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
Vvi3g426 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g427 Blo02g00835 . . . . . Bma05g00518 . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1099 . . . . . . . . . . . . . . . . . . . . . . . Cpe01g00442 . . . . . . . . . . . . . . . . . .
Vvi3g428 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g429 . Blo15g00739 Bda06g01058 . Bpe07g00391 . . Bma12g00463 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe01g00444 . . . . . . . . . . . . . . . . . .
Vvi3g430 . Blo15g00737 Bda06g01055 . Bpe07g00392 . . Bma12g00464 . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1101 Cone8ag1142 . . . . . . . . . . . . . . . . . . . . . Cpe14g00299 Cpe01g00449 . . . . . . . . . . . . . . . . . .
Vvi3g431 . . . . . . . . Cmo19g00628 . . . . . Sed11g0972 . Cpe15g00494 Bhi05g01128 Tan02g1874 Cmetu03g0548 . Hepe02g0579 . . . . . . . . . . . . . . Csa07g00768 . . . . . . . . . . . Cmo02g00566 . Cma11g01757 Cma19g00610 . Car19g00463 . . . . . . . . . . . . . . . . . . . .
Vvi3g432 . . . . . . . . . Cmo11g01356 . . . . . Cpe04g00274 . . . . . . . . Cla02g00594 . . . . . . . . Cone3ag1105 . . . . Cme01g00041 . . . . . . . . . . . . . . . . Cpe01g00450 . . . . . . . . . . . . . . . . Chy01g00047 .
Vvi3g433 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g434 Blo02g00836 Blo15g00736 Bda06g01054 Bda08g00853 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1106 . . . . . . . . . . . . . . . . . . . . Cpe14g00300 Cpe01g00451 . . . . . . . . . . . . . . . . . .
Vvi3g435 . . . . . . Bma05g00520 . Cmo19g00630 Cmo11g01354 . . . . Sed10g2039 Cpe04g00273 Cpe15g00495 Bhi05g01129 Tan02g0899 Cmetu01g0736 . Hepe02g0578 . . Cla02g00593 Cam02g0622 Cec02g0621 Cco02g0637 Clacu02g0626 Cmu02g0622 Cre02g0946 . . . . Lsi10g00565 Csa07g00769 . Cme01g00040 . . . . . . . . . Cmo02g00567 . Cma11g01758 Cma19g00611 . Car19g00464 . . . . . . . . . . . . . . . . . . Chy01g00046 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 37436023 37438708 + Bda022811.1 Bda06g01054 1054
6 37441991 37477507 - Bda022812.1 Bda06g01055 1055
6 37612485 37626914 + Bda022818.1 Bda06g01058 1058
8 14240862 14243336 + Bda029422.1 Bda08g00853 853
5 40633506 40646060 - XM_039031908.1 Bhi05g01128 1128
5 40659434 40662181 - XM_039032423.1 Bhi05g01129 1129
2 30365116 30368467 + BLOR10565 Blo02g00835 835
2 30369426 30371960 - BLOR10566 Blo02g00836 836
15 24725560 24729236 + BLOR07130 Blo15g00736 736
15 24773047 24800554 - BLOR07131 Blo15g00737 737
15 24948720 24977914 + BLOR07133 Blo15g00739 739
5 25777111 25796537 + Bma021463.1 Bma05g00518 518
5 25968790 25969861 - Bma021468.1 Bma05g00520 520
12 12037328 12052152 - Bma007476.1 Bma12g00463 463
12 12158878 12186944 + Bma030502 Bma12g00464 464
7 3511392 3525784 - Bpe021207.1 Bpe07g00391 391
7 3542153 3571337 + Bpe021208.1 Bpe07g00392 392
2 7142920 7145071 + CaPI482276_02g006220.1 Cam02g0622 622
19 6314735 6317688 - Carg22061-RA Car19g00463 463
19 6322881 6324690 - Carg22060-RA Car19g00464 464
2 6307203 6328823 + CcPI632755_02g006370.1 Cco02g0637 637
