 . . Cma08g01075 Cma17g00153 Car08g00947 Car17g00135 Cpe12g00130 Cpe17g00203 Bhi12g01600 Tan06g2394 Cmetu05g0124 . . . Lcy13g0389 . . . . . . . . . . Cme05g00583
Vvi5g736 . . . . . Bpe14g01266 . . . . Cma06g01312 . Car06g01126 . . Cpe08g00343 . Bhi01g00710 . . . Hepe05g1669 . . . . . . . . . . . Cone7ag0334 Cone4ag0341 Lsi05g01746 . . Cme06g00476 Blo02g00754 Blo07g00272 . Bda13g00052 . Bpe13g00548 Bma02g00765 . . Cmo06g01320 . . . . . . . . . . . . . . Cla05g00432 Cam05g0470 Cec05g0479 Cco05g0479 Clacu05g0467 Cmu05g0446 Cre05g0507 . Csa03g01194 Chy06g00458 .
Vvi5g737 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g738 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 10811009 10812454 - Bda017120.1 Bda03g01076 1076
11 6366340 6367764 - Bda033045 Bda11g00638 638
11 6368547 6369038 + Bda033046 Bda11g00639 639
13 751909 754241 + Bda032831 Bda13g00052 52
13 763157 763969 + Bda000898.1 Bda13g00053 53
13 766275 768795 - Bda000899.1 Bda13g00054 54
13 823725 825183 + Bda032832 Bda13g00056 56
1 13256437 13258896 + XM_039044059.1 Bhi01g00710 710
1 13259123 13260265 - XM_039044078.1 Bhi01g00711 711
1 13262175 13265396 - XM_039022307.1 Bhi01g00713 713
1 13270736 13271901 - XM_039022578.1 Bhi01g00714 714
1 13360612 13362452 + XM_039024523.1 Bhi01g00717 717
12 51957490 51961199 + XM_039051095.1 Bhi12g01600 1600
12 51963111 51964743 + XM_039050866.1 Bhi12g01601 1601
1 3466377 3472233 + BLOR00274 Blo01g00274 274
2 21029835 21032933 - BLOR10426 Blo02g00696 696
2 25002134 25005740 + BLOR10482 Blo02g00752 752
2 25048909 25051172 - BLOR10484 Blo02g00754 754
7 3210296 3212554 - BLOR18202 Blo07g00270 270
7 3215828 3219373 + BLOR18203 Blo07g00271 271
7 3220883 3222585 - BLOR18204 Blo07g00272 272
12 10397772 10406445 + BLOR04171 Blo12g00152 152
2 39713435 39715694 + Bma030900 Bma02g00765 765
2 39716341 39719957 + Bma015476.1 Bma02g00766 766
2 39721029 39723772 - Bma015477.1 Bma02g00767 767
2 39731057 39732637 + Bma015478.1 Bma02g00768 768
4 16103766 16105207 - Bma019595.1 Bma04g00990 990
5 51616794 51618121 + Bma022410.1 Bma05g01219 1219
6 52226733 52228152 - Bma031338 Bma06g01605 1605
6 52229117 52229612 + Bma024720.1 Bma06g01606 1606
4 6971553 6973075 + Bpe015665.1 Bpe04g00999 999
5 23253860 23255217 + Bpe018489.1 Bpe05g01074 1074
13 12743706 12745570 + Bpe010251.1 Bpe13g00548 548
13 12753118 12753694 - Bpe010253.1 Bpe13g00550 550
13 12754522 12755979 + Bpe010254.1 Bpe13g00551 551
14 9535011 9538435 - Bpe014622.1 Bpe14g01263 1263
14 9547925 9550676 + Bpe014623.1 Bpe14g01264 1264
14 9551757 9555394 - Bpe014624.1 Bpe14g01265 1265
14 9556028 9558349 - Bpe014625.1 Bpe14g01266 1266
5 4198137 4199778 + CaPI482276_05g004700.1 Cam05g0470 470
5 4203715 4206669 - CaPI482276_05g004720.1 Cam05g0472 472
5 4213967 4214770 - CaPI482276_05g004730.1 Cam05g0473 473
5 4223205 4224746 + CaPI482276_05g004750.1 Cam05g0475 475
6 9828987 9835983 - CaPI482276_06g007270.1 Cam06g0727 727
6 8411955 8413616 + Carg06231-RA Car06g01126 1126
6 8414342 8416579 - Carg06230-RA Car06g01127 1127
6 8417357 8421045 - Carg06229-RA Car06g01128 1128
6 8425250 8427481 + Carg06227-RA Car06g01130 1130
8 6337364 6340526 + Carg10976-RA Car08g00947 947
8 6342671 6344434 + Carg10975-RA Car08g00948 948
14 13095919 13100627 - Carg16556-RA Car14g01631 1631
14 13102251 13102765 + Carg16555-RA Car14g01632 1632
14 13104087 13107524 + Carg16554-RA Car14g01633 1633