2 6216278 6218693 + CePI673135_02g006210.1 Cec02g0621 621
1 339236 340548 + Chy1G000460.1 Chy01g00046 46
1 341056 348568 + Chy1G000470.1 Chy01g00047 47
2 6145568 6146949 + ClG42_02g0062600.10 Clacu02g0626 626
2 6432214 6434460 + ClCG02G005840.2 Cla02g00593 593
2 6446635 6454569 + ClCG02G005860.2 Cla02g00594 594
11 11718981 11720320 - CmaCh11G017570.1 Cma11g01757 1757
11 11725036 11726840 - CmaCh11G017580.1 Cma11g01758 1758
19 6650761 6653614 - CmaCh19G006100.1 Cma19g00610 610
19 6658073 6660367 - CmaCh19G006110.1 Cma19g00611 611
1 332449 336456 + MELO3C018442.2.1 Cme01g00040 40
1 339525 342208 + MELO3C018443.2.1 Cme01g00041 41
1 388228 392041 + PI0018014.1 Cmetu01g0736 736
3 1461092 1463601 - PI0024306.2 Cmetu03g0548 548
2 3282669 3286599 - CmoCh02G005660.1 Cmo02g00566 566
2 3287684 3289547 - CmoCh02G005670.1 Cmo02g00567 567
11 9422647 9423920 + CmoCh11G013540.1 Cmo11g01354 1354
11 9429577 9437894 + CmoCh11G013560.1 Cmo11g01356 1356
19 6853976 6857816 - CmoCh19G006280.1 Cmo19g00628 628
19 6862480 6863990 - CmoCh19G006300.1 Cmo19g00630 630
2 6052389 6053770 + CmPI595203_02g006220.1 Cmu02g0622 622
3 29632091 29633681 - Conep03aG0160900.1 Cone3ag1105 1105
3 29641245 29644735 - Conep03aG0161000.1 Cone3ag1106 1106
8 10003237 10008409 + Conep08aG0117400.1 Cone8ag1142 1142
12 8947511 8953912 + Conep12aG0113500.1 Cone12ag1099 1099
12 8956358 8959456 + Conep12aG0113700.1 Cone12ag1101 1101
1 2546992 2557555 + Cp4.1LG01g02290.1 Cpe01g00442 442
1 2560631 2573650 - Cp4.1LG01g02160.1 Cpe01g00444 444
1 2592785 2602502 + Cp4.1LG01g02300.1 Cpe01g00449 449
1 2603336 2607895 - Cp4.1LG01g01950.1 Cpe01g00450 450
1 2611157 2614643 - Cp4.1LG01g01980.1 Cpe01g00451 451
4 3402982 3405053 + Cp4.1LG04g08110.1 Cpe04g00273 273
4 3411573 3419388 + Cp4.1LG04g08130.1 Cpe04g00274 274
14 1752913 1763678 + Cp4.1LG14g04290.1 Cpe14g00299 299
14 1764983 1769087 - Cp4.1LG14g04020.1 Cpe14g00300 300
15 5895248 5898453 - Cp4.1LG15g04980.1 Cpe15g00494 494
15 5904481 5906826 - Cp4.1LG15g04970.1 Cpe15g00495 495
2 6660035 6677099 + CrPI670011_02g009460.1 Cre02g0946 946
7 5384625 5387622 - CsaV3_7G008670.1 Csa07g00768 768
7 5392056 5394889 - CsaV3_7G008680.1 Csa07g00769 769
2 5868752 5870685 + Hsped.02g05780.1 Hepe02g0578 578
2 5887397 5890480 + Hsped.02g05790.1 Hepe02g0579 579
10 8276113 8277892 + Lsi10G005650.1 Lsi10g00565 565
10 36899216 36901001 - Sed0006444.1 Sed10g2039 2039
11 24432551 24435054 - Sed0019706.1 Sed11g0972 972
2 10245453 10247084 + Tan0004558.1 Tan02g0899 899
2 86648614 86651082 - Tan0020046.1 Tan02g1874 1874
3 4070577 4072718 - Vvi3g426 Vvi3g426 426
3 4075993 4091628 + Vvi3g427 Vvi3g427 427
3 4095046 4095827 - Vvi3g428 Vvi3g428 428
3 4095877 4121942 - Vvi3g429 Vvi3g429 429
3 4130581 4162043 + Vvi3g430 Vvi3g430 430
3 4170183 4173696 - Vvi3g431 Vvi3g431 431
3 4176728 4178437 - Vvi3g432 Vvi3g432 432
3 4180638 4183390 - Vvi3g433 Vvi3g433 433
3 4192398 4198551 - Vvi3g434 Vvi3g434 434
3 4207532 4210487 - Vvi3g435 Vvi3g435 435
       

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