14 13108052 13109893 + Carg16552-RA Car14g01635 1635
17 827466 831338 + Carg10097-RA Car17g00135 135
17 832421 834046 + Carg10096-RA Car17g00136 136
5 3861998 3863640 + CcPI632755_05g004790.1 Cco05g0479 479
5 3867657 3870403 - CcPI632755_05g004810.1 Cco05g0481 481
5 3876429 3878054 - CcPI632755_05g004820.1 Cco05g0482 482
5 3886564 3888103 + CcPI632755_05g004840.1 Cco05g0484 484
6 8473333 8476700 - CcPI632755_06g007440.1 Cco06g0744 744
5 3852997 3854639 + CePI673135_05g004790.1 Cec05g0479 479
5 3858666 3861414 - CePI673135_05g004810.1 Cec05g0481 481
5 3868815 3869598 - CePI673135_05g004820.1 Cec05g0482 482
5 3878538 3880084 + CePI673135_05g004840.1 Cec05g0484 484
6 8511126 8511413 - CePI673135_06g007350.1 Cec06g0735 735
5 3085292 3090851 + Chy5G093570.1 Chy05g00311 311
6 3073182 3074803 + Chy6G109860.1 Chy06g00458 458
6 3075672 3076619 - Chy6G109870.1 Chy06g00459 459
6 3078367 3081355 - Chy6G109880.1 Chy06g00460 460
6 3084699 3085269 - Chy6G109890.1 Chy06g00461 461
6 3089464 3094116 + Chy6G109900.1 Chy06g00462 462
5 3906682 3908324 + ClG42_05g0046700.10 Clacu05g0467 467
5 3912267 3914999 - ClG42_05g0046900.10 Clacu05g0469 469
5 3922415 3923224 - ClG42_05g0047000.10 Clacu05g0470 470
5 3931583 3933117 + ClG42_05g0047200.10 Clacu05g0472 472
6 8389403 8392766 - ClG42_06g0071900.10 Clacu06g0719 719
5 3882203 3884449 + ClCG05G004210.1 Cla05g00432 432
5 3889354 3896230 - ClCG05G004230.2 Cla05g00434 434
5 3899799 3900666 - ClCG05G004240.1 Cla05g00435 435
5 3907219 3912501 + ClCG05G004250.2 Cla05g00436 436
6 8585807 8593412 - ClCG06G007100.2 Cla06g00677 677
6 8675049 8677252 + CmaCh06G013120.1 Cma06g01312 1312
6 8678011 8679676 - CmaCh06G013130.1 Cma06g01313 1313
6 8679798 8684396 - CmaCh06G013140.1 Cma06g01314 1314
6 8685219 8691899 + CmaCh06G013150.1 Cma06g01315 1315
8 6696503 6703040 + CmaCh08G010750.1 Cma08g01075 1075
14 13030295 13031004 + CmaCh14G018200.1 Cma14g01820 1820
14 13032158 13035597 + CmaCh14G018210.1 Cma14g01821 1821
14 13036299 13037831 + CmaCh14G018220.1 Cma14g01822 1822
17 769429 776079 + CmaCh17G001530.1 Cma17g00153 153
5 5911383 5912882 - MELO3C023012.2.1 Cme05g00582 582
5 5914591 5918441 - MELO3C023013.2.1 Cme05g00583 583
6 3017859 3020484 + MELO3C006407.2.1 Cme06g00476 476
6 3022967 3026607 - MELO3C006409.2.1 Cme06g00478 478
6 3029851 3030670 - MELO3C006410.2.1 Cme06g00479 479
6 3037003 3038926 + MELO3C006412.2.1 Cme06g00480 480
5 18063253 18066529 + PI0011420.1 Cmetu05g0124 124
6 3266297 3271441 + PI0022036.1 Cmetu06g1413 1413
6 9864058 9868059 + CmoCh06G013200.1 Cmo06g01320 1320
6 9867219 9873560 - CmoCh06G013210.1 Cmo06g01321 1321
6 9878155 9879380 + CmoCh06G013230.1 Cmo06g01323 1323
8 6775393 6780953 + CmoCh08G010500.1 Cmo08g01050 1050
14 14012755 14015142 - CmoCh14G018590.1 Cmo14g01859 1859
14 14017361 14018188 + CmoCh14G018600.1 Cmo14g01860 1860
14 14019754 14022739 + CmoCh14G018610.1 Cmo14g01861 1861
14 14023227 14024723 + CmoCh14G018620.1 Cmo14g01862 1862
17 867353 873968 + CmoCh17G001520.1 Cmo17g00152 152
5 3742804 3744446 + CmPI595203_05g004460.1 Cmu05g0446 446
5 3745308 3751110 - CmPI595203_05g004470.1 Cmu05g0447 447
5 3758523 3759332 - CmPI595203_05g004480.1 Cmu05g0448 448
5 3767750 3769284 + CmPI595203_05g004500.1 Cmu05g0450 450
6 8198136 8205047 - CmPI595203_06g007030.1 Cmu06g0703 703
4 1558434 1560086 - Conep04aG0034800.1 Cone4ag0336 336
4 1560257 1561792 + Conep04aG0034900.1 Cone4ag0337 337
4 1565034 1566716 - Conep04aG0035200.1 Cone4ag0340 340
4 1567139 1569224 - Conep04aG0035300.1 Cone4ag0341 341
7 1448136 1449980 - Conep07aG0033900.1 Cone7ag0331 331
7 1450136 1451890 + Conep07aG0034000.1 Cone7ag0332 332
7 1457077 1459125 - Conep07aG0034200.1 Cone7ag0334 334
14 767910 771202 + Conep14aG0016100.1 Cone14ag0157 157
14 772061 772516 + Conep14aG0016300.1 Cone14ag0159 159
14 772811 774898 + Conep14aG0016400.1 Cone14ag0160 160
14 775053 777957 - Conep14aG0016500.1 Cone14ag0161 161
15 822063 822455 + Conep15aG0017400.1 Cone15ag0170 170
15 825099 827222 + Conep15aG0017500.1 Cone15ag0171 171
15 827359 830411 - Conep15aG0017600.1 Cone15ag0172 172
3 11911539 11914196 - Cp4.1LG03g09780.1 Cpe03g01523 1523
3 11915720 11916591 + Cp4.1LG03g09850.1 Cpe03g01524 1524
3 11917767 11921332 + Cp4.1LG03g09840.1 Cpe03g01525 1525
8 2117288 2123635 - Cp4.1LG08g03320.1 Cpe08g00340 340
8 2124061 2127542 + Cp4.1LG08g03340.1 Cpe08g00341 341
8 2128775 2130111 + Cp4.1LG08g03380.1 Cpe08g00342 342
8 2131453 2133932 - Cp4.1LG08g03300.1 Cpe08g00343 343
12 825503 829707 + Cp4.1LG12g01290.1 Cpe12g00130 130
12 830458 832122 + Cp4.1LG12g01270.1 Cpe12g00131 131
17 1309079 1311240 - Cp4.1LG17g02270.1 Cpe17g00202 202
17 1312524 1316530 - Cp4.1LG17g02250.1 Cpe17g00203 203
5 4538585 4540862 + CrPI670011_05g005070.1 Cre05g0507 507
5 4544178 4546928 - CrPI670011_05g005090.1 Cre05g0509 509
5 4554365 4555144 - CrPI670011_05g005100.1 Cre05g0510 510
5 4563618 4565134 + CrPI670011_05g005120.1 Cre05g0512 512
6 9306389 9311017 - CrPI670011_06g014750.1 Cre06g1475 1475
2 10183474 10187261 + CsaV3_2G012640.1 Csa02g01048 1048
2 10187951 10189692 + CsaV3_2G012650.1 Csa02g01049 1049
3 9253257 9255819 + CsaV3_3G011940.1 Csa03g01194 1194
3 9255512 9257320 - CsaV3_3G011950.1 Csa03g01195 1195
3 9258369 9262193 - CsaV3_3G011960.1 Csa03g01196 1196
3 9265117 9266412 - CsaV3_3G011970.1 Csa03g01197 1197
3 9269829 9274896 + CsaV3_3G011980.1 Csa03g01198 1198
5 66526238 66528320 - Hsped.05g16650.1 Hepe05g1665 1665
5 66551774 66553209 + Hsped.05g16660.1 Hepe05g1666 1666
5 66561813 66565542 + Hsped.05g16670.1 Hepe05g1667 1667
5 66566722 66568857 + Hsped.05g16680.1 Hepe05g1668 1668
5 66569641 66571639 - Hsped.05g16690.1 Hepe05g1669 1669
13 4421254 4423539 - Maker00023837 Lcy13g0388 388
13 4426591 4430264 - Maker00023919 Lcy13g0389 389
5 24827289 24829679 - Lsi05G017420.1 Lsi05g01742 1742
5 24833589 24835297 + Lsi05G017430.1 Lsi05g01743 1743
5 24840392 24844001 + Lsi05G017440.1 Lsi05g01744 1744
5 24845470 24847117 + Lsi05G017450.1 Lsi05g01745 1745
5 24847239 24849659 - Lsi05G017460.1 Lsi05g01746 1746
9 19641710 19649810 + Lsi09G012220.1 Lsi09g01222 1222
2 50321277 50322706 - Sed0018658.1 Sed02g1415 1415
9 8690095 8694737 - Sed0025447.1 Sed09g0662 662
6 76241428 76244877 + Tan0002942.1 Tan06g2394 2394
6 76256341 76257600 + Tan0004006.1 Tan06g2396 2396
5 8545811 8546558 + Vvi5g729 Vvi5g729 729
5 8549657 8553417 - Vvi5g730 Vvi5g730 730
5 8586197 8587539 + Vvi5g731 Vvi5g731 731
5 8594493 8604824 + Vvi5g732 Vvi5g732 732
5 8606636 8607245 + Vvi5g733 Vvi5g733 733
5 8609832 8611014 - Vvi5g734 Vvi5g734 734
5 8611048 8614480 - Vvi5g735 Vvi5g735 735
5 8615162 8617937 - Vvi5g736 Vvi5g736 736
5 8648516 8650936 + Vvi5g737 Vvi5g737 737
5 8652755 8665137 + Vvi5g738 Vvi5g738 738
       

